I think the whole area of study looking at the human biome has been heavily distorted by fashion, health claims and financial interests. People like to imagine that our biome is in some way an example of a benign, mutually beneficial, natural alliance. That contains more good bacteria when we eat what is currently defined as a healthy diet and provides all sorts of benefits. In fact we have yet to classify most of the inhabitants, have little knowledge of how they interact, many that have been identified are major causes of human disease and the by-products we can use nutritionally are of minor significance. We also know that probiotic supplements have little chance of changing the resident population and can be dangerous when people are immune compromised. In fact our immune system invests considerable effort and resources into the control of our resident population.
It has been suggested that the gut biome is capable of producing compounds that are absorbed and that can influence our mental state, presumably such compounds would be proteins, and would be identified by our immune system as none self and initiate an immune response. This current finding takes this idea even further suggesting an internal population of bacteria, a brain microbiome, however this would be very different to bacteria living on our external surface's, a bacteria inhabiting our internal cells and using our internal resources would be better described as a disease.
We need to think about the evolutionary logic to all of this, our biome consists of many hundreds of different species, each competing for the limited resources in an effort to improve their fitness. The reason that they offer protection from colonisation by pathogens isn't because they are being nice its because they have no intention of allowing interlopers to steal their homes. While we know that some bacterial populations can cooperate , to further their needs, these types of cooperation are usually temporary and linked to the environment, and I haven't seen anything that has identified 500 - 1000 different species engaged in a cooperative activity and the smaller ones that have been described still feature competition. Like these bacteria, humans as a species have their own needs and have developed an elaborate set of defences to prevent other species exploiting our resources, there is no reason to believe that our systems would allow the needs of another species to control or influence our behaviour or even live internally as parasites. This bacteria would have to leave the gut, presumably an environment it was optimised for, evade layers of immune defences simply to get to the brain and while the brain is "immune privileged" it still has its own systems of defences. OK some disease causing organisms can do this, but virtually all of these have been identified and described and the brain has been studied extensively, I notice the bacteria isn't classified and is described as intracellular, this isn't very common and may suggest it would be a very old human disease like TB.
Much of what I say is guesswork, but this suggests a very important finding and one which seems counter intuitive, I think considering the generally low quality of the evidence that has been used to promote the significance of the microbiome so far, colour me unconvinced.