Pangenome analysis of Nocardia brasiliensis reveals phylogenetic divergence, high genomic diversity and widespread distribution of biosynthetic gene clusters involved in secondary metabolite biosynthesis.
Jul 2026· Molecular Phylogenetics and Evolution· pp.
108686
· 0 citations· 61 references
Medicine
TL;DR
Significant genomic diversity and a wide distribution of biosynthetic clusters within the Nocardia brasiliensis pangenome are revealed, demonstrating its genomic plasticity and the variability in metabolic potential across strains.
Abstract
Actinobacteria are a diverse and heterogeneous group of bacteria with complex taxonomy that produce most of the natural products used in medicine. Although comparative genomic studies of Nocardia species have been reported, comprehensive species-level analyses integrating phylogenomics, pangenome structure, and biosynthetic gene cluster distribution in N. brasiliensis remain limited. In this study, we performed phylogenomic orthology inference, analyzed pangenome composition, and evaluated the potential of Nocardia brasiliensis as a source of secondary metabolites using comparative genomics. Four clinical strains from Mexico and 22 publicly accessible genomes were included. Genomic identification was performed, orthologous genes were identified, core genome and pangenome composition were estimated, and phylogenomic orthology inference was assessed. All genomes were searched for known BGCs, secondary metabolites were predicted, and data on reported biological activity were collected. A pangenome comprising 17,715 clusters was calculated, with the core genome accounting for 22.76 % and the cloud genome for 48.17 %. The trend in the gene accumulation curve indicated that the species had an open pangenome, as the continuous increase in gene clusters with the addition of new genomes suggests a high level of genomic diversity and ongoing gene acquisition within the species, reflecting its capacity for environmental adaptation and evolutionary plasticity. Phylogenomic analysis showed that geographical origin and isolation conditions affect evolutionary divergence within N. brasiliensis. Computational BGC prediction detected PKS, NRPS, NAPAA, terpenes, aminopolycarboxylic acids, hybrids, and other clusters coding for secondary metabolites with antimicrobial activity (ε-Poly-L-lysine, brasiliquinones A-B), antitumor activity (rhizomides A-C, anthramycin), antioxidant activity (isorenieratene), and a fertilizer for calcareous soils ([S, S]-EDDS). The results reveal significant genomic diversity and a wide distribution of biosynthetic clusters within the Nocardia brasiliensis pangenome, demonstrating its genomic plasticity and the variability in metabolic potential across strains.
Understanding of the metabolic capabilities and genomic landscape of the P. fluorescens species is enhanced, providing a foundation for natural product discovery using bioinformatic approaches.
Sajid Iqbal, Farida Begum· Discover Genetics and Evolut...· 0 citations
The genus Erwinia comprises a diverse group of bacteria associated with plants, insects, and the environment, including several economically important phytopathogens. The genus has been revised taxonomically many times, yet a thorough and genome-wide assessment of its evolutionary relationships and genomic diversity has been lacking. In this research, we carried out an extensive phylogenomic and comparative genomic analyses of the genus Erwinia using 104 genomes including historically important strains. Genome-wide analyses integrating average nucleotide identity (ANI), digital DNA–DNA hybridization (dDDH), core-genome phylogenomics, pan-genome analysis, and comparative genomics resolved evolutionary relationships across the genus and identified multiple taxonomic inconsistencies. The pan-genome analysis revealed a relatively small core genome alongside an extensive accessory genome, underscoring the substantial genomic plasticity and ongoing diversification within the genus. The comparative analyses further showed pronounced lineage-specific variation in secretion systems, exopolysaccharide biosynthetic loci, flagellar gene clusters, genomic islands, prophages, and iron acquisition systems, suggesting that virulence-associated determinants have evolved through differential gene gain, loss, and conservation across distinct lineages, thereby facilitating host and ecological niche adaptation. This lineage-specific variation indicates that pathogenicity in the genus is not driven by a single conserved set of virulence determinants but instead reflects distinct combinations of virulence-associated genes. These findings refine the genomic framework of the genus Erwinia, provide evidence for taxonomic revision of several lineages, and improve our understanding of the evolutionary relationships, genomic diversification, and lineage-specific adaptations associated with host interactions and ecological specialization. Impact Statement This study provides the first comprehensive genome-wide phylogenomic framework for the genus Erwinia, integrating taxonomy, pan-genome diversity, virulence-associated determinants, and mobile genetic elements across all 18 currently recognized species. Analyses resolve evolutionary relationships, uncover multiple taxonomic inconsistencies, identify previously unrecognized species-level lineages, including a putative novel Erwinia species PL328 isolated from Cornus florida (dogwood), and reveal lineage-specific genomic features. These findings establish a valuable genomic foundation for future studies of Erwinia evolution, taxonomy, and plant-microbe interactions. Data Summary Genomes sequenced in this study were submitted to the NCBI database under the accession numbers: JCBCPT000000000
