Biology subjects

Vidal-Veuthey, B.

Publications and source records attributed to Vidal-Veuthey, B..

2 recordsLinked to original sources

bioRxiv2025

Genomic analysis of the probiotic candidate Bifidobacterium bifidum strain 900791 in the context of the B. bifidum pangenome

BackgroundBifidobacterium bifidum is a key commensal bacterium in the human gut microbiota with recognized probiotic properties and health benefits. An underinvestigated strain called 900791, isolated from meconium of a Siberian infant and with a validated role in lactose tolerance, requires more understanding of the genomic basis of its potential probiotic functionality. MethodsWe performed whole genome sequencing of strain 900791 using hybrid sequencing (Illumina NextSeq and Nanopore). The genome was functionally annotated and compared against 228 B. bifidum genomes to elucidate probiotic determinants and evolutionary relationships. Antibiotic resistance profiling was conducted using three independent approaches, carbohydrate-active enzymes (CAZymes) were characterized using dbCAN analysis; additionally different markers for desired phenotypes in probiotics (such as adherence to epithelial cells, resistance to low pH, bile salts and oxidative stress, and the ability to produce bacteriocins) were also investigated. ResultsThe complete genome comprises 2.28 Mb with 62.43% G+C content, encoding 1,852 ORFs, 53 tRNAs, and three complete 16S rRNA genes. Phylogenomic analysis revealed 900791 belongs to a distinct clonal subgroup of nine closely related strains sharing almost identical allelic similarity (observed via cgMLST). The pangenome analysis of 229 B. bifidum genomes showed an open structure with 4,679 orthogroups, including 1,212 core families.The strain 900791 harbors extensive CAZymes from families GH2, GH20, GH33, and GH84 associated with mucin and human milk oligosaccharide degradation, plus GH2 and GH42 families for lactose metabolism. Safety assessment revealed only intrinsic resistance to mupirocin and rifampicin, with no acquired resistance markers or virulence factors. The strain possesses multiple stress tolerance systems including acid resistance (FF-ATPase), bile salt resistance (MFS transporters, BSH hydrolase), and oxidative stress response mechanisms. Predicted probiotic features include adhesion proteins (FimA/FimB, FimM), bacteriocin production capabilities, and comprehensive stress response systems. ConclusionB. bifidum 900791 harbors markers for significant probiotic potential with genetic features optimized for gut colonization, host interaction, and antimicrobial competition. This genomic characterization provides a framework for understanding B. bifidum diversity and supports B. bifidum strain 900791-specific probiotic applications, particularly given its demonstrated efficacy in improving lactose tolerance in human subjects.

microbiology↗

bioRxiv2025

Clade-wide proteome analysis shows widespread non-canonical Dcr proteins in fungi.

Dicers (Dcrs) are central proteins involved in the biogenesis of small RNAs (sRNAs) in eukaryotes. Most of the knowledge on Dcr structure, function and evolution comes from studies conducted in animal and plant species. Comparatively, much less is known in fungi, which are a genetically and ecologically diverse group with important roles in ecosystems, agriculture, medicine, and biotechnology. While canonical Dcrs in plants and animals contain a well-defined domain architecture, most fungal Dcrs with experimentally validated functions lack one or more identifiable canonical domains, raising questions about how RNA-binding and precise sRNA processing is retained. Here, we conducted the most extensive survey of fungal Dcr proteins, analyzing 1,593 proteomes across eight phyla. We found a diversity of Dcr domain architectures, with some of them lacking an identifiable PAZ, Helicase, and/or double-stranded RNA binding domains. Phylogenetic analyses showed that different Dcr classes are distributed across distinct clades that often align with fungal taxonomic groups. Despite the lack of canonical domain architectures, we found that fungal Dcrs fold into a characteristic L-shaped structure and show PAZ-like folds, even in proteins without detectable PAZ sequences. Molecular docking and electrostatic analyses further indicate that these divergent Dcrs maintain key RNA-binding surfaces for proper sRNA processing. Our results indicate a remarkable evolutionary plasticity of Dcr in fungi, showing that essential sRNA processing functions can be retained through structural conservation, and highlighting fungi as models to study the modular evolution of the RNAi machinery in eukaryotes. Significance statementDicer (Dcr) proteins are central to RNA interference (RNAi), a gene regulatory mechanism conserved across eukaryotes. However, current models of Dcr structure, function, and evolution are largely based on studies in animals and plants. Here, we present the most comprehensive analysis to date of Dcr proteins in fungi, a diverse eukaryotic group including many societally important pathogens and symbiotes which are reliant on RNAi. Our findings reveal that despite widespread divergence from canonical Dcr architecture, fungal Dcrs conserve critical folds and RNA-binding features, further suggesting that core RNAi functions are maintained. This work establishes fungi as key models for studying the evolution and functional robustness of the RNAi machinery, offering broader insight into the diversity and plasticity of sRNA biogenesis pathways across eukaryotes.

genomics↗