Unless there is any special selective protocol in a kit for different types of bacteria, it is highly likely that the kit you use will extract DNA from any bacteria that are in the culture. So you will end up with a mixture of DNA from all types bacteria that were there. Any commercial kit will do fine, but if you want to do large scale DNA extraction from many samples it can get expensive. I can recomend you using a method I've been using for fungi, which works very well for bacteria as well and it's very cheap and simple! Take a look here:

https://www.researchgate.net/publication/236197011_The_cdr1B_efflux_transporter_is_associated_with_non-cyp51a-mediated_itraconazole_resistance_in_Aspergillus_fumigatus

Hope it helps.

Article The cdr1B efflux transporter is associated with Non-cyp51a-m...

Hi, If your interest is to work with total DNA after extraction any kit can be fine. But if your interest if for a specific bacteria, then you should look for a specific kit. You should also consider the type media from which your culture is made, because inhibitors can affect the downstream process after extraction. In my lab I am using powersoil DNA extraction so that I extract total DNA for all bacteria found in a sample, the kits works perfect, you can try in your culture.

Good luck

I think that you should used of selective culture for your bacteria

Dear Marcin Fraczek

thanks for the reply. I have read your paper and seems to be a good method. As I want to extract DNA from mixture of bacteria (gram + and -) and work with total DNA do you think I can use your method for my experiment exactly as you described.

Dear Samson Kilaza

Thanks for you reply.

yes I want to work with the total bacterial DNA. After extraction, I need to amplify V2 of 16s rRNA and then 454 pyrosequencing to identify the total bacterial composition of the cultured media.

Do you think it is possible to extract total DNA from bacterial culture media and then identification and quantification of total bacterial composition in the media by 454 sequencing?

Try extracting using Chelex. It is simple and quite efficient. We used it to Extract DNA from sorted bacterial cells. Take a look at these papers.

Also this recent paper that used Chelex

http://www.ncbi.nlm.nih.gov/pubmed/23252765

Mohsen, the method described works on bacteria, fungi and plants. You can also extract DNA from human cells and it disrupts cells, releasing DNA to the solution. When you have a mixture of different organisms (in your case bacteria), you need to do sequencing to be able to distinguish between DNAs, which you will be doing anyway.

Use the DNA extraction method exactly as described, apart from the first step, which is harvesting spores (this is only for fungi). Instead, take 1 or 2 ml of your bacteria culture, centrifuge it for 2-3 min and resuspend the pellet in the extraction buffer. All remaining steps stay the same.

Good luck :)

PureLink Microbiome DNA Purification Kit –  http://www.thermofisher.com/order/catalog/product/A29790?ICID=search-product