Trichoderma virens, a plant- beneficial fungus, has the ability to produce volatile and non-volatile secondary metabolites that possess antimicrobial properties and contribute to promoting plant growth and development. Gliovirin, viridin, viridiol, and heptelidic acid are among its major non-volatile metabolites. In our previous study, we observed that the deletion of heptelidic acid synthase (has1), a terpene cyclase, abolished the biosynthesis of major non-volatile metabolites, in addition to heptelidic acid. Conversely, deletion of the Tex7 gene, a non-ribosomal peptide synthetase, led to an increase in heptelidic acid production, along with other major secondary metabolites. Additionally, disruption of a GAPDH gene located within a secondary metabolite gene cluster abolished heptelidic acid biosynthesis and, consequently, all major secondary metabolites. These findings suggest that heptelidic acid might act as a microbial hormone that regulates secondary metabolism. To investigate this further, we conducted transcriptomic and metabolomic comparisons between the wild-type strain and a Δhas1 mutant lacking heptelidic acid biosynthesis. Transcriptome analysis revealed a major proportion of transcripts were down regulated. Of them, nine transcripts belonged to gliovirin biosynthesis cluster, 14 for viridin cluster and five for volatile sesquiterpene and heptelidic acid biosynthesis cluster; metabolite analysis couldn't detect any heptelidic acid along with viridin, viridiol and gliovirin in the Δhas1 mutant. Additionally, several other secondary metabolites were significantly down regulated. Our results are indicative of a possibility that heptelidic acid might function as a microbial hormone regulating secondary metabolism in this biotechnologically important fungus.

4-methylcyclohexane methanol (MCHM), an alicyclic alcohol, is a synthetic hydrotrope that induces a starvation response by upregulation of biosynthetic pathways despite the availability of nutrients. To investigate how Saccharomyces cerevisiae adapts its metabolism to tolerate MCHM, we evolved MCHM-resistant strains in In-Lab Evolutions (ILEs). We sequenced the parental (YJM789) with long read sequencing and the evolved strain using short sequencing, increasing the quality of the YJM789 genome. We identified thousands of SNPs and indel variants per ILE strain, which was a consistent number between strains that evolved resistance and control strains that remained sensitive. However, one gene, PDR3, was consistently mutated in all resistant strains. Because it controls the pleiotropic drug response, recurrent mutations in PDR3 across resistant strains indicate that it is a key driver of adaptive resistance to MCHM in yeast. While many of the evolved alleles of PDR3 would likely produce functional proteins, a PDR3 knockout in the parent YJM789 strain was sufficient to reproduce resistance to MCHM. We found that the pdr3 resistance is mediated through Med15, a component of the Mediator complex which regulates activation by mediating interactions between transcription factors of RNA Pol II. Pdr3 can homodimerize or dimerize with Pdr1, another transcription factor paralog and loss of Pdr1 also confers MCHM resistance. The pleiotropic drug response (PDR) pathway facilitates the export of amino acid catabolites, and deletion of PDR3 disrupted glutathione metabolism and its intermediates. Thus, mutations in PDR3 represent the first identified mechanism conferring resistance to this novel hydrotropic chemical.

The genus Kluyvera has gained increasing attention due to their emerging role as opportunistic pathogens and their antibiotic resistance determinants. Various approaches have been employed to reveal genomic insights into the evolution and pathogenicity of Kluyvera species. However, detailed knowledge about Kluyvera-specific clustered regularly interspaced short palindromic repeats (CRISPR) is still missing. In this study, a genome-mining approach was employed for the characterization of CRISPR-Cas loci in a total of 13 complete Kluyvera genomes using CRISPRCasFinder and related tools. Out of 13 species, only K. ascorbata displayed multiple CRISPR-Cas arrays and a complete set of cas genes characteristics of a type I-E system. Spacer analysis revealed potential targets within phage and plasmid sequences, indicating historical exposure to mobile genetic elements. Furthermore, a phylogenetic tree constructed using the Cas3 protein sequence positioned K. ascorbata closely with other enteric bacteria, including Salmonella spp. and Citrobacter spp. This study provides the first detailed insight into the CRISPR-Cas architecture of K. ascorbata. Although there is no significant diversity of the CRISPR-Cas system identified in this species, it can emphasize a role as active immune defenses against invaders and offer a foundation for future functional and evolutionary investigations. Moreover, difficulties in identification of the genus Kluyvera can be overcome through the CRISPR-Cas system using next-generation diagnostics tools.

