I am using 16S rRNA gene analysis for identification of bacteria. But for an organism show 100% 16S rDNA sequence (~1400 bp) homology to two species B. megaterium and B. ariyabattai according to the NCBI database (Nucleotide collection and ref-sequence). Anybody know any other specific method to identify B. megaterium?
You can explore new primer design. Have you tried all the biochemical tests? Also check if some one has performed PCR-Restriction fragment length polymorphism analysis on it. Hope this helps
Hi: This is some useful papers:
http://www.microbiologyresearch.org/docserver/fulltext/micro/130/7/mic-130-7-1871.pdf?expires=1489680199&id=id&accname=sgid025581&checksum=DACCFDC6812909CEDD0CE49DB315DA2D
http://www.ec.gc.ca/ese-ees/2BA6CA56-B883-4159-AE17-7EC5EC2159AC/DSAR%20B.%20megaterium%20EN-clean%20CR.pdf
http://www.ec.gc.ca/ese-ees/2BA6CA56-B883-4159-AE17-7EC5EC2159AC/DSAR%20B.%20megaterium%20EN-clean%20CR.pdf
Another way is use seqmatch from rdp database: https://rdp.cme.msu.edu/seqmatch/seqmatch_intro.jsp
Is reallly difficult discover specie using only 16S rDNA, but you can try. Make comparations in distinct databases, ncbi, embl (ena database:http://www.ebi.ac.uk/ena), rdp database, ez taxon (https://rdp.cme.msu.edu/seqmatch/seqmatch_intro.jsp).
Phylogentic analyses could be help you.
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