The leaky gut is caused by the pathogens. These pathogen create strong immune reactions including radical oxides that are generated from the white blood cells. These oxides are generated to destroy pathogens (destroys the cell membranes of the pathogens, thus destroying them). But these oxides also create a plethora of free radical damage including damage to the gut lining, thus leaky gut.
The parasite present taxonomy unknown is probably b. hominis. If you want additional info on why I think this then pm me or post a response.