Plant-microbe interactions in the rice rhizosphere play a pivotal role for crop productivity. Acinetobacter spp. are known for their plant growth-promoting (PGP) abilities, including phytostimulation, phosphate solubilization, and siderophore production. In this study, we isolated the bacterial strain Acinetobacter lwoffii DJPGP01 from rice rhizosphere soil and conducted comprehensive genome sequencing and analysis. Techniques included serial dilution for bacterial isolation, genomic DNA purification, and Illumina sequencing followed by whole genome data analysis. Genome assembly was performed using multiple assemblers with subsequent annotations through PROKKA and RAST, while pathway analysis utilized KEGG-KAAS server. The genome assembly revealed a high-quality sequence of 3.2 Mb with substantial coverage and a GC content of 43.06%. Species identification confirmed as Acinetobacter lwoffii, closely related to Acinetobacter lwoffii strain DSM 2403 based on 16S rRNA analysis. Antismash analysis identified five secondary metabolite gene clusters, potentially linked to PGP traits. Comparative genome analysis provided insights into the phylogenetic placement of Acinetobacter lwoffii DJPGP01 within its genus, showing a close relationship with Acinetobacter lwoffii NCTC 5866 based on digital DNA-DNA hybridization (DDH). The genome data underlines the potential of Acinetobacter lwoffii as a PGP agent, highlighting specific genes involved in nitrogen assimilation, phosphate uptake, and stress response mechanisms. This study contributes to our understanding of the Acinetobacter role in agricultural settings, suggesting strategies for enhancing crop resilience and productivity.

Vancomycin-resistant enterococci (VRE) are critical nosocomial pathogens, classified as high priority by the World Health Organization (WHO) due to rising antibiotic resistance. Among these, Vancomycin-resistant Enterococcus faecium (VREfm) presents a significant clinical challenge, frequently detected in healthcare-associated infections and exhibiting resistance to multiple antibiotics. This study presents a genomic surveillance analysis of 63 Enterococcus faecium (E. faecium) isolates obtained from the public database from India during the period January 2017 to December 2021. These isolates were confirmed as VREfm, making them valuable for understanding the key resistance genes and mutations commonly associated with strains. Genomic analysis revealed diverse plasmid replicons such as pRE25, pRUM, and pIP501, often coexisting in single isolates, indicating active horizontal gene transfer. Multiple antimicrobial resistance genes, such as vanHAX, ermB, optrA, and blaOXA-232, were identified along with insertion sequences (IS3, ISL3, IS256), integrons, and transposons (Tn1546, Tn917). Mutations in GyrA, ParC, and PBP5 proteins associated with fluoroquinolone and β-lactam antibiotics were also detected in each isolate. Amino acid substitutions associated with daptomycin resistance were identified in the encoded proteins of the liaR (LiaR-W73C), liaS (LiaS-T120A), cls (Cls-T298S), and rpoB (RpoB-S491F) genes. Three novel deleterious amino acid substitutions were also observed in Cls-R424S, RpoB-M475V, and RpoC-T634K, encoded by the cls, rpoB, and rpoC genes, respectively, that may impact protein function. Overall, this genomic survey provides a framework for hypothesis-driven studies exploring resistance evolution and gene mobility in E. faecium.

Histone modifications regulate vital pathogenic features necessary for opportunistic fungi to cause disease. More specifically, histone modification via acetylation and methylation are two major ways that fungi regulate their growth, replication, and ability to respond to stress. This is critically important, as these genes can be potential targets for drug therapies in these difficult-to-treat pathogens. For fungi to rapidly respond to changes in their environment, they must quickly and efficiently adapt to their surroundings. Epigenetic control mechanisms, such as histone modification, allow the fungus to adapt to conditions without altering its DNA. As in other eukaryotes, fungal DNA is tightly packaged into an organized complex known as chromatin and wound around histone proteins. As these histones are modified by methylation or acetylation, specific sections of DNA can become accessible to transcriptional machinery. These histone modifications may interact with various other proteins to accomplish their functions, as well. In this way, histone modifications allow microorganisms to rapidly modify gene expression and respond to their environment. In this review, histone modifications via methylation, demethylation, acetylation, and deacetylation for select model and pathogenic fungal species are summarized concerning how they affect growth, stress response, and gene expression, as applicable. Additionally, the roles of epigenetic regulation in virulence factor expression, toxin formation, and disease are explored. Lastly, current knowledge pertaining to novel drugs and drug targets related to histone acetylation, deacetylation, and demethylation is discussed. Understanding the diverse roles of epigenetic regulation in fungal disease is a crucial first step in exploiting this critical linchpin for novel antifungal treatments of these important human pathogens.

