Dear Mostafa, the gold standart to show genetic relatedness of the bacterial strains from the same species is pulsed-field gel electrophoresis (PFGE). If you carry out PFGE, you can find clonal relationships of the strains isolated from the same or different regions. You can find details related to foodborne staph in our papers. Some other methods are also used to identify clonal relationships, e.g. MLST, DNA sequence based methods.

Best regards.

Those bacteria isolated from two contrasting regions  , may or may not be different based on metabolomics or proteomics studies...

DNA finger printing can help in distinguishing  both isolates

Is it true that 16s rRNA method is not good enough to identification bacteria? please introduce new methods...

It will be interesting to know from our colleagues..how  two  similar bacterial species isolated from two contrasting soil conditions, will be different in what context..

16 S rRNA is very useful in your case to show the phylogenetic relationship between 2 isolates.

Two bacterial isolates from two different places may be of the same genus and species. You can determine their strains to check and confirm their difference at subspecies level through 16 S rRNA analysis. It' will hopefully help you unveil the their phylogenetic relationship.

"For the same, indeed, are those things of which the substance is one; but similar are those things of which the quality is one; and equal are those of which the quantity is one. And the one is the first principle and measure of number." --Aristotle

The same genus and same species does not means that these are same bacteria. They may different strains with several different traits. It also depends how could you established that both bacteria from different region is same. If you have took one criteria e.x. 16S rRNA gene similarity criteria then you have to do MLSA to check if really both bacteria are genetically and phylogenetically same. 

16  RNA has not been so effective in identifying bacteria of different strains. My experience is when same bacterial strains are subjected to 16 RN!A different times, reveals different strains..

In order to know if you have the same strain type, I would suggest an MLST approach. Or a genotyping method alternative to the one I refer above.There are currently alternative approaches to sequencing seven housekeeping genes (in general) available in the lierature, such as several SNPapshot approaches.MLST is time consuming but the fact that you have a database with information on strain types from all over the world may provide you with a better knowledge on the genetic relatedness of the strain you are studying.

I would suggest that you consult the MLST webpage http://www.mlst.net/databases and search for the species you are dealing with. Maybe there is already a well established method  such as sequencing protocols and priners used or performing this genotyping assay.

Good luck with your research.

The same species is, in fact, the same species, however, it is in the sequencing that and species determination that most of the differences become apparent.  Long reads can alleviate this with 16S to a certain extent, however, the bacteria may have differing sub-species too!

Bacteria may have difference at  strain level?  Source of sample is not a matter, molecular identification is the main method for differentiating the bacterial species using 16S rDNA. It should follow for exact identification by comparing the DNA sequence of 2 bacterial species using BLAST.  It will say you whether it is same or different?

I suggest whole genome sequencing.

Sequencing of 5 housekeeping protein coding genes and draw phylogeny would be enough to designate novel strains comparing with closest type strains. I agree that 100% similarity in 16S rRNA gene that of closest match with strain type strains can also be novel based on MLST. 

There are reports that bacteria may have multiple copies of 16S rRNA, so it is now days essential to go for MLST using at least 4-5 house keeping protein coding genes instead of only based on 16S rRNA phylognetic analysis. 

I suggest either  for whole genome sequencing or MLST using 4-5 housekeeping genes,