Actifensin Evolution in the Human Oral Cavity over the Past 100,000 Years

Bacterially produced antimicrobial peptides (AMPs), or
bacteriocins,
play key roles in shaping microbial communities via interspecies competition.
Unlike the more temporally dynamic gut microbiome, the oral microbiome
exhibits long-term stability and is preserved into deep time in dental
calculus, enabling evolutionary analysis across time. Here, we combine
metagenomics, structural modeling, and experimental validation to
investigate AMP diversity in ancient and modern dental biofilms from
humans, Neanderthals, and nonhuman primates spanning 100,000 years.
Using our newly developed platform, AMPcombi, we uncover evolutionary
trajectories of bacteriocins and elucidate their ecological functions.
Among these, we identify a conserved family of Actinomyces-derived
defensin-like peptides, termed actifensins, present across all time
periods. Phylogenetic, structural, and functional analyses revealed
shared ancestry and adaptive diversification between ancient (paleo-)
and modern actifensins, with evidence of positive selection and maintained
antimicrobial activity. Our findings position the oral microbiome
as a valuable reservoir for natural product discovery. In the face
of rising antimicrobial resistance, evolutionary insights into AMP
function open a door to next-generation therapeutics. AMPcombi streamlines
this process, linking ancient biomolecules with biotechnology.