Fusarium species are pathogens affecting the broodstock of farm-raised Fannabin prawns, resulting in significant economic losses. However, the genomic characteristics and pathogenic mechanisms of these causative Fusarium strains remain incompletely understood. We isolated a novel Fusarium strain, designated 1-Jan, from diseased prawns and confirmed its pathogenicity through artificial infection experiments. Whole-genome sequencing was performed using both PacBio and Illumina platforms. The assembled genome is 51.8 Mb in size, consisting of 54 scaffolds with an N50 length of 1,974 kb. Gene prediction using AUGUSTUS identified 9,769 putative genes. Comparative genomic analysis revealed that strain 1-Jan is closely related to Fusarium solani JS-169 and Nectria haematococca. Candidate pathogenicity genes were identified through annotation against the PHI, FCPD, DFVF, and CAZy databases, yielding 1,101, 126, 479, and 497 hits, respectively. Within the 1-Jan genome, SNP mutations were identified in 737 potential pathogenicity genes, and 859 out of 4,255 single-copy genes were classified as potentially pathogenic. Additionally, 95 of the 967 genes unique to strain 1-Jan were predicted to be involved in pathogenicity. The genome sequence of the 1-Jan strain and the pathogenicity-related genes identified in this study provide valuable insights into the molecular basis of Fusarium-induced diseases in prawns and offer insights for improving the management of fungal infections in aquaculture.

Cyanobacteria are ecologically pivotal microorganisms with immense biotechnological potential, particularly due to their capacity to synthesize fatty acids, terpenes, and other metabolites with applications ranging from biofuels to nutraceuticals. Despite this, many genera remain genomically underexplored. In this study, we present a polyphasic genomic analysis of two native strains, Aphanothece microscopica RSMan92 and A. stagnina RSMan2012, isolated from the Patos Lagoon estuary in Southern Brazil. Whole-genome sequencing and annotation enabled characterization of both genomes: RSMan92 spans 3.69 Mb in 701 contigs with 3,279 protein-coding sequences, while RSMan2012 comprises 3.28 Mb in 153 contigs with 3,567 protein-coding sequences. Phylogenetic analyses using MUSCLE and RAxML positioned these strains within a well-supported clade closely related to other Aphanothece RefSeq genome, highlighting their evolutionary relatedness and reinforcing the integrative taxonomic placement of the genus. Both strains reveal conserved gene repertoires associated with stress response, fatty acid biosynthesis, and secondary metabolite production (terpenes). Functional classification based on COG and KEGG annotations indicated strong representation of genes involved in lipid metabolism. To investigate how variations in temperature and light intensity modulate metabolite profiles, cultures were subjected to different environmental conditions. GC/EI-MS analysis revealed distinct patterns of fatty acid methyl ester production across conditions: both strains synthesized saturated and monounsaturated fatty acids, whereas only strain RSMan92 exhibited the capacity to synthesize polyunsaturated fatty acids, including linoleic acid derivatives, under variable cultivation conditions. This polyphasic genomic approach, providing novel genomic records, also reveals the fatty acid biosynthetic capacity and metabolic plasticity of Aphanothece strains, emphasizing their biotechnological relevance.

Klebsiella pneumoniae, identified by the World Health Organization (WHO) as a critical priority pathogen, presents a growing public health concern due to increasing multidrug-resistant (MDR) and extended spectrum β-lactamase (ESBL)-producing strains. This study assessed the antimicrobial resistance (AMR) profiles of K. pneumoniae isolates from 288 cattle farm samples in Punjab, India. The bacterium was detected in 10.06% (29/288) of the samples, with 65.51% (19/29) of the isolates being MDR and 6.89% (2/29) exhibiting an ESBL-like phenotype. Resistance genes for β-lactams (blaTEM-62.06%, blaAmpC-51.72%, blaSHV-51.72%), quinolones (qnrS-13.79%), and tetracyclines (tetA-10.34%) were identified. Whole-genome sequencing (WGS) was conducted on two representative phenotypically ESBL-positive and MDR K. pneumoniae isolates, selected for detailed genomic analysis within the limitations of available funding. The analysis revealed the presence of multiple antimicrobial resistance genes (ARGs) conferring resistance to quinolones, cephalosporins, carbapenems, tetracyclines, macrolides, and several other antibiotic classes. Virulence factors detected included Type I and Type III fimbriae, capsules, efflux systems, siderophores, and secretion systems. Plasmid replicon types (IncFIB(K), IncFIB, IncFII(K)), integrons harboring ARGs, and insertion sequences (ISKpn24, ISKpn1, ISKpn19, IS26) were also identified. Multilocus Sequence Typing (MLST) assigned isolates to sequence types ST-160 and ST-4232, with core-genome MLST identifying additional types ST-14,733 and ST-13,365. These findings highlight the potential risk of transmission of resistant K. pneumoniae strains between animals and humans and underscore the urgent need for integrated One Health surveillance and intervention strategies to contain the spread of AMR across sectors.

