Genome-based revision of the family Gordoniaceae
The isolation and characterization of microbial species from their natural environments remain among the most practical and important ways microbiologists study microbial biodiversity, ecology, and evolution. As whole-genome sequencing has become increasingly central to microbial taxonomy, many historically described groups now require re-evaluation using genome-scale data. This is especially important for bacterial families in which species and genera were originally defined using a combination of morphology, chemotaxonomy, limited physiological testing, and 16S rRNA gene comparisons. While these approaches remain valuable, whole-genome relatedness indices and phylogenomic methods now provide much greater resolution for determining species boundaries and higher-level taxonomic relationships.
One major project in my lab focuses on the genome-based taxonomic revision of the family Gordoniaceae. This family includes environmentally and biotechnologically relevant actinobacteria, including members of the genus Gordonia, many of which are associated with hydrocarbon degradation, environmental persistence, and complex cell envelope chemistry. Our work uses comparative genomics, phylogenomics, whole-genome relatedness indices, and phenotypic data to reassess relationships across the family and determine whether current genus-level classifications accurately reflect evolutionary history.
Our analyses suggest that the current taxonomy of Gordoniaceae does not fully capture the diversity present within the family. Phylogenomic reconstruction and genome relatedness comparisons indicate that several groups currently treated within existing genera form well-supported, genomically coherent lineages that may be more appropriately recognized as separate genera. Based on these patterns, we are proposing the addition of four new genera within the family. These proposed genera are supported by genome-scale phylogenetic structure, relatedness indices, and emerging patterns in shared physiological and genomic traits.
In addition to recognizing new genus-level lineages, this project is also clarifying multiple heterotypic synonyms within the family. These cases occur when separately named taxa appear to represent the same or highly overlapping taxonomic entities based on modern genome comparisons. Resolving these issues is important because taxonomic redundancy can obscure biodiversity estimates, complicate comparative studies, and make it more difficult to interpret ecological and physiological data across related organisms.
A key part of this work is connecting genome-based taxonomy with organismal biology. We are using in silico physiology and comparative genome analyses across family members to identify traits that may distinguish the proposed genera from one another. These genomic predictions are being compared with available laboratory-based physiological and chemotaxonomic data from described type strains. By integrating these approaches, we aim to avoid a purely sequence-based revision and instead produce a taxonomic framework that reflects both evolutionary relationships and biologically meaningful differences among lineages.
Together, these results indicate that Gordoniaceae is more diverse at the genus level than previously recognized. This project will provide a clearer and more stable classification for the family, support the description of newly recognized genera, and improve the use of whole-genome relatedness indices in prokaryotic systematics. More broadly, the work highlights how modern microbial taxonomy can combine cultivation, classical phenotypic characterization, and genome-resolved analyses to better describe bacterial diversity.
One major project in my lab focuses on the genome-based taxonomic revision of the family Gordoniaceae. This family includes environmentally and biotechnologically relevant actinobacteria, including members of the genus Gordonia, many of which are associated with hydrocarbon degradation, environmental persistence, and complex cell envelope chemistry. Our work uses comparative genomics, phylogenomics, whole-genome relatedness indices, and phenotypic data to reassess relationships across the family and determine whether current genus-level classifications accurately reflect evolutionary history.
Our analyses suggest that the current taxonomy of Gordoniaceae does not fully capture the diversity present within the family. Phylogenomic reconstruction and genome relatedness comparisons indicate that several groups currently treated within existing genera form well-supported, genomically coherent lineages that may be more appropriately recognized as separate genera. Based on these patterns, we are proposing the addition of four new genera within the family. These proposed genera are supported by genome-scale phylogenetic structure, relatedness indices, and emerging patterns in shared physiological and genomic traits.
In addition to recognizing new genus-level lineages, this project is also clarifying multiple heterotypic synonyms within the family. These cases occur when separately named taxa appear to represent the same or highly overlapping taxonomic entities based on modern genome comparisons. Resolving these issues is important because taxonomic redundancy can obscure biodiversity estimates, complicate comparative studies, and make it more difficult to interpret ecological and physiological data across related organisms.
A key part of this work is connecting genome-based taxonomy with organismal biology. We are using in silico physiology and comparative genome analyses across family members to identify traits that may distinguish the proposed genera from one another. These genomic predictions are being compared with available laboratory-based physiological and chemotaxonomic data from described type strains. By integrating these approaches, we aim to avoid a purely sequence-based revision and instead produce a taxonomic framework that reflects both evolutionary relationships and biologically meaningful differences among lineages.
Together, these results indicate that Gordoniaceae is more diverse at the genus level than previously recognized. This project will provide a clearer and more stable classification for the family, support the description of newly recognized genera, and improve the use of whole-genome relatedness indices in prokaryotic systematics. More broadly, the work highlights how modern microbial taxonomy can combine cultivation, classical phenotypic characterization, and genome-resolved analyses to better describe bacterial diversity.