Microbiome research traditionally focuses on highly abundant microbes, often overlooking low-abundant species despite their potential to significantly impact microbial community function and contribute to dysbiosis. Our scoping review highlighted this issue, finding that many human microbiome studies using NGS employ arbitrary abundance cut-offs (e.g., <1%), which hinders a complete understanding of microbial diversity and the roles of rarer members like fungi and archaea, which abundances were infrequently reported. Addressing the specific challenge of studying low-abundant archaea in the oral cavity, we developed a specialised bioinformatic pipeline to re-analyse publicly available oral shotgun sequencing data (from 7 datasets). This targeted approach successfully detected low-abundance archaea (mainly Euryarchaeota, Thermoplasmatota, Nitrosphaeria) in saliva and plaque from individuals with and without dental caries. While methanogenic archaea were present in both groups, the analysis revealed methanogenesis genes were underexpressed in caries-active samples.