Ammonia-oxidizing archaea in host-associated environments and the oral microbiome: Ecological evidence and molecular...

Ammonia-oxidizing archaea (AOA) are key contributors to environmental nitrogen cycling. Reliable detection methods are needed to investigate these low-abundance microorganisms. This review aims to: (1)synthesize and contextualize the evidence on AOA, with an emphasis on the oral microbiome; and (2)evaluate primer sets targeting the amoA gene (encoding ammonia monooxygenase) to support the selection of molecular markers for future investigations of AOA in oral samples.

A narrative review with an exploratory in silico primer analysis was performed. Evidence of AOA detection across environmental and host-associated microbiomes was synthesized, including AOA findings in oral microbiome studies. Published amoA-targeting primer pairs developed for environmental communities were evaluated against reference genomes representing AOA lineages reported in human-associated samples. Reference amoA coding sequences were retrieved from genomes and aligned with each primer pair to compare primer-template compatibility, annealing characteristics, and sequence mismatches across AOA representatives.

AOA was predominantly detected in the oral microbiome based on molecular detection and does not yet distinguish active oral residents from transient organisms or environmental exposure. AOA-related sequences, including signatures assigned to Nitrososphaerota, have been found in oral and caries-associated samples. Although their residency is plausible, stability and metabolic activity still have to be studied. For that, an exploratory analysis showed good performance of four primers, but also the need of more reference sequences to have definitive information.

Current evidence remains insufficient to define the ecological or functional role of AOA in the oral microbiome. Broader in silico assessment and experimental validation in oral samples are required before specific primer sets can be recommended.