Linking genomic evolutionary transitions to ecological phenotypic adaptations in Spirochaetes

Area of Science:

• Evolutionary Biology
• Microbial Genomics
• Bacteriology

Background:

• Spirochaetes are ancient, diverse bacteria with significant medical relevance, yet their evolutionary history and adaptations remain poorly understood.
• The discovery of non-spiral lineages necessitates a re-evaluation of the Spirochaetes phylum's evolution.
• Limited curated genomic data has historically hindered comprehensive studies of Spirochaetes.

Purpose of the Study:

• To conduct the most comprehensive phylogenomic and functional analysis of the Spirochaetes phylum to date.
• To reconstruct the evolutionary rooting and ancestral characteristics of Spirochaetes.
• To identify genomic signatures of adaptation, including morphological changes and host association.

Main Methods:

• Phylogenomic analysis of 172 curated Spirochaetes genomes representing all cultivable species.
• Ancestral genome reconstruction to infer characteristics of the Last Spirochaetal Common Ancestor (LSCA).
• Functional genomic analysis and phylogenetic profiling to identify adaptive genes and pathways.

Main Results:

• The LSCA was determined to be a motile, endoflagellated bacterium with a heterotrophic metabolism.
• Spirochaetes diverged into two major clades, with *Brachyspira* species diverging early.
• Loss of endoflagellar genes correlated with the emergence of non-spiral species and host-associated lineages.
• Novel motility-associated gene families were identified and experimentally validated.

Conclusions:

• This study provides a robust evolutionary framework for the Spirochaetes phylum, clarifying their deep evolutionary roots.
• Genomic insights reveal key adaptations, including the loss of spiral morphology and development of host association, driven by ecological specialization.
• The findings offer a foundation for further research into the evolutionary mechanisms shaping this clinically important bacterial group.