Dear Heba,

I think the best alternative to using real time PCR in quantitation of a particular bateria in a human stool sample is deep sequencing of 16S rRNA gene(V3-V4 or V4 region) amplicon via Illumina Hiseq or Miseq platform.

Best regards,

Gui-Hua

You could deploy the traditional bacteriological technique of dilution plate counting, particularly if you have a selective medium or antibiotic available for your target. Good luck! 

Dear Gui-Hua ,

Thank you so much for answering .  That was very helpful. 

Best regards

Heba

Dear  Anthony , 

Thank you so much for your answer. I have another question . If I use the conventinal method , which would give better results,  pour plate method  or spread method? ?

Hi Heba. I would do triplicate plates using the spread method, ensuring you dilute to extinction. This will give you the viable cell count which might vary from the qPCR count. Good luck with it! 

Hi Anthony. If a selective medium is used for the same bacteria but in dog stool , could it be used in human stool samples too ? 

Hi Heba. If it's the same bacterium, the same medium will be effective. Cheers, Ant.