microorganisms database

[Serhat Sevli]

Hello at all,

I am a recent follower of DIY Bio and this is my first e-mail here. So please forgive me if I am asking a question discussed previously.

I am going to start a research on developing new microorganisms for endustrial applications. I am looking for a database that provide phenotypic features of both commonly used and other microorganisms. I am not interested in classification, philanthropy or genomic sequences since there are plenty of resources on the net. I need to search info such as H2S metabolizing bacteria or high pressure resistant x-molecule consuming microbe...etc

thanks in advance

--

Serhat Sevli, MSc

Genetikçi (Geneticist)

erke....@gmail.com

[Patrik]

Does not exist, sorry...

At least not for the *general* case. I actually wasted over a year of
my research career at one point trying to chase down and compile this
type of information and eventually gave up in frustration. One of the
big problems is that there are/were no controlled vocabularies for any
of this. (Heck, try looking up in different microbiology text books
what is considered the temperature boundary between "mesophile" and
"thermophile" and see what happens... 5 textbooks, 5 different
answers!)

Now, for specific subsets of phenotypes, you can find useful tables
left and right. Just not all in one convenient place. For example,
NCBI has a nice table that at least shows basic microbial phenotypes
such as cell shape, motility, salinity, etc:

http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi/lproks.cgi (click on
"Organism info" tab, top right)

The Genomes OnLine Database (GOLD) has some more general phenotypes
such as energy source, etc:

http://www.genomesonline.org/cgi-bin/GOLD/MetadataSearch.cgi

The JCVI's old Comprehensive Microbial Resource database actually
still has the best developed ontology for "genome properties",
including metabolism, biological niche, etc. Not sure whether it's
been maintained over the past 5 years though:

http://cmr.jcvi.org/cgi-bin/CMR/shared/GenomePropertiesHomePage.cgi
http://pathema.jcvi.org/cgi-bin/Bacillus/shared/GenomePropertiesHomePage.cgi

Finally, for metabolic pathways, best thing to do is probably looking
up the pathway of interest at one of the big metabolic pathway
resources such as KEGG (http://www.genome.jp/kegg/pathway.html) or
MetaCyc (http://metacyc.org/META/new-image?object=Pathways), and then
checking which organisms have that pathway. If you can narrow it down
to a specific enzyme, BRENDA (http://www.brenda-enzymes.org/) is an
excellent resource.

Tying all of these different sources of information together is
obviously a huge nightmare - that's why I gave up on it. Things *are*
getting somewhat better though. Ontologies and controlled vocabularies
are being developed, thanks in part to the efforts of the Genomic
Standards Consortium and Open Biomedical Ontologies. Getting people to
actually *use* them is another matter, but at least the GSC is getting
a lot of buy-in from funding agencies and sequencing centers.

And then lastly... the best database for queries such as "H2S

metabolizing bacteria or high pressure resistant x-molecule consuming

microbe" may simply be the scientific literature (pubmed or Google
scholar), or just plain Google. Google really excels at searching
through craploads of material with no discernible organization - which
is sadly the current state of affairs for much biological knowledge...

> *Serhat Sevli, MSc*
> *Genetikçi (Geneticist)
>
> erke.bi...@gmail.com*

[Serhat Sevli]

Hi Patrik,

Thank you very much for your effort of giving these info.

So, I think I will spend some months to find the most suitable organisms. Starting from these links will ease my work.

thanks again

serhat

11 Şubat 2012 04:24 tarihinde Patrik <pat...@gmail.com> yazdı:

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Serhat Sevli, MSc

Genetikçi (Geneticist)

+90-535-628-7887
erke....@gmail.com