Pangenomic and genomic plasticity analyses of the genus Rickettsia

Phylogenomic analysis of Paenibacillus larvae isolates from Slovakia predicts regional genomic clustering

The Paenibacillus larvae is known as the causative agent of American foulbrood, which is widespread throughout the world. It is a highly contagious, fatal disease of honeybees. The aim of this study was to investigate the phylogenomic relationships of ERIC II genotype P. larvae isolates from Slovakia and to compare them with ERIC II genotype isolates originating from other countries. Phylogenomic analyses of P. larvae D3, 5S, and M1 isolates from Slovakia revealed a very low level of genetic diversity among our isolates, with low genome size variability (3.56 ± 0.04 Mbp) and average nucleotide and amino acid identity levels above 99%. Genomes showed similar gene counts (3,700 ± 59 genes per genome), with the highest variability in the mobile elements, especially bacteriophage-related genes (from 220 to 281 genes per genome). Comparative genomic analyses of several ERIC II and ERIC I types of P. larvae genomes available in the GenBank showed a clear geographical pattern, indicating that P. larvae strains spreading in the Slovak region differ from strains found in other parts of Europe and the rest of the world, thus indicating the possible existence of regionalism in the P. larvae species distribution.

Faecalibacterium harmsenii sp. nov., an abundant but previously overlooked Faecalibacterium in the human gut

Faecalibacterium is one of the most abundant anaerobes in the human colon. At the genus level, this bacterium shows a strong positive association with human health. Expanding collections of isolates and metagenome-assembled genomes have revealed its species diversity, yet species-level functions remain so far underexplored. Here, we describe a novel species, Faecalibacterium harmsenii. In addition, we reclassify another isolate as a member of the recently reported F. langellae species. Despite close genomic relatedness, these isolates exhibit distinct physiological and biochemical traits, including differences in carbohydrate utilization, stress tolerance, enzymatic activity, Gram-staining and fatty acid composition. Our present comparative genomics analyses further uncover extensive functional diversity and plasticity across type strains, with F. harmsenii being distinguished by an expanded carbohydrate gene repertoire and reduced defense systems, mobile genetic elements and antibiotic resistance genes. Extending to the species, we identify species-specific ecological niches across hosts and differential sensitivities to human diseases, highlighting certain species as reliable biomarkers of gut health. Together, these findings refine our understanding of Faecalibacterium diversity and provide a framework for its use in microbiome-based diagnostics and therapeutic development.

Genomic exploration of Serratia rubidaea MJ24 uncovers diverse biosynthetic capacity and agricultural relevance

The findings reveal S. rubidaea MJ24 as a metabolically versatile bacterium with a rich secondary metabolite repertoire and significant agricultural and biotechnological promise.

Automated pangenomic profiling of Pediococcus acidilactici genomes via Snakemake: uncovering genomic plasticity and specialized antimicrobial potential

Polyphasic and genomic characterisation of Streptomyces zimensis sp. nov., a halotolerant Actinomycetota from the Saline Lake Zima in Morocco

Members of the phylum Actinomycetota are widely distributed across diverse environments and are well known for their metabolic versatility and capacity to produce bioactive compounds. In this study, strain ZE1316R2Aᵀ was isolated from the saline water collected from Lake Zima (Morocco) and subjected to comprehensive polyphasic taxonomic characterisation. Phylogenetic analysis based on the 16 S rRNA gene placed strain ZE1316R2Aᵀ within the genus Streptomyces , showing highest sequence similarity with S. albidoflavus DSM 40,455 T (99.71%). However, genome-based indices, including average nucleotide identity (ANIb = 94.84%, ANIm = 96.09%) and digital DNA-DNA hybridization (dDDH = 64.9%), supported its distinction as a separate species. The draft genome (7.41 Mb; G + C = 73.26 mol%) comprises 6,464 coding sequences and reveals the presence of strain-specific genomic regions and biosynthetic gene clusters. Comparative analyses highlighted both a conserved core genome and a substantial accessory genome component, reflecting genomic differentiation relative to closely related taxa. Phenotypic and chemotaxonomic characteristics were consistent with assignment to the genus Streptomyces , while supporting its differentiation at the species level. Based on the combined genomic, phenotypic, and chemotaxonomic evidence, strain ZE1316R2Aᵀ represents a novel species of the genus Streptomyces , for which the name Streptomyces zimensis sp. nov., is proposed. This study expands current knowledge of Streptomyces diversity associated with saline environments and highlights the genomic diversity present within closely related taxa. The type strain is ZE1316R2Aᵀ (= CCMM B1331 T  = DSM 120541 T ).

Genomic, spatial, and evolutionary insights into a dominant Mycoplasmatota symbiont colonizing the body wall of deep-sea holothurians

This study provides genome- and spatially resolved views of dominant SCB in holothurians and offers evolutionary insights into host-interface diversification in the deep-sea holothurian body wall.