Why does BLAST results give 100% similarity to two bacterial species and only identified to the genus level?
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?
Hi there!
It sounds like you've encountered a common issue with BLAST results when dealing with closely related bacterial species. When BLAST gives you 100% similarity to two different bacterial species, it usually means that the sequences in the database for those species are extremely similar or even identical in the region you amplified. This can happen because 16S rRNA gene sequences, which are commonly used for bacterial identification, sometimes don't have enough variability to distinguish between very closely related species.
For your lignolytic organism, the identical matches to two different species suggest that the 16S region you sequenced is conserved between those species, making it impossible for BLAST to differentiate between them based solely on that sequence.
Here are a few things you can consider:
- sequence a longer or different region
- use a different database
- tools like RDP (Ribosomal Database Project) or SILVA can sometimes provide more insights into bacterial taxonomy based on 16S rRNA sequences
Good luck with your research!
Some things to keep in mind when interpreting BLAST results are listed in Article Five simple guidelines for establishing basic authenticity a...
The 16S annotations in INSDC are messy. You could try a BLAST against type strains only: https://www.ncbi.nlm.nih.gov/refseq/targetedloci/
But BLAST does local alignment and so may not always give you what you probably want: similarity statistics based on a full-length global alignment. Download the (type) sequences of interest and use MAFFT to align your sequence to them.
bacteria[ORGN] AND sequence from type[FILTER] AND 16S[TITL]
gives you only type-derived sequences. Replace "bacteria" with the species name you have in mind.
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