Microbial Taxonomy

Microbial taxonomy underpins our ability to catalogue and compare the immense diversity of bacteria and archaea. Historically, classification relied on phenotype—cell morphology, metabolic tests and staining characteristics—augmented in the late twentieth century by ribosomal RNA sequencing. Today, taxonomy has shifted towards genome-centred approaches, using whole-genome similarity metrics and phylogenomic inference to define species and higher ranks. Average nucleotide identity (ANI) and digital DNA-DNA hybridisation (dDDH) now replace laborious laboratory hybridisation, while high-throughput pipelines integrate type-strain genome repositories, allow automated phylogenetic tree construction and provide objective species-boundary estimates. This genomic framework reveals microdiversity within natural populations, uncovers cryptic lineages among uncultured taxa and supports consistent taxonomic revision across phyla. Accurate taxonomy is crucial for tracking pathogen emergence, mapping antimicrobial resistance, guiding probiotic development, informing environmental monitoring and underpinning biotechnology, highlighting its global significance and practical applications.

Research from Nature Portfolio

Recent deep sequencing efforts in a model hypersaline bacterium uncovered a bimodal distribution of genome-aggregate ANI values, defining natural “genomovars” and higher-threshold “strains.” Thousands of rare variants were detected in single saltern ponds, exposing cultivation bias and demonstrating that only a small fraction of in situ diversity is recovered by standard methods. Complementing these ecological insights, a fully automated web platform now enables researchers to upload draft or complete prokaryote genomes, infer large-scale phylogenies anchored on reference type strains and receive objective species- and subspecies-boundary estimates. The service integrates nomenclatural data and synonymy, streamlining both novel-taxon description and the reclassification of problematic lineages, and has become a central resource for genome-based bacterial systematics.

Research from all publishers

A taxonomically united database has merged over 61 000 quality-controlled 16S rRNA gene sequences with more than 62 000 whole-genome assemblies, each linked to type-strain metadata. The resource employs initial gene-based searches followed by ANI computations to assign genomes at genus, species and subspecies levels, and provides genome-property summaries for comparative studies of environmental and clinical microbiomes.

A phylogenomic survey of over 1000 alphaproteobacterial type strains assembled draft genomes to infer genome-scale trees, leading to proposals for new orders, families and genera and prompting numerous taxonomic transfers. The work confirmed the superior resolution of whole-genome phylogenies over single-gene trees, demonstrated the taxonomic value of genome size and G + C content, and highlighted the power of gene-content analysis to resolve complex relationships.

A recent review of prokaryotic systematics has charted the transition from phenotype-based classification, through polyphasic approaches, to the current genome-centred paradigm. It details the roles of key reference works and professional societies in guiding metadata standards, addresses challenges posed by the metadata era and outlines focal priorities—from nomenclature consistency to database interoperability—to sustain innovation in microbial systematics.

Microbial Taxonomy publication trend

The graph below shows the total number of articles in microbial taxonomy across all publications each year (not limited to Nature Index journals).

Technical terms

Average nucleotide identity (ANI): A genome-wide measure of nucleotide similarity between two microbial genomes, used to delineate species.

Digital DNA-DNA hybridisation (dDDH): A computational analogue of laboratory DNA-DNA hybridisation, estimating overall genomic relatedness.

Phylogenomic inference: Reconstruction of evolutionary relationships using genome-scale sequence data rather than single loci.

Type strain: A reference microbial isolate to which a species name is formally attached and against which other strains are compared.

Core genome: The set of genes shared by all strains of a species or higher taxon, reflecting essential functions.

References

1. Towards estimating the number of strains that make up a natural bacterial population. Nature Communications (2024).
2. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nature Communications (2019).
3. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. International Journal of Systematic and Evolutionary Microbiology (2017).
4. Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria. Frontiers in Microbiology (2020).
5. Advancements in prokaryotic systematics and the role of Bergey's International Society for Microbial Systematicsin addressing challenges in the meta-data era. National Science Review (2024).