Why Scientists are Changing the Names of Bacteria and Archaea
The hidden world of microorganisms is getting a major makeover, and it's revolutionizing how we communicate about the building blocks of life.
Imagine a world where scientists in different countries use different names for the same animal, or where a dog is suddenly reclassified as a fish. This is the kind of chaos that microbiologists have faced for decades when studying the invisible world of prokaryotes—the bacteria and archaea that shape our health and environment.
In 2022, a significant change began sweeping through microbiology labs: the renaming of entire phyla, the fundamental categories of life. This article explores the science behind this taxonomic revolution and why getting names right matters for everything from disease treatment to environmental conservation.
Single-celled organisms found in nearly every habitat on Earth
Microorganisms often found in extreme environments
Revolutionized our understanding of microbial relationships
Biological taxonomy, the science of naming and classifying organisms, dates back to Carl Linnaeus in the 1700s. His binomial system provided a universal language for scientists, but microorganisms have always been tricky to categorize 1 . Traditionally, microbiologists classified prokaryotes based on their physical traits and biochemical capabilities. But this approach had limitations—many microbes that look similar under a microscope turned out to be genetically distant cousins.
The problem deepened with the discovery that most microbial diversity had been completely overlooked because the vast majority of microbes cannot be easily grown in laboratory cultures 6 . As one researcher noted, "Fewer than 0.2% of prokaryotes have been named" under traditional classification systems 5 .
The game-changer came with DNA sequencing technology, particularly the analysis of the 16S rRNA gene—a piece of genetic code present in all prokaryotes that acts like a molecular clock, revealing evolutionary relationships 6 . When this genetic evidence showed that the traditional names didn't reflect true evolutionary relationships, scientists knew the system needed an overhaul.
The 16S rRNA gene contains both highly conserved and variable regions, making it ideal for comparing evolutionary relationships across different microorganisms.
The movement to rename prokaryotic phyla culminated in 2021 when the International Committee on Systematics of Prokaryotes (ICSP) voted to formally include the rank of phylum in the International Code of Nomenclature of Prokaryotes 2 . This decision triggered what some scientists called "the great phylum flip."
The new rules were simple but transformative: a phylum's name must be formed by adding the suffix -ota to the stem of its designated type genus 2 . This brought consistency to microbial naming, similar to systems long used for animals and plants.
Researchers compared genome sequences across thousands of microbial species to map their evolutionary relationships 6 .
For each phylum, scientists identified a representative genus that embodied the group's characteristics.
Following the new -ota rule, they created new phylum names based on these type genera.
The new names underwent peer review and were formally published in the International Journal of Systematic and Evolutionary Microbiology 2 .
This process wasn't merely academic—it established names that reflect true evolutionary relationships, creating a more accurate map of the microbial world.
The renaming initiative produced dramatic changes to microbiology's vocabulary. Some of the most significant changes included:
Based on the type genus Pseudomonas, this phylum includes many medically important bacteria.
Based on the type genus Bacillus, this phylum includes many Gram-positive bacteria.
Based on the type genus Actinomyces, this phylum includes many antibiotic-producing bacteria.
Based on the type genus Bacteroides, this phylum includes many gut bacteria.
Based on the type genus Methanobacterium, this phylum includes many methane-producing archaea.
Based on the type genus Thermoproteus, this phylum includes many thermophilic archaea.
Based on the type genus Nitrososphaera, this phylum includes ammonia-oxidizing archaea.
As of early 2024, names of 49 phyla had been validly published under the new system 2 . The changes went beyond mere labels—they corrected misclassifications that had persisted for decades. For instance, the well-known pathogen Clostridium difficile was reclassified as Clostridioides difficile when genetic analysis revealed it was only distantly related to the type species of the genus Clostridium 2 .
Modern microbial classification relies on an array of sophisticated tools and techniques:
Provides genetic "fingerprint" for comparison. Primary method for initial classification and phylogenetic placement.
Determines complete DNA sequence. Allows for precise comparison of evolutionary relationships.
Reconstructs genomes from environmental samples. Enables study of unculturable prokaryotes.
Calculates genome similarity between organisms. Helps define species boundaries.
Computes theoretical DNA pairing between organisms. Determines relatedness at the species level.
Despite this progress, the renaming initiative has faced challenges. Not all scientists have embraced the changes, leading to a period of transition where both old and new names appear in scientific literature 2 . This can create confusion, especially in fields like medical diagnostics where precise communication is crucial.
Looking ahead, the International Code of Nomenclature of Prokaryotes is preparing for its 2025 revision , which will likely address these ongoing challenges and continue refining how we name the microbial world.
The reorganization of prokaryotic phyla represents more than taxonomic housekeeping—it reflects science's continual progress toward greater accuracy and consistency. As microbiologists harmonize nomenclature with evolutionary relationships, they create a more reliable framework for communication across all biological disciplines.
of pathogens in medical diagnostics
of environmental microbes in ecosystem studies
among scientists worldwide
of evolutionary relationships across life's domains
The microbial world may be invisible to our eyes, but its impact on our lives is profound. By giving microorganisms names that reflect their true biological relationships, scientists are not just rearranging labels—they're creating a more accurate map of life itself.
For those interested in exploring the fascinating world of prokaryotic nomenclature further, the List of Prokaryotic names with Standing in Nomenclature (LPSN) provides up-to-date information on validly published names 3 .