I understand it’s thought that probiotics don’t add the higher numbers of good bacteria in the gut over time. That is to say, they don’t take up residency. They are just helpful in transit. I just can’t help feeling that if they, for instance, are keeping pathogenic bacteria in check, this must give time and space for proliferation of good bacteria and therefore they must make some changes that remain after they pass through. What are your thoughts on this?

Chris Kresser:  The studies that I was referring to, they actually looked. They looked at patients who were taking probiotics and they measured their fecal microbiota over a pretty long period of time as I recall, and they just found that there wasn’t a significant change in the composition of their microbiota so that would even argue against what you suggested.

However, again like I said, that doesn’t mean that there aren’t clinical benefits. The patients could have been experiencing improvements in their immune function. It’s also possible that they could be experiencing changes in the gut mucosa that can’t be detected by looking at stool. One of the biggest shortcomings of looking at microbiota sequence in the stool is that we’re not capturing a lot of what’s happening in the gut. The mucosal bacteria that don’t shed into the stool cannot be measured by looking at the stool. So if taking probiotics affects the bacteria or microbes in the mucosa, we’re not going to know about it, but the patient will know about it if it improves their symptoms.

So again, we’re kind of like in the Wild West here with this microbiota research. I think there are a lot of claims that are being made that are interesting and worth investigating. There is absolutely no doubt in my mind that microbiota is just a hugely important part of our health and what contributes to disease. But there’s still a lot we don’t understand so I think we have to be careful about getting a little too crazy with it.