I did BLAST of the two cellulolytic species and one lignolytic species of bacteria after 16S amplification using PCR. However, my results indicate that the lignolytic organism is 100% similar to two different bacterial species. BLAST have only identified up to the genus level in my cellulolytic bacterial species. Can anyone assist to explain what has happened?
That's exactly what you would expect to happen. The 16S gene can only get you genus level resolution in bacteria.
Pick another region or two to sequence to get to species level resolution.
BLAST results may show 100% similarity to two bacterial species but only identify to the genus level because the sequence is highly conserved among species within the genus, the query sequence is too short to distinguish species, the database is incomplete or lacks detailed annotations
Katie A S Burnette , What should I do? Can you explain further? I am new this field
You'll have to find a few other genes to sequence to get species-level resolution. The 16S is identical in many different bacteria genera.
Talk with your research advisor, they can help you choose the additional genes.
Katie A S Burnette Thank you very much. We are going for whole genome sequencing of the isolates
Keep in your mind, that there is not "gold standard" genomes of type strains. Unfortunately this is not possible ! Live bacteria change his own genomes by normal way and this is necessary for adaptation and evolution.
16S is not discrimination method for species definition in all cases. Very often databases are polluted with sequences from non-corect identified species. Your decision for full genome seq is correct.
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