Help - microbiology databases - (May/08/2007 )
Hello to all
I've just searched the forum about my problem and find exactly what i'm looking for (post from jpopesku).
So, jpopesku and the others, is there any database in which I can find these parameters? I find something, but all I've find is an incomplete databases.
And who is that Bergey? Author of microbiology book? I'm not a microbiologist, I'm a molecular biologist and I don't know lots of microbiology, but i have to collect all these parametars for all bacteria and archaea that have sequenced genome ( that is a part of my PhD)
Thanks a lot
Any help would be great
Some parameters I'm interested in:
-biomass yield on a particular substrate
Does anyone know if something like this exists online, or will I have to spend massive amounts of time in Bergey's?
I'm not sure that there is a database set up for this . . . at least not that I've seen. Bergey's Manual of Systematic Bacteriology or Bergey's Manual of Determinative Bacteriology have always been the go-tos for this sort of thing. (Beware, the MSB is huge!) Failing access to that from a library, I'd maybe suggest hitting the systematic bacteriology journals? International Journal of Systematic and Evolutionary Microbiology is where the valid nomenclature is published, but there might be something there, or in a related journal. Possibly, the only other thing to do is hit Pubmed and hope you get a winner.
Is there Bergey's Manual of Systematic Bacteriology on-line edition?
I also thought that cultivation database would also be helpful, because optimal growth conditions are approximatley same as the enviroment conditions( at least for parameters that I need). Is that also in Bergey's?
If I can find right and good book, I can ask my boss to buy it, but it would be bad if I ask for buying a book that would not be helpful.
I seem to recall once upon a time that there was supposed to be an online version . . . but I can''t find one at the moment. (It'd probably be expensive too.) I don't know what sorts of bacteria you're studying, but I think I'd recommend checking out the Manual of Determinative Bacteriology first since you're not familiar with the books.
The MDB is a condensed version of the Systematic for quick reference use, but being condensed it doesn't have all info. Furthermore, it's not a culture book as such . . . it will tell you how to differentiate species, serotypes etc. based on testing characteristics in common bacteriological tests. It should have info, say, on growth temp and overall nutrient requirements, but it's not a recipe book for media nor will it have arcane knowledge like radiation susceptibility unless that's pertinent to identifying the species from others. It's also not cross-referenced, that I recall, which would likely be a feature of a database. The MSB is of course more extensive and in-depth.
You can have a look, but it may not have all you need. I'd recommend borrowing one or buying the MDB off a used books site for cheap (I had to buy it for an undergrad course, so it's not too dear). Be advised--I think the Manaul of Systematic goes for about $700/volume or something crazy like that.
Correction: I found it for $400/volume (though you'd probably only need one) but still, awful costly for something you'd not 100% sure you'd need.