- Philosophy: NCBI - Curator-driven, phenotypic and genotypic data; GTDB - Genome-based, phylogenetically consistent.
- Data source: NCBI Refseq and Genbank; GTDB - NCBI Refseq and Genbank
- Species definition: NCBI - Less stringent, often based on 16S rRNA gene sequence similarity [1]; GTDB - Stricter, based on ANI values (>95% for bacteria) [2].
- Higher-rank classification: NCBI - Traditional Linnaean ranks (phylum, class, order, etc.); GTDB - Ranks are normalized based on evolutionary divergence (phylum level for Bacillota can be Bacillota, Bacillota_A, Bacillota_B; ) [2].
- Schoch, C.L., Ciufo, S., Domrachev, M., Hotton, C.L., Kannan, S., Khovanskaya, R., Leipe, D., McVeigh, R., O’Neill, K., Robbertse, B., Sharma, S., Soussov, V., Sullivan, J.P., Sun, L., Turner, S. and Karsch-Mizrachi, I., 2020. NCBI Taxonomy: a comprehensive update on curation, resources and tools. Database, 2020, baaa062.
- Parks, D.H., Chuvochina, M., Waite, D.W., Rinke, C., Skarshewski, A., Chaumeil, P.-A., and Hugenholtz, P., 2018. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nature Biotechnology, 36(10), pp.996-1004