We recently hosted a guest in our Undoctored Inner Circle weekly Virtual Meetup (via Zoom), noted microbiologist Dr. Raul Cano.
Dr. Cano has had a long career in generating unique findings in the world of the human microbiome, including sequencing ancient stool from naturally mummified humans dating back many centuries and retrieving bacterial and fungal species from amber a la Jurassic Park. He even brewed beer from a fungus retrieved from the stomach of an ancient bee that was 25-45 million years old.
Among many of Dr. Cano’s insightful statements was one that really stuck in my mind. In response to a question regarding the reliability of various gut flora testing methods, he made the point that microbes inhabiting the human colon (as well as upper gastrointestinal, GI, tract) vary inch-by-inch. As we proceed through our days, we eat different foods, drink different liquids, experience different emotions, engage in different activities, experience different hormonal changes, etc., all of which influence microbial composition of the GI tract. It means that, by submitting a small sample of bowel movement for analysis, we are only sampling a small snapshot of stool microbial composition but failing to analyze the much broader range of microbes (and metabolites) that could be found all throughout the GI tract.
For this reason, Dr. Cano, via an organization called the BioCollective, uses entire bowel movements for analysis, rather than small samples. They homogenize (mix) the sample, and then perform genetic analyses to define the microbes present. Dr. Cano and BioCollective founder, Martha Carlin, told me that, by analyzing whole samples, numerous unique observations have been made that are very different from evidence gathered from small stool samples.
The normal adult human colon is approximately five feet in length, or 60 inches. It is a virtual record of the prior 24 or more hours: what you ate for breakfast, lunch, dinner, snacks; how much prebiotic fibers, polysaccharides, polyphenols, and sugars you ingested; how many herbs, spices, and other foods with antimicrobial properties you consumed; how much stress you experienced (recall that the gut-brain axis is bidirectional); how well or how long you slept; what drugs you took; the quality of the air you breathed (air pollution also has microbiome implications); circadian and age-related changes in hormones and other factors. Analyzing whole stool samples is therefore at least a big step in the right direction of obtaining a broader perspective on bowel flora composition. (Unfortunately, the BioCollective is only performing such analyses for research, not for clinical purposes.)
It means that, regardless of whether you submit a stool sample for analysis to GI Map, GI Effects, Viome, Thryve, Vibrant’s Gut Zoomer, Verisana, or other methods, all you are going to receive is a small snapshot of bowel flora composition. Submit a different poop sample from the same bowel movement and you are likely to receive different results. One of our Undoctored Inner Circle Members recently submitted stool samples, all from the same bowel movement, to four different testing services. Each service reported different results, with some results in direct contradiction of each other.
What to do with such widely variable, discrepant, and incomplete results? The BioCollective method of whole stool analysis would be a start of a solution, though I know of no laboratory currently doing this commercially. Another way, though costly, would be to submit several samples either within a single bowel movement or over several bowel movements.
Bottom line: Be careful with interpretations of bowel flora analyses, as they can only provide a limited view of what is going on in your GI tract, just a snapshot with limited ability to characterize the entire microbiome. Physiologic measures provided by such testing services, however, such as pancreatic elastase or calprotectin levels, are more reliable and carry greater certainty. Clear-cut overgrowth of, say, Enterobacteriacea such as Klebsiella or E. coli should be taken seriously.