I have fed the 2-3 weeks old swiss albino mice with E. coli (by gavage) and am trying to get a count of these bacteria that has caused infection in the colon region. After oral gavage the mice were sacrificed at day 7. I tried homogenization of the tissue with beads but after plating the homogenate, there was no bacteria at all. Is it possible that the bacteria did not infect at all? or the technique of homogenization was not correct? In that case:

How can I homogenize the tissue so that only the mice cells are lysed but not the bacterial cells; so that I can get a plate count of these bacteria on LB agar plates (CFU/mL) ?

(1) Is sonication a right method for such kind of lysis, then what amplitude can be used for the same?

(2) Or can the cells be burst open to release the bacteria with specific concentrations of Triton-X-100 or SDS?

(3) Or the method for bursting the cells with beads could be the right way for the experiment? 

(4) Can any other method be used for the lysis without affecting the bacteria within?

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