A database of "evidences" and "hypotheses" for the study
of culture conditions of obligate parasitic bacteria.
Reference: Ogata & Claverie, Nucleic Acids Res. (2005)
There are many pathogenic bacteria that we cannot cultivate
in a cell-free ("axenic") culture medium. The development of an appropriate
culture condition is critical to implement modern microbiological techniques
to characterize the pathogens.
In the previous work, we analyzed the genome sequence of a human pathogen,
Tropheryma whipplei, and identified putative metabolic deficiencies
(Raoult et al., 2003).
This genome sequence-derived knowledge guided the first successful design of the
cell-free culture medium to cultivate
this bacterium, that was previously cultured only in human fibroblast cells
(Renestro et al., 2003; pdf).
We believe this type of approach should lead to other successes
in growing previously uncultured parasitic pathogens.
Metagrowth is a new type of database aiming to guide experimental studies and
in silico simulation studies on the culture conditions of obligate parasitic
Now we are gathering biological data relevant to the improvement of culture
conditions of different obligate parasitic bacteria, and organizing a database
The data were collected from literature, genomic sequence
information, metabolic databases and transporter databases.
Each database entry is composed of evidences and derived hypotheses.
The hypotheses are physical conditions or supplementation of molecules
in culture media, that may lead to the improvement of the bacterial growth.
Currently about 200 entries are available for six different bacteria.
Bacteria in the Metagrowth database:
About the bacteria
Components of known culture media for fastidious ("difficult-to-culture") bacteria
Start to design culture media
Flat file distribution
Metabolic pathway data (Tropheryma whipplei)
Great thanks to the developpers of the following databases and software that are used to develop Metagrowth:
We look forward to your feedback about Metagrowth.
This web page is maintained by
Hiroyuki Ogata at
Structural & Genomic Information Laboratory.
(c) Hiroyuki Ogata (Last update Oct 7, 2004)