when someone want to describing a novel bacterial subspecies , he or she asked to do extra testes such as molecular, which testes are the best and necessary for this case?
Are you referring really to subspecies? or to species?
Well the best way for you to identify a novel species of bacteria is to amplify its 16S rDNA gene. It is about 1,600 bp and you need to compare its 16S rDNA to different species (called type strains) under the same genus using Phylogenetic methods. Please go to this website to see the different species of your organism and assigned type strain to use for comparison http://www.bacterio.net/index.html
If you plan to publish your nov.sp. then please try to look at the requirements of this journal http://ijs.sgmjournals.org/ There are several tests other than molecular methods that you need to include and compare it to the type train species
Now if it is subspecies, then it depends on the organisms you are working on. You may use different molecular markers that are deemed for that organism to be a subspecies. Better yet, you can use MLST... but like I said previously, you will be needing the markers for identification of a subspecies.
Dear Thaddeus Carvajal
Thank you for your replay
My strain is from genus salicola I did all the required testes and sent its manuscript to IJSEM. but they replayed that 16s rRNA and DNA-DNA hybridization results are not as enough to name the strain as novel sp. And the strain is subsp.
16s rRNA similarity with the closest sp. was 99.2% and DNA-DNA hybridization is 76% so I think I should do interspecies molecular testes. I am looking for that kind of testes
Dear Mushtaq,
Please do try and research on Multi-Locus Sequence Typing for molecular techniques.
Did you include biochemical tests for your submission and FAME profiling?
Dear Thaddeus
I did fatty acid profiling. and want to do GTG-PCR and RFLP are These testes enough on not?
Dear Mushtaq,
Yes you may use either of the two. But I prefer GTG-PCR on the subspecies question you are pertaining to.
Dear Thaddeus
I did GTG-PCR and I ordered 5 RAPD -PCR primers for RAPD.
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