Hi there,
I was trying to identify and compare the bacterial community of primates from two areas, and at the same time trying to identify zoonotic bacteria.
But the problem is how is a database (specifically zoonotic bacteria) created, and where can we get the up-to-date official database of these zoonotic bacteria?
You’d have to do this yourself. I’m not sure how well a “zoonotic bacteria” classification would work since there are so many bacteria that can easily transition between environments.
Pat
Thanks Pat. Do you think instead of creating a database, it would be easier/better to get representative sequence of each OTU and BLAST it instead?
Eh, probably not. Besides blastn having worse performance than the naive Bayesian classifier, I’m not a big fan of environment or phenotype specific databases. Why not run the data through one of the available general databases and see what comes out? Based on the taxonomy you get you can then make these types of further associations.
Pat
Heyya Pat.
Thanks for the reply. I did run it using SILVA database. But then my PI also wants to look for “zooonotic” bacteria/ pathogens from those result. However, I think it is quite hard since not all of the bacterial species in a certain genus is pathogenic, and some are merely opportunistic. It’s quite vague on what is termed as “zoonotic”.
I think that’s the exact problem with trying to create a “zoonotic” database. Often what makes something pathogenic is a set of genes or plasmids that have little relation to the 16S rRNA gene (e.g. E. coli)
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