Cannabidiol (CBD) as an active ingredient is widely used in cosmetics, food, medical products, and dietary supplements. Recent studies suggest that CBD consumption may influence the gut microbiome, impacting overall health. The mechanism of CBD action on the intestinal microbiome may be linked to the endocannabinoid system, which plays a role in the normalization of the functions of the immune system. Additionally, CBD may have a direct influence on the gut by interacting with the intestinal microflora, regulating intestinal permeability, modulating immune responses, and affecting the gut-brain axis communication through the vagal signaling pathway. A study was conducted to analyze how different doses of CBD injected intraperitoneal could alter the microbial composition of the duodenum contents in a mouse model. Obtained results suggest that the impact of CBD on the intestine microbiome may be dosage-dependent. Statistical analysis revealed significant differences compared to the control group in the 0.2 mg/kg CBD and 20 mg/kg CBD dose groups for the genera Campilobacteriota, Firmicutes, Proteobacteria, and, specifically in the 0.2 mg CBD group, Cyanobacteria. In contrast, the 10 mg CBD dose group showed no statistically significant differences relative to the control. The Firmicutes phylum had the highest relative abundance in all groups, wherein its share was lower in the CBD-treated groups than in the control group. Lachnospiraceae_NK4A136_group, Muribaculaceae, and Akkermansia were predominant, with Lachnospiraceae_NK4A136_group decreasing and Akkermansia increasing in relative abundance in CBD-treated groups. Of the genera that showed statistically significant differences between groups, most belonged to the phylum Firmicutes, including the dominant Lachnospiraceae_NK4A136_group. These findings suggest that intraperitoneal CBD administration induces alterations in the duodenal microbiome, particularly affecting the Lachnospiraceae_NK4A136_group and the Akkermansia genera.

Trichoderma species exhibit remarkable versatility in adaptability and in occupying habitats with lifestyles ranging from mycoparasitism and saprotrophy to endophytism. In this study, we present the first high-quality whole-genome assembly and annotation of T. lixii using Illumina HiSeq technology to explore the mechanisms of endophytic lifestyle and plant colonization. The genome size was 41.1 Mbp, comprising 15,430 predicted genes, of which 7,918 were functionally annotated. Comparative analysis identified 82 CAZyme families involved in cellulose and hemicellulose degradation, notably Glycoside Hydrolases (GHs) (43) [e.g., GH3 (14), GH5 (10), GH7 (4) ], Carbohydrate Esterases (CEs) (10), and Auxiliary Activities (AAs) (29) [e.g., AA3 (20), AA9 ]. GHs primarily degrade cellulose, while Polysaccharide Lyases (PLs), along with other CAZymes like CEs and Lytic Polysaccharide Monooxygenases (LPMOs), assist in modifying substrates or targeting specific bonds. These enzymes facilitate substrate breakdown, host tissue penetration, and nutrient acquisition, supporting a non-pathogenic, endophytic lifestyle. The presence of 53 secondary metabolite biosynthetic gene clusters indicates a strong biosynthetic potential. KEGG analysis assigned 2,469 genes to multiple metabolic and signaling pathways, highlighting an enriched profile for carbohydrate metabolism, signal transduction, and antibiotic biosynthesis. Comparative genomics also revealed both preserved and distinctive traits of T. lixii, confirming its ecological flexibility and promise as a source of new bioactive molecules. These findings reveal genetic diversity among the species, providing a foundation for future studies on biocontrol and endophytic functions. The growing availability of Trichoderma genomes deepens understanding of their unique features and offers new prospects for agricultural and biotechnological applications.

