Firmicutes are higher in number and then comes Bacteroidetes. But the data on microbiota, especially in mouse is confusing and contradictory. In my experiments using fat induced obese mice I have found contradictory number of bacterial colonies of Firmicutes and Bacteriodetes. However, there are a lot of literature available on this topic.

Thank you Anindya Mukhopadhya. I found also high number of Firmicutes using a culture dependent-MALDI Tof identification of bacteria from mouse caecum

What mice model were you using for your experiment, if you don't mind saying it. I had used mice which were fed with high fat diet... I had read in literature that in healthy mice gut, Bacteroidetes are higher than Firmicutes and this ratio is inverted due to obesity... However, when I compared the colony numbers of these 2 bacterial colonies i did not see such a phenomena in my fat and lean mice.. both groups had higher firmicutes than bacteroidetes with fat mice having highest numbers.

it was just the beginning of our project. I used normal mice and some with restriction of food. We want to see if maldi-biotyper is a good alternative for identification of gut microbiota in mice.