Table 1 Proposed standards for high-quality taxa descriptions of uncultivated Bacteria and Archaea

From: Uncultivated microbes in need of their own taxonomy

Characteristic Standards
(1) Genome quality >80% completeness with <5% contamination
(2) Species genetic discreteness <95% ANI to the closest species
(3) Phylogenetic affiliation Based on 16S rRNA gene or housekeeping gene analysis and tree reconstruction with the closest relatives
(4) Category thresholds
For (same) family, genus and species
For a new domain, phylum, order, class and family
AAI: 45–65%, 65–95%, 95–100%
16S: 92–95%, 95–98.6%, >98.6%
16S: <75%, 75–83%, 83–86%, 86–89%, 89–92%
(5) Phenotypic discreteness Bioinformatics annotation of metabolic pathways using the minimum standards for a genome sequence description
(6) Ecological characteristics Recruit a shotgun metagenome against the genome sequence, define area of sequence discreteness, quantify intrapopulation sequence diversity level and estimate relative abundance. Similarly, assess abundance in additional metagenomes/samples (when available) and gene content or sequence identity differences between populations from different samples
(7) Experimental validation Verify bioinformatics predictions experimentally using methods, such as MAR-FISH, NanoSIMS or meta-transcriptomics/proteomics and so on
(8) Cell morphology Microscopic identification by FISH or another visualization technique
(9) Data release Submit genome sequence and Protologue to webserver
  1. Abbreviations: AAI, amino-acid identity; ANI, average nucleotide identity; MAR-FISH, microautoradiography and fluorescence in situ hybridization; NanoSIMS, nanoscale secondary ion mass spectrometry. Characteristics 1–6 and 9 should accompany every new species description; characteristics 7 and 8 should be obtained, whenever possible, in order to provide richer descriptions and facilitate future research.