What is the best molecular method to identify the novel bacterial specie, if we can use MLSA as a replacement of DNA-DNA Hybridization for this regard? Please post your suggestion here.
If you can get WGS data then ANI can accurately replace DDH values. DDH techniques can be time-consuming, and are not easy to carry out in routine laboratories.
Sensors based on DNA-DNA hybridization could be applied, e.g. in attached publication.
Article Pulsed amperometric detection of DNA with an ssDNA/polypyrro...
Muhammad,
It depends on taxonomic position of your strain. If it belonged to well-known taxa with available type strains of related species - you can use DNA:DNA hybridization to prove that it is different. MLST/MLSA is good for such case as well, but not useful for poorly studied genera. Complete genome sequencing is a method of choice for any strain, if you can do it.
If you can get WGS data then ANI can accurately replace DDH values. DDH techniques can be time-consuming, and are not easy to carry out in routine laboratories.
Dear Andrew, yup agreed and i go through many studies, where it is clearly elaborated DDH is time consuming, laborious as well as not available in all Laboratories, recalling all these factor, i am working on its replacement, like MLSA so want to know how much effective in this regards?
Dear Alex
its means MLSA as effective as DDH to well-known taxa with available type strains of related species and we can use it for species identification and WGS is too difficult as DDH also not easy to carry out in routine, so if you suggest any study regarding MLSA effectiveness as compared to DDH and WGS???
Again, it depends on taxonomic position of your bacterium.
All works known to me have supported MLST data by ANI or DDH (see http://dx.doi.org/10.1016/j.ijmm.2014.02.002, et al.).
I believe that journal publication on new species designation could be accepted if you provide enought MLST data for all previously known species in the same genus ( I would suggest to sequence parts of 7-9 genes, again, depending on your bacterium) and study AFLP profiles + all phenotypic traits demanded for new species.
But, so far MLST was used to deny newly described bacterial species (Boité MC, Mauricio IL, Miles MA, Cupolillo E. New insights on taxonomy, phylogeny and population genetics of Leishmania (Viannia) parasites based on multilocus sequence analysis. PLoS Negl Trop Dis. 2012;6(11):e1888.).
Be careful with calculation of recombination events based on MLST - we have got completely opposite conclusion based on WGS analysis.
Sure, if you bacterium represents new genus, you should not do DDH or ANI. 16S rRNA and MLST would be sufficient.
I might be tempted to side with DDH for novel phyla/family rather than species, which might have varied genes that cannot be captured by MLST.
DDH is performed at institutions for a fee like DSMZ where one can expect a consistent lab protocol and performance.
But if the isolate is close phylogenetically to a well established strain then one can expect the MLST to work well.
One more option is to apply molecularly imprinted polymers, as it is presented in attached paper:
Article Molecularly Imprinted Polypyrrole for DNA Determination
Dear Jay,
but DDH is laborious and time consuming then what will be the substitute of it for identification of phyla/genus ???
for DDH i suggest either have it done professionally like at DSMZ or find a collaborator who can do it reproducibly.
Yup means still time consuming and laborious. Want to search and work on new alternatives methods which done on simple and economical way that,s way posted this query. Thanks to all but if find any new updates in this regards please post a comment. Stay happy
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