Nucleocytoplasmic large DNA and Mirusviricota viruses exhibit taxonomic richness which continually expands due to metagenomic sequencing. Here we curate a database of giant virus metagenome-assembled genomes (GVMAGs V2), comprising 8,508 species-level representatives from 18,727 GVMAGs, a sixfold increase from the previous giant virus phylogenetic frameworks. Phylogenomics revealed 712 previously undescribed genera, 13 previously unknown viral families and an order we propose named Mycodnavirales. By accounting for alternative and custom genetic codes, we improved gene calling in over 1,300 GVMAGs, enabling more accurate identification of protein-coding genes. Database mining uncovered putative endogenous viral elements in hosts spanning algae, fungi and parasitic protists, highlighting that giant virus integration is widespread and evolutionarily persistent. Protein-level analysis revealed enriched genes for pollutant degradation in Algavirales and widespread biosynthetic gene clusters linked to antimicrobial-like and antibiotic resistance gene-like activity. This public resource will serve as a foundation for expanding giant virus diversity, uncovering virus–host interactions and exploring viral evolution. This curated genome-resolved, metagenomic resource expands the known diversity of Nucleocytoviricota and Mirusviricota lineages.
Yumary M. Vasquez, Tiago Nardi, G. M. Terasaki et al.· Nature Microbiology· 1 citation
Diarrheagenic Escherichia coli (DEC) pathotypes are commonly defined by molecular detection of discrete virulence genes, yet how quickly these diagnostic genes emerge and move among co-circulating lineages remain unclear. Here, we classified 248 whole-genome-sequenced E. coli isolates from the EcoZUR case-control study in northern Ecuador into intra-species genomovar units using the recently described 99.5% ANI threshold. This framework exposed cryptic population structure, revealing that single sequence types, representing identical multilocus sequence types (MLST), can harbor multiple distinct genomovars. Within individual genomovars, we observed a few cases of different pathotypes among isolates showing ∼99.7% ANI (and many such cases between genomovars). Coupled with synteny and phylogeny analyses that revealed pervasive incongruences between pathotype-diagnostic virulence genes and the core genome, these findings suggest recent horizontal gene transfer as the primary driver of pathotype evolution. Virulence gene profiling further revealed that accessory virulence repertoires are hierarchically structured by phylogroup across pathotypes, with genomovars assigned to phylogroups B2 and D exhibiting more conserved virulence architectures than those in phylogroup A and B1. Among DAEC isolates specifically, the B2- and D-associated genomovars showed elevated diarrhea-association rates relative to their phylogroup A counterparts. Rare virulence genes, including Type VI secretion systems, further distinguished diarrhea-associated from asymptomatic genomovars. These findings demonstrate that, although there seems to be within-lineage (phylogroup) conservation of virulence, pathotype identity is a labile state defined by horizontally acquired virulence genes at the genomovar level, and that the genomovar framework provides a biologically meaningful unit for linking intra-species diversity to pathogenic potential and outbreaks. Importance Efforts to diagnose diarrheal Escherichia coli infections depend on our ability to reliably identify which strain is dangerous, a task that for decades has rested on sorting strains into pathotypes defined by a few virulence genes. Whether these labels mark stable lineages or fleeting states is hard to judge with traditional typing methods such as Sequence Types (STs), which group together isolates with identical sequences in a handful of housekeeping loci. Using a recently defined genome-wide threshold (99.5% ANI), we resolved isolates into fine-scale genomovars and found that individual STs often conceal multiple distinct genomovars, some carrying conflicting virulence repertoires. At this resolution, the loci that define pathotypes are gained and lost far faster than the core genome diverges, and a genomovar’s genomic background shapes its association with disease. Genomovars therefore complement MLST with the resolution needed to interpret genomic surveillance data and to build robust diagnostic and public-health frameworks.
Dorian J. Feistel, K. Jesser, K. Levy et al.· bioRxiv· 0 citations
4-Isopropylnitrobenzene (4-IPNB) is a nitroaromatic compound commonly employed as an intermediate in pesticide synthesis and chemical manufacturing. Despite its potential environmental persistence and ecological risks, the microbial degradation pathway of 4-IPNB remains largely unknown. In this study, a Gram-negative bacterium, designated Sphingobium yanoikuyae strain SG1, was isolated from a pesticide manufacturing site in Brazil for its ability to utilize 4-IPNB as the sole added source of carbon, nitrogen, and energy. Aerobic degradation of 4-IPNB by strain SG1 was accompanied by nitrite release, and intermediate-trapping experiments revealed the transient accumulation of 4-isopropylcatechol (4-IPC). Together, these findings support the initial conversion of 4-IPNB to 4-IPC through oxidative denitration and dihydroxylation. Genomic and transcriptomic analyses further inferred several candidate nitroarene dioxygenases that may catalyze this initial reaction. Furthermore, the downstream metabolism of 4-IPC proceeded via both meta- and ortho-cleavage pathways, with cell-extract enzyme assays demonstrating predominant meta-cleavage activity under the tested conditions. Strain SG1 also degraded 4-IPNB in nonsterile soil slurry microcosms, extending its degradation capability beyond defined liquid culture. This study provides the first comprehensive insight into the microbial aerobic degradation of 4-IPNB, advances our understanding of the environmental fate of emerging nitroaromatic contaminants, and supports the potential of strain SG1 in 4-IPNB biodegradation and removal.
Na Yang, Isabelle Câmara, Sharmin Afroz et al.· Journal of Hazardous Materia...· 0 citations
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