A. Hiergeist, J. Ruelle, S. Emler, A. Gessner. PLOS ONE. 16 February 2023, Article Link:  doi: 10.1371/journal.pone.0280870. 

Reliable and reproducible microbiome testing in clinical practice requires standardization of methods and comprehensive, representative, up-to-date reference databases. In this article in PLOS ONE, read how SmartGene's BiomeScan Apps for Microbiome analysis and SmartGene's proprietary Centroid reference databases can meet these needs. This email address is being protected from spambots. You need JavaScript enabled to view it.

Citation: “... For data analysis with the SmartGene pipeline, FASTQ files were uploaded to the protected cloud-platform. The SmartGene IDNS-5 Bacteria 16S Microbiome App is a commercial CE-IVD labeled automated cloud application service of SmartGene (SmartGene, Unteraegeri, Switzerland, www.smartgene.com). It uses a proprietary SmartGene "16S Centroid" database of non-redundant representative bacterial 16S rRNA sequences covering 15,960 species across 3,161 genera as of May 2020, which is maintained and updated using AI and algorithms (patent #EP02215578). A sliding-window filter eliminates low quality sections of reads, and the resulting contigs are mapped against the reference sequences without prior binning. Results are grouped according to match quality (e.g. % of coverage, number of mismatches, etc.), match specificity (matching a single species or not), and match consistency (close matches belonging to the same genus). The system produces a confidence score for the matching taxon, and if a species cannot be called specifically, the system assigns the next taxon level and indicates all possibly matching species and genera. Results are displayed in a table format, along with the number of reads and the relative abundance, and can be consolidated to the species, genus, and family levels, along with a dynamic Krona diagram. Abundances are measured by the count of reads mapped to a specific species/genus/family. ... Algorithm-curated databases such as SmartGene’s 16S Centroid databases hold the promise of more frequent updates with adequate representation of natural diversity. In order to appreciate the quality of the curation, users should have access to [the database's] principals, to a list of species covered in the database, the number of sequences evaluated to select representative records, and be aware of the frequency of updates. ... ”