Nimisha Maurya, S. Dobhal, George W. Sundin et al.· bioRxiv· 0 citations
Introduction Fish nocardiosis is a chronic and economically significant bacterial disease in aquaculture, yet its genomic basis remains poorly resolved beyond single-species studies. It remains unclear whether fish-associated Nocardia share conserved persistence-associated features or exhibit lineage-specific genomic diversification. Materials and methods We conducted a comparative genomic analysis of 22 Nocardia genomes, including 20 N. seriolae isolates and single representatives of N. salmonicida and N. crassostreae. Genome-wide analyses included phylogenomics, gene-content comparison, pangenome analysis, functional annotation, virulence-associated homolog screening, genomic island detection, and secondary biosynthetic gene cluster prediction. Results The conserved genome core was enriched in central metabolism, lipid-associated cell envelope biogenesis, iron acquisition, and stress-response pathways. Virulence-associated homologs were dominated by persistence-associated and metabolic functions, whereas classical toxin systems were limited, although several transport- and secretion-associated homologs were detected, consistent with their potential contribution to host interaction and intracellular persistence. Phylogenomic and gene-content analyses revealed clear species-level divergence but limited host-associated structuring within N. seriolae. Pangenome analysis supported a robust open pangenome structure (γ = 0.386), with extensive accessory gene diversity enriched in regulatory functions, mobile genetic elements, and secondary metabolic pathways. Genomic islands were dominated by insertion-sequence-associated genes, recombinases, regulators, and hypothetical proteins, whereas prophage- and toxin-related signatures were rare. Secondary metabolite analysis revealed extensive biosynthetic diversity, with most biosynthetic gene clusters showing low similarity to characterized reference pathways. However, ectoine- and nocobactin-associated pathways were broadly conserved. Conclusion These genome findings are consistent with a persistence-associated pathogenicity model in which fish-associated Nocardia, particularly N. seriolae, may depend more on metabolic resilience, stress adaptation, iron acquisition, and accessory genome plasticity than on classical toxin-mediated virulence. Collectively, the results highlight the importance of accessory genome diversification, iron acquisition, and stress adaptation in shaping host-associated lifestyles and provide a comparative genomic foundation for future functional investigations and aquaculture disease-management strategies.
Kiran Kumar Eripogu, P. Maharathi, Wen-Hsiung Li· Frontiers in Microbiology· 0 citations
Aquirufa
is a widespread and diverse bacterial genus inhabiting freshwater ecosystems. Analyses of genomes from cultured strains and metagenome-assembled genomes (MAGs) of the genus revealed four phylogenetically distinct branches that differed markedly in the proportions of cultured strains and MAGs they contained. In total, 56 species or species-like taxa were identified, including eight novel species described here. Proteorhodopsin genes were detected in many of the genomes and were found across a wide range of habitat types, but their prevalence differed considerably among the four phylogenetic branches. Detailed analyses of two branches with markedly different proteorhodopsin gene frequencies suggested differences in the occurrence, size, structure, and pangenomes of their populations. Comparative whole-genome analyses showed that proteorhodopsin genes in
Aquirufa
consistently co-occurred with two key genes involved in retinal chromophore biosynthesis. These three genes exhibited distinct evolutionary patterns, most likely reflecting differences in recombination and co-evolution. Phylogenetic analyses placed the
Aquirufa
proteorhodopsins within the proteorhodopsin-xanthorhodopsin clade, specifically in a lineage comprising proteorhodopsins from species of the phylum
Bacteroidota
. Extending the analyses to related proteorhodopsins revealed additional patterns. Thirteen distinct gene arrangement types and all three common spectral-tuning residues were identified, with variation occurring not only among genera but occasionally even among species within the same genus. Overall, our findings indicated that the evolution, acquisition, horizontal transfer, and recombination of proteorhodopsin genes and associated genes have proceeded differently across taxonomic groups.
