Recommended guidelines for use of 16S rRNA gene sequencing for microbial identification

Strain to be sequencedPhenetic profile of strain is not known by general grouping to present difficulties for identification by 16S rRNA gene analysis (Table 2)
For strains such as those in Table 2 requiring molecular identification, another housekeeping gene is required (e.g., rpoB)
16S rRNA gene sequencingMinimum: 500 to 525 bp sequenced; ideal: 1,300 to 1,500 bp sequenced
    <1% position ambiguities
Criteria for species identificationMinimum: >99% sequence similarity; ideal: >99.5% sequence similarity
Sequence match is to type strain or reference strain of species that has undergone DNA-relatedness studies
For matches with distance scores <0.5% to the next closest species, other properties, including phenotype, should be considered in final species identification