What does a zero result for a bacteria mean? Does it mean the bacteria is extinct?

Tests such as Biomesight do not have the sensitivity of targeted qPCR tests. We can only detect a bacteria if it's present at a relative abundance of at least 0.001% of your microbiome. Many species can be present and can even cause symptoms at levels below this. Essentially, that means that if you are concerned that key species such as Akkermansia and Oxalobacter are extinct, is it more likely that it's presence is so low that it is undetected rather than extinct.