I did 16S rRNA sequencing and SEM analysis for the morphological characterization, but I want to know, how can I be certain that this is a new species?.
Go for Polyphasic taxonomic analysis, deposit your strain atlleast to two culture collections for confirmation and importantly use EzTaxon database, not GenBank.
You should go for poly phasic taxonomy and also follow Nanomura 1974 article. Although you give the pure strain for 16 s identification, it may be chances of miss leading of the appropriate sequencing. So before sequencing you kindly repeat your biochemical test. It also the chances of getting bacterial contamination during the handling of the culture in Sequencing laboratory.So the best to do in your lab and after getting confidence than go for sequencing.