It seems that firmicutes are associated with obesity because they increase energy availability from food.If you come to a place where you are replacing everything, you are in the same rabbit hole as mainstream medicine, i.e cut out and replace. We can see the results of long term allopathic medicine
Peat's advice about the microbiome is simplistic
He treats all bacteria as having endotoxin
Firmicutes are not gram negative and have no endotoxin. If you skew your ratio of firmicutes to bacteroidetes towards firmicutes, you can have both healthy gut bacteria as well as low endotoxin.