Alexandra Pitt, Stefan Lienbacher, J. Schmidt et al.· Microbial Ecology· 0 citations
The genus
Streptomyces
is one of the richest sources of bioactive natural products; however, a substantial proportion of its biosynthetic gene clusters (BGCs) remain cryptic and their metabolic products are unresolved. Advances in genome mining and computational prediction now enable comprehensive exploration of this hidden biosynthetic repertoire. In this study, whole-genome sequencing and comparative genomic analyses were performed on three three newly isolated
Streptomyces
strains to evaluate their specialized metabolic potential. Genome assemblies were annotated and systematically analyzed using antiSMASH, DeepBGC, GECCO, and PRISM to identify, cross-validate, and functionally characterize BGCs while predicting their associated secondary metabolite scaffolds. Taxonomic analyses based on Average Nucleotide Identity (ANI), phylogenomics, and BLAST identified the isolates as
Streptomyces thinghirensis, Streptomyces novocaesareae
, and
Streptomyces griseorubens
. Applying the consensus framework across the three
Streptomyces
genomes yielded 43 cryptic BGCs, lacking close similarity to reference BGCs in the MIBiG database, of which 26 were classified as HIGH, 10 as MEDIUM, and 7 as LOW confidence. Notably, numerous BGCs exhibited low abundance to characterized reference clusters, indicating a high potential for previously undescribed biosynthetic pathways and novel metabolite scaffolds. Comparative analyses further revealed strain-specific biosynthetic architectures together with putative metal-responsive regulatory systems;
Fur, Zur
, and
Nur
, which were frequently associated with specialized metabolite biosynthetic loci. Collectively, these findings demonstrate the effectiveness of integrated genome-mining strategies for prioritizing cryptic biosynthetic gene clusters and highlight the remarkable biosynthetic potential of newly identified
Streptomyces
isolates as a source of novel natural products.
Nada S. Al-Theyab, Haila M. Alnassar, Mohanad A. Ibrahim et al.· Frontiers in Microbiology· 0 citations
The SAR11 clade, also known as the order Candidatus Pelagibacterales, is among the most abundant bacterial lineages in the ocean and plays central roles in marine biogeochemical cycles. However, many SAR11 genes remain functionally uncharacterized, highlighting the need for a comprehensive, integrated catalog that supports genomic, functional, and ecological analyses across the clade. Here, we present the SAR11 Genome Atlas, an interactive ortholog group (OG)-centered web resource that integrates 542 SAR11 genomes, including all 132 cultured strain genomes, with functional annotations, synteny, phylogenetic distribution, metatranscriptomic expression, and predicted protein structure information. To demonstrate its utility, we used environmental expression profiles to identify OGs associated with high-latitude environments, recovering OGs known to be involved in cold adaptation and proposing a hypothesis for the function of uncharacterized protein. We further analyzed phylogenetic distribution patterns to identify mutually exclusive functional modules, including candidate alternative systems for Mn/Zn homeostasis and phosphate acquisition, and to associate these modules with distinct oceanographic environments. Together, these case studies demonstrate that the SAR11 Genome Atlas supports complementary analyses that connect environmental signals to genes of interest and use phylogenetic or functional distributions to generate hypotheses about ecological specialization. Through a user-friendly web interface, the SAR11 Genome Atlas enables researchers to explore genomic, environmental, and structural information without specialized computational expertise. All data and analysis outputs are freely accessible online at [https://stsnsn.github.io/SAR11_Atlas/]. The SAR11 Genome Atlas thus provides a scalable framework for generating and testing hypotheses that connect SAR11 genomic variation to protein function and oceanographic context, supporting advances in marine microbial ecology and biogeochemistry.