Hello Oluwaseyi, 

A lot of natural product laboratories utilize a variant of methanol extraction for secondary metabolites. In bacterial realms, you want to filter off the (assuming liquid) media and place the cells in methanol. Some labs stir/shake the mixture for an extended period of time, so as to extract as much as possible. This would then be followed up by filtration and your resulting supernatant is of interest. The methanol will lyse the cells and your compounds may be happily soluble in it. If they are not, then a mixture of solvents may be of interest. 

Largely though, this would need to go through some sort of chromatographic separation, so you can tell what you're looking at. Otherwise, you will be overrun by a number of primary metabolites and sugars from your extract.  

I have seen variants of solvent mixtures depending on what metabolites you are looking for. For instance, the metabolites may be more soluble in a water: methanol mix than just methanol, or Chloroform: methanol mix. Just a heads up, I have seen ethanol being used a lot, especially for dietary supplement extraction. However, methanol has a higher extraction potential, so if it fits into your protocol well, I would suggest that. 

Additionally, some labs do liquid partitioning of the extracts once they have extracted from the cells to remove fatty acids and the like. Methanol: Hexanes or something of that nature tends to be standard. 

Admittedly, I am unfamiliar with what sorts of compounds you wish to look at, so just take into account this protocol may have some decomposition problems if your compounds in question are air/solvent sensitive. 

Cheers, 

Joe

in my opinion, first you have to determine which kind of metabolite you are looking for and then you can use one of the methods cited above. I tell you that because the rhiznbacteria can use a multiple of mechanisms for the biocontrol of others bacteria and this needs a large number of primary and secondary metabolits

Hi Oluwasey

I agree with Bouznad, there are many solvents

thanks everyone for your responses.