Phylotype

A phylotype is a population or group of organisms that share a high degree of similarity in their genetic sequence, typically the 16S rRNA gene for prokaryotes (bacteria and archaea) or other suitable phylogenetic markers. It is a pragmatic classification used in microbial ecology and molecular biology to group organisms that are closely related phylogenetically but may not be formally classified into specific species due to challenges in applying traditional taxonomic definitions, such as reproductive isolation, to microorganisms.

Phylotypes are defined based on a chosen similarity threshold for the genetic marker sequence. For example, a commonly used threshold for 16S rRNA genes is 97% sequence similarity, meaning that organisms with 16S rRNA gene sequences that are 97% or more identical are considered to belong to the same phylotype. This threshold can be adjusted depending on the research question and the target group of organisms. Lower similarity thresholds (e.g., 95%) are sometimes used for broader classifications, while higher thresholds (e.g., 99%) may be employed for finer-scale differentiation.

The concept of phylotypes is particularly useful when analyzing complex microbial communities using techniques such as amplicon sequencing (e.g., 16S rRNA gene sequencing) or metagenomics. These methods generate large datasets of genetic sequences, which are then clustered into phylotypes based on sequence similarity. The relative abundance of different phylotypes in a sample can provide insights into the composition and diversity of the microbial community.

Phylotypes should not be confused with species. A single phylotype may encompass multiple distinct species, and conversely, a single species may be represented by multiple phylotypes if there is significant intraspecies variation in the chosen phylogenetic marker. The use of phylotypes reflects the practical challenges of definitively classifying microorganisms based solely on genetic information.

The term phylotype is often used interchangeably with other terms, such as "operational taxonomic unit" (OTU), although there are subtle differences in their usage. OTUs are typically defined based on clustering algorithms applied to sequence data, while phylotypes emphasize the phylogenetic relatedness of the clustered sequences. However, both terms serve the same general purpose of grouping organisms based on genetic similarity for ecological and evolutionary studies.