Question: --Strain-level sensitivity for Bacillus--
0
gravatar for estybri
3.1 years ago by
estybri0
estybri0 wrote:

Hello,

After performing shotgun sequencing, I would like to know if it's possible to achieve strain-level sensitivity for Bacillus. I am not sure if Kraken, GOTTCHA and other tools can lead to the strain level.

I have a metagenomic data which I want to characterize, qualitatively and quantitatively. Genus: Bacillus -> different Species: ...->Strains: ...

Thanks!

ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by estybri0

Please clarify, if you want to discriminate species with the genus Bacillus, or if you would like to discern strains within a certain species. Please also note that the term 'strain' is not well defined on the level of whole genome sequences.

ADD REPLYlink written 3.1 years ago by piet1.6k

I added some details above. I am not sure if I undersatnd your note about the term 'strain'.

ADD REPLYlink written 3.1 years ago by estybri0

Your are doing some metagenomics, but I still do not know exactly what kind of experiment you have done. Why do you believe that you have sequenced only Bacillus?

Strains of a certain species can be differentiated either based on SNP in some genes belonging to the core genome of the species (Multilocus Sequence Typing), or by the presents of absents of certain groups of genes in the accessory genome (Regions of Difference).

ADD REPLYlink written 3.1 years ago by piet1.6k

Thank you piet, I get and sequence a sample from a researcher, which I want to characterize. I don't know which species there are but I assume that I will find different strains of Bacillus. Moreover, I would also like to see which other bacteria there are in the sample. I am interested in the best resolution as possible

ADD REPLYlink modified 3.1 years ago • written 3.1 years ago by estybri0

All strains of a species are still the same species (infra-specific level).
It sounds like you are using those two terms interchangeably, which is not correct. Do you expect multiple species of Bacillus (and other microorganisms), in addition to multiple strains within each species?

ADD REPLYlink written 3.1 years ago by genomax65k

Theoretically, we expect to have different strains of Bacillus, BUT we also want to make sure there are no other genus/species/strains.

ADD REPLYlink written 3.1 years ago by estybri0
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