Which sequencer or sequencing technique are you used, check the adapter (Seq. flanking at end of the desired gene to be sequenced and complementary seq. to the lane sequences, where does get bind for sequencing) primers quality.

What do you mean exactly saying "Sequencing was attempted for 3 times but failed"?

Are you sequencing with Sanger or NGS? What bacteria are you trying to sequence, pure culture in the case of Sanger, I assume.

Hi,

If you are doing sanger sequencing then you have multiple bacteria spp. In the sample.

If next gen sequencing then the adaptors are probably the problem 

The problem could also be multiple copies of the 16S rRNA gene with sequence variations in your organism. Then the sequencing with Sanger fails.

I have out sourced my sample for sequencing. They have used ABI 3500 DNA sequencer. My sample is a pigmented bacteria, so the chances of contamination is also negligible as the DNA is isolated from an isolated colony. 

You have to be more specific on the type of failure you had. I.e. .If you could obtain a sequence but is plenty of "N", probably you have a bug with several rrn operons, but if you don't have any sequence at all, then you have to check your sequencing reaction; componente, conditions, etc.

I think that you must start with a pure culture and  that you know the genius of your bacteria. You could align several 16s ribosomal DNA of the same genius. Then it allows  to determine the more conserved region flanking the hypervariable regions. Then  after AT cloning of the PCR product ( aproximatively 400-600 bp) you could obtain an informative sequence.

A other problem is that if you have nomber of differents bacteria, you will obtain a PCR product containing a mixed of 16S ribosomal DNA  (one part of one bacteria and an other  part from an other bacteria on the same PCR product more specificaly if you uses commercialy avialable generic primers able to amplify 1.400 bp) that is unable to be use to identify a specific bacterai after sequencing.