How do I translate phylogenetic tree-Neighbor joining to explain the related species to my identified isolate. Because my sequencing results indicated 99% relation with my isolate and other species. So I need to know which one should I consider
Your tree attached as PDF show a 16S rRNA sequence apparently more closely related to Bacillus anthracis 16S rRNA than to other isolates of Bacillus cereus and other Bacillus species. But a tree with meaningless branch lengths such as the one you show, is a cladogram rather than a tree, and without knowing the sources of the sequences it is impossible to say much about this cladogram.
There are dozens of complete genomes of B. anthracis in GenBank now, and each genome has 8 or more copies of the 16S rRNA gene in it. On top of this, there are many more dozen 16S genes or cDNAs sequenced from other strains and isolates. If you BLAST any one of these 16S rRNA sequences against GenBank you find that there are hundreds of entries listed as B cereus, B. thuringensis, B. anthracis, and other species names all with 99% to 100% identity to each other. So sequencing the 16S rRNA is enough to determine if a bacteria is in this general group of bacteria, but not enough to identify which species it is for sure.
Refer to Emerging Infectious Diseases 8(10) Oct 2002 page 1117-23. There is debate on usefulness of 16S sequence to identify B. anthracis/cereus/thurigiensis. As you must be knowing, Bacillus cereus, B. thurigiensis and B. anthracis have been considered as genomospecies. So you may not be able to consider identification of your isolate on the basis of your phylogeny (cladogram here) in this case. Now you have to carry out discrete phenotypic testing of your isolate to identify it. You can culture it in Sheep Blood agar to see hemolysis (B. anthracis is non-hemolytic on SBA), motility (B. anthracis is non-motile, is susceptible to penicillin disc and has mucoid medusa like colonies on Nutrient Agar. By the way, 16S sequence may be good for species level identification in some other cases, and as mentioned by Dr Brian, test your sequence with phylogeny construction using type strains. One phenotypic character of thurigiensis is parasporal crystals. Hope this helps.
I sugget to use some additional regions which are phylogenetically informative for species description or better resolved phylogenies.
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