I'm trying to find the absolute abundance of bacterial species in a bovine fecal sample (fecal microbiome). Can anyone suggest the best method to achieve this?
Do qPCR for absolute quantification.
CFU is not at all a good method, as CFU is not defined, what is an CFU, its a arbitrary unit.
Colony forming unit is an arbitrary unit. I actually did not mean its full form, I meant it can be anything from single bacterium to a clamp of 50 bacteria. Exactly, I meant what you said in your last sentence.
For quantification of the bacterial community: Article A method for simultaneous measurement of soil bacterial abun...
Does somebody know of a similar method for fungal communities?
Yes, but I mean if somebody has used an internal standard (spike) for absolute quantification of fungal communities (by sequencing the ITS region).
Abhijeet Singh Thank you very much for the response Abhijeeth. Can you please elaborate on the experimental setup you suggest for this. Including what housekeeping gene can be used to generate baseline expression values etc. ?
TIA.
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