Introducing Clinical Nanorachaeaology: Isolation by Co-Culture of Nanopusillus massiliensis sp. nov

Background: Nanoarchaeota, obligate parasites of some environmental archaea with reduced genomes, have been described in marine thermal vent environments, yet never detected in hosts, including humans. Methods: Here, using laboratory tools geared towards the detection of nanoarchaea including PCR-sequencing, WGS, microscopy and culture. Results: We discovered a novel nanoarchaea, Nanopusillus massiliensis, detected in dental plate samples by specific PCR-based assays. Combining fluorescent in situ hybridization (FISH) with scanning electron microscopy disclosed close contacts between N. massiliensis and the archaea Methanobrevibacter oralis in these samples. Culturing one sample yielded co-isolation of M. oralis and N. massiliensis with a 606,935-bp genome, with 23.6% GC encoded 16 tRNA, 3 rRNA and 942 coding DNA sequences, of which 400 were assigned to clusters of orthologous groups. Conclusion: The discovery of N. massiliensis, made publicly available in collection, extended our knowledge of human microbiota diversity, opening a new field of research in clinical microbiology here referred to as clinical nanoarchaeology. Funding Information: This work was supported by the French Government under the «Investissements d’avenir» (Investments for the Future) program managed by the Agence Nationale de la Recherche (ANR, fr: National Agency for Research), (reference: Mediterranee Infection 10- IAHU-03). Declaration of Interests: All the authors declare that there are no conflicts of interest. Ethics Approval Statement: The ethics committee of the University-Hospital Institute Mediterranee Infection approved this study under number No. 12-008. Accordingly, all patients received information about the study and gave an informed consent prior to the reported investigation.