One thing I try never to do is to take cheap shots at research studies. I’ve acknowledged that my expertise in the methodologies of microbiome analysis is limited. I think that these research groups did something unique in their approach to assessing the microbiome. That doesn’t prevent me from pointing out some obvious issues with the studies that could have impacted the outcomes.
 

The Problems

The first issue was the lack of diet control in either study; diets vary between people, and that could have significantly impacted the results. The foods you eat can directly impact your microbiome for hours, and what the subjects ate the days before the sampling may have skewed the results. Before the study, they used a Food Frequency Questionnaire and determined there were no unique dietary issues that could have impacted the results, but not using a diet record during the entire 28-day study is curious. For the thousands of data points they did collect, they ignored the most basic.

What shocks me is that they knew better: these are the same laboratories that have shown both foods and synthetic additives can substantially impact the microbiome. Without studying the diet of the subjects, and only eight subjects at that, you don’t know who had a diet conducive to the restoration of the microbiome after antibiotics or not.

Second, they used a novel approach. They collected samples from the digestive system using endoscopic techniques in addition to the fecal samples typically collected. Very interesting, but they also used the typical colonoscopy prep which means no food and the complete cleansing of the colon. To their credit, they did test two subjects with and without the typical pre-colonoscopy prep and found few differences. Two subjects. I don’t need to say anything more. While the prep is not going to erase all the bacteria and other microbes, it will eliminate the food supply and could impact what bacteria are growing at the time of the sampling.

Third, they gave healthy people antibiotics; that may bear no resemblance to the microbiome of someone who has a serous infection. The best we can say is that taking antibiotics when you’re not sick may not be a good idea.

Finally, I’ve read research by this group in Israel before. They’re developing a weight loss program based on their microbiome research. It may have no relationship to these studies but it does demonstrate a willingness to monetize their research results, and that always raises my suspicions.

Sure enough, the purpose of these studies was to support a patent application. It may be for the collection technique or more likely, a test to ascertain what probiotics might benefit specific groups of people while healthy or with specific conditions. While they claim no conflicts of interest in the paper, I can’t think of a bigger one than this. While there’s nothing wrong with establishing tests and treatments based on your research, the procedures need to be tested in other laboratories before rushing to market. This strikes me as premature.
 

The Bottom Line

I think these two studies illustrate where we are with microbiome research: at the very beginning. They contribute to the body of knowledge but little else. Probiotics will impact everyone differently, and they may not be desirable for everyone under every condition. But unless we get a radical change in our diet that encourages the microbiome to grow healthy and strong, taking a probiotic every day is still a good idea. My family and I, including my grandson Riley, will continue taking our probiotics because nothing in this research raises any questions about the safety or potential everyday benefit of regularly taking a probiotic supplement, preferably with a prebiotic.

What are you prepared to do today?

Dr. Chet

 

References:
1. DOI:https://doi.org/10.1016/j.cell.2018.08.041.
2. DOI:https://doi.org/10.1016/j.cell.2018.08.047.