Telomerase plays an important role in sustaining eukaryotic linear chromosomes, as elongation of telomeres is needed to counterbalance the shortening occurring in each replication round. Nevertheless, in telomerase-deficient cells, Alternative Lengthening of Telomeres (ALT) pathways can maintain telomeres by employing recombination-based mechanisms. In the budding yeast Naumovozyma castellii, effective activation of the ALT pathway leads to bypass of senescence and supports long-term growth. We found that telomere structures in N. castellii ALT cells are stably maintained at a shortened uniform length over extensive numbers of generations. This is correlated to the spreading of a subtelomeric sequence, TelKO element, to all telomeres. Genome sequencing of the wild-type strain revealed variants of the TelKO element, differing in their lengths, and separate ALT strains are maintained by spreading of distinct TelKO element variants. Although short uniform telomere structures are predominant, sporadic telomere lengthening events occur by addition of long repeated arrays of TelKO elements. The telomere-binding protein Rap1 can bind to TelKO sequences in vitro, indicating a functional role of TelKO elements in providing stability to shortened ALT telomeres. Our results suggest that stable maintenance and telomere functionality may be achieved by incorporating the distal subtelomeric TelKO sequences into the telomeric chromatin cap.

Clearance and adaptation to reactive oxygen species (ROS) are crucial for cell survival. As in other eukaryotes, the catalases in Neurospora crassa are the main enzymes responsible for ROS clearance, primarily by decomposing hydrogen peroxide (H2O2), a major type of ROS. Their expression is tightly regulated by growth and environmental conditions. Histone modifications are frequently linked to the regulation of gene transcription. Histone H3 trimethylation at lysine 4 (H3K4me3) is one of the most studied histone modifications and is associated with transcription initiation. We showed that the abolishment of H3K4me3 in N. crassa led to a low CAT-3 expression level and increased sensitivity to H2O2-induced ROS stress. On the other hand, overexpression of the histone methyltransferase SET-1 led to increased expression of CAT-3. Furthermore, ChIP assays revealed that SET-1 mediated H3K4me3 modification at the cat-3 TSS and ORF 5' region, which regulates RNAPII recruitment for cat-3 transcription. Together, these results demonstrate that histone methyltransferase COMPASS (complex of proteins associated with Set1) complex-mediated H3K4me3 plays a key role in activating cat-3 expression in N. crassa.

Advances in diagnostics, therapeutics, and large-scale clinical studies have significantly expanded our understanding how human health is shaped by the microorganisms that colonize the body since birth. This article explores the rapidly evolving field of human microbiome research, focusing upon how microbial communities influence neurological health and contribute to the development of neurodegenerative diseases (NDs). Multiple factors, including age, lifestyle, and immunological memory, are recognized as major determinants of an individual's microbiome composition, which in turn can influence the onset and the progression of disorders such as Alzheimer's disease, Parkinson's disease, Huntington's disease, and amyotrophic lateral sclerosis. These conditions have been linked to mechanisms including the aggregation of pathogenic proteins (e.g., amyloid-β and α-synuclein), inflammation driven by activation of the Toll-like receptor (TLR) signaling pathway, the NLRP3 inflammasome, as well as the modulatory effect of microbial metabolites such as short-chain fatty acids (SCFAs) and lipopolysaccharides (LPS). The article also highlights ongoing research and emerging strategies aimed at leveraging the human microbiome for better diagnosis, and management of NDs.

Cadmium, a significant environmental heavy metal contaminant, poses considerable threats to human health. Cadmium detoxification by microbes, especially yeast, would serve as a potential strategy for coping with cadmium contamination. Based on the screening assay, the non-conventional yeast Wickerhamomyces anomalus BT3 exhibits cadmium stress resistance with a MIC of CdCl2 exceeding 1000 µM. A prolonged lag phase was observed when BT3 was exposed to > 400 µM cadmium prior to resuming growth in log phase. Thus, suggesting the presence of a cadmium-tolerant genotype in BT3 genomes. Based on the whole genome sequencing analysis, BT3 has a genome size of ~ 14Mbp with 35.0% GC content. Functional gene annotation against the EggNOG and KEGG databases revealed that most of the genes are involved in the genetic translation process. Several key genes potentially involved in cadmium tolerance were identified, including the Yeast cadmium factor (YCF1) gene, which encodes a transporter protein important for cellular homeostasis and detoxification. Genes involved in glutathione synthesis (GSH2) were detected to support the activity. In addition, genes related to oxidative stress response pathways, such as SOD1/2, TRX1, GLRX, and PRX1, were present in BT3 genomes, which promote survival under cadmium-induced oxidative stress conditions. Comparative genome analysis revealed that 2212 gene clusters (36% of BT3 gene clusters) were shared between yeasts. Interestingly, 121 gene clusters were found to be unique to BT3, which predominantly correlated with the gene ontology terms of transmembrane transport activity, integral membrane component, and dimethyl sulfide monooxygenase for the sulfur cycle. Further studies are required to clarify the potential involvement of these unique genetic properties of BT3 in coping with cadmium exposure.