What do Our Microbes Tell Us?

Dr. Rob Knight, researcher and founder of American Gut, recently shared some fantastic and exciting insights on current microbiome research and the promising future ahead. The human body harbors an estimated ten times as many microbial cells as human cells. By studying these microbes, we can learn more about ourselves and potentially influence our health.

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What do Our Microbes Tell Us?

In this week’s podcast, we talked with Dr. Rob Knight, researcher and founder of American Gut. He shared some fantastic and exciting insights on current microbiome research and the promising future ahead.

We are only 10% human cells. The human body harbors an estimated ten times as many microbial cells as human cells. By studying these microbes, we can learn more about ourselves and potentially influence our health. Researched has discovered that the microbial ecosystems in different parts of our bodies differ dramatically, but also demonstrate unique intra-personal signatures which develop in early life and are generally stable over time.

However, the overall composition of our microbiota can be influenced by the way we are born and may change in response to our diets and hygiene, who we live with, and different conditions and diseases.

It’s important to point out that your microbiome is not just bacteria. It’s fungi, viruses, archaea, and more that comprise a complex ecosystem in and on your body.

You microbiome affects every aspect of how your body functions. It impacts you liver, your joints, your brain, and more. These microbes contribute not just to gastrointestinal diseases but also to other conditions such as atherosclerosis and autism.

In fact, there’s a lot of research analyzing the role your microbes play on obesity. It’s been determined that microbes certainly play a role in obesity, but we have to be careful not to put a label on which microbes cause obesity and which ones reverse it. Some animal studies have shown certain bacteria to increase obesity, but that does not correlate with humans. In different human populations, we see different things. We must remember that just because something worked in a rodent study, does not mean it will deliver the same results in humans.

Rodents have completely different microbiomes than humans. What works in one species does not necessarily work in another species. It’s not enough to rely on animal data alone. We need more human studies to draw more accurate conclusions.

FMT as a treatment option

FMT (fecal microbiota transplant) is gaining a lot of popularity in the natural health world, and it’s approved for many conditions outside the US. However, FMT in the US is only FDA approved for resistant c. difficile, which is a potentially lethal bacterial infection. FMT has delivered incredible results at curing this infection. It works in 90% of human cases and has saved many lives. However, that does not mean it’s going to work for everything else that the microbiome is involved in.

There are no guarantees when using FMT for IBS, IBD, multiple sclerosis, or other conditions.

Perhaps the next condition that FMT may be approved for is IBD (inflammatory bowel disease). The trials done in IBD patients, both Crohn’s and ulcerative colitis, have been a lot more mixed, than the results with recurrent c. diff. One thing that’s interesting with c. diff is that it seems anyone’s stool sample will work as a transplant.  You don’t need to match up donors to recipients. However, with other conditions such as IBD, that may not be the case. We may find that matching donors to recipients will deliver the best results.

What about testing your microbiome?

Research is now showing that microbiota assay results may serve as a future predictor of IBD. At this point it’s still very researched-based and is not to be used in a clinical setting for diagnostic purposes. It’s still too early to take a microbiota assay and confirm any predictive markers since guidelines have not yet been established, and there’s much we still don’t know.

We encourage that everyone continue to participate in these projects because we need to keep collecting data, but we’re not at the point where we can make clinical interpretations with it yet. So, if you’re into this stuff and want to test your microbiome, then visit americangut.org to get your sample kit. Just remember, this is not a diagnostic test. It’s more for the point of collecting data and furthering research, so one day we will have diagnostic criteria.

What about the small intestine?

We don’t get a good assay of the small intestine with these stool samples. Is that relevant? Should we be collecting this data on the environment in the small intestine?

Sometimes it’s important and sometimes it’s not. It really depends on the person and the condition. There are cases where you’ll need to do a biopsy to see what’s going on in the small intestine. Other times a breath test is all you need. We want to consider where we can use with the least invasive option and get the results we need.

Sometimes you don’t even need to get samples from the colon, which is great because not many people enjoy doing stool tests. Research is showing that testing the oral microbiome is promising for type 2 Diabetes, Cirrhocis, and Rheumatoid Arthritis. So, for some cases you might not need to go to the gut at all. You may be able to get away with something as simple as tongue swab.

What is the American Gut Project?

The American Gut Project is an Earth Microbiome Project study co-founded by Dr. Rob Knight and Jeff Leach. It’s world’s largest crowd-funded citizen science project in existence.

The American Gut Project enables participants to learn about their own body’s microbes while also contributing to the greater scientific effort to learn how the human microbiome is associated with various aspects of our health; from associations with diet to the amount of alcohol someone drinks to whether or not someone has autism or IBD. Because all de-identified data are made freely available, researchers from all over the world can access the data to ask questions about the microbiome and its association with a variety of health and lifestyle factors.

Key preliminary findings from American Gut:

1. The American Gut project has many more samples representing more groups of people than other studies, such as the Human Microbiome Project, Global Gut, or Personal Genome Project.
2. The microbiome changes as we grow! As you get older, your gut microbiome becomes more diverse.
3. Antibiotic usage also affects our microbiomes, by reducing diversity and thereby creating a less healthy gut environment.
4. The more different types of plants a person eats, the higher their gut microbiome diversity.
5. Alcohol consumption also affects microbiome diversity-those who had at least one drink per week had a more diverse microbiome than those who abstained from alcohol.
6. People from different countries tend to have different gut microbes, probably due to distinct diets. However, there are also factors, like age, that impact gut bacteria similarly, regardless of what country a person lives in.

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What do you think? I would like to hear your thoughts or experience with this.