Photo: National Human Genome via Flickr (CC BY-NC 2.0)
Thank you for your response to my “Ask the Health Coach!” email.
I received this great question from Tonja Hall (actually she had two questions but I thought I would leave the other for a later date!)
“There is a lot of discussion about microbiome and the health of our gut. How does one know the best probiotic to buy for my gut flora and is there a test to let me know the makeup of my microbiome?”
Great question, Tonja! There is a lot of research and discussion going on in this area of health and nutrition. New information is coming out almost daily and it can be confusing. I have been reading up on this topic and have a few great references that I will list below. Additionally, I recently listened to a detailed interview with Dr. Lucy Mailing, a research scientist specializing in how diet and lifestyle impact the gut microbiome in both health and disease states. She addressed many of the issues brought up in Tonja’s question. (You can listen to the entire podcast here.) I agree with Dr. Mailing’s take on the microbiome and the advice she gives, especially at the end (spoiler alert!) where she states:
“The same lifestyle practices that support health overall also support a healthy microbiome. Eat a nutrient-dense diet, move every day, get enough sleep, and manage stress. This will do more than any probiotic or prebiotic supplement.”
The following are excerpts from the transcripts from her discussion on the Phoenix Helix podcast. (I have put my comments in parenthesis.) Topics covered include:
- What we know about the microbiome and why it is so difficult to study
- What a healthy microbiome looks like
- How probiotics function in our bodies, what to look for, and two brands she recommends (I will also include a couple I have used.)
- Some microbiome myths
- The efficacy of stool testing
Phoenix Helix Podcast
First, for everyone, let’s just quickly review what the microbiome is and what we know about it so far.
The microbiome is all the bacteria, viruses, fungi, and archaea that live in and on the human body. The microbiome wasn't generally recognized until the late 1990's and since the early 2000’s the field has grown exponentially. Tens of thousands of studies have been published, and there are labs worldwide either focused on microbiome research, or discovering unintentionally how the microbiome impacts their research.
The gut microbiome is integral to human health. Beneficial microbes aid in digestion, synthesize vitamins, outcompete pathogens, produce important signaling molecules, and help regulate the immune system. When the gut microbiome is out of balance, it can contribute to inflammation and disease.
That said, there is a lot we don't know. For example, half of the microbiome is still unknown. Future research will focus on identifying unknown microbes, learning about microbial interactions, understanding their individual roles in health and disease, and developing targeted therapeutics.
What we do know is there's a great deal of variability between individuals. Human beings only share about 1/3 of their gut microbiota. The rest is influenced by genetics and environment.
Some of the factors that shape and change the composition and function of the gut microbiome include vaginal birth, breastfeeding, diet, exercise, sleep, stress, antibiotics, medications, toxins, and geography.
(Evey’s note: This is one of the reasons just one brand of probiotic won’t work for everyone.)
The gut can also change rapidly. For example, diet can change the gut microbiota in less than 48 hours. That said, this is not a permanent change. To have a healthy gut microbiome, you need long-term healthy practices, and an unhealthy gut also takes time to heal. A healthy gut microbiome becomes resilient and can then recover more quickly from negative influences (Evey: such as stress, travel, compromised food options, antibiotics.)
What Is a Healthy Gut Microbiome?
There is no such thing as a universally healthy gut microbiome. We are all unique, and there's a wide variability in microbiota among healthy people. Two common characteristics of a healthy gut are microbial diversity and community stability, but there are even exceptions to this rule.
The definition of a healthy gut microbiome is one that supports your individual health.
Lactobacillus and Bifidobacterium are two bacterial strains that are well-studied in the literature and are naturally found in fermented foods like yogurt, as well as in probiotic formulas. In the Western gut, they seem to