I used a 16s rRNA universal primer for identification of unknown bacteria . Is it possible to identify bacteria as the PCR product size near 1000 bases, because 16s rRNA gene is of 1500 base?
I think, 1000 nt sequence of 16S rRNA gene is enough to provide you the preliminary identification of the bacterium; however, to identify the strain you will need to sequence some more region/genes like intergenic 16S-23S rRNA spacer regions (ISR), several house keeping genes etc. Lipid profiling and nucleic acid hybridization are also suggested.
Dear Amit Pande
I agree with Md Firoz Mortuza.
In addition, 16S rRNA gene contain of conservative and signature sequences. If you know partial sequence of 16S rRNA gene, you can recognise of unknown bacteria.
Best, Roshdi
Hi
its dependent to your bacteria . if your bacteria is a common bacteria you can do. what is your bacteria?
Did you perform BLAST search? It should give you an idea about your bacteria. You can use the Nucleotide BLAST tool of NCBI (http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&BLAST_PROGRAMS=megaBlast&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&LINK_LOC=blasthome) and see the similarity result.
Yes i did BLAST search but difficult to find exact isolate bcoz there are number of species in results.
The usual thing to do is to perform a BLAST search, but you should be aware that every hit that has >98% similarity
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