This letter defends a molecular-based reclassification of Chlamydiales bacteria that divides the order into two genera and nine species, responding to critics who favored maintaining the traditional classification or developing one based on biological markers. The authors argue that the previous classification system, based on a unique developmental cycle and later expanded using serology and host-specificity, became inadequate as new chlamydial species were discovered in unexpected hosts. They demonstrate that traditional biological markers—such as sulfadiazine sensitivity and glycogen accumulation—are unreliable for species identification, citing swine isolates that lack these characteristics yet are genetically distinct from C. trachomatis. The authors support their molecular approach using 16S and 23S ribosomal RNA sequence analysis, which reveals distinct evolutionary lineages with partial chromosome deletions and rearrangements separating the two genera. Multiple independent genetic markers (MOMP, GroEL, RNase P RNA, and others) confirm this evolutionary history. The authors contend that molecular markers provide standardized, reproducible identification applicable across laboratories, enabling reliable species designation and facilitating Internet-based comparisons. They conclude that DNA-based classification is not arbitrary but reflects genuine biological divergence while providing a framework for identifying new taxa as knowledge expands.

Key findings

• Previous chlamydial classification based on biological markers (sulfadiazine sensitivity, glycogen accumulation) is unreliable; the same species show variable phenotypes across different hosts.
• Molecular markers including 16S/23S rRNA, MOMP, GroEL, and chromosome structure consistently support division of Chlamydiaceae into two distinct monophyletic genera with nine species.
• The reclassification reflects genuine evolutionary divergence marked by partial chromosome deletions and rearrangements between genera.
• DNA-based identification provides reproducible, standardized results comparable across laboratories without requiring difficult culture and transport of isolates.
• The new taxonomy provides a framework for understanding selective pressures affecting gene evolution and for classifying new chlamydial taxa as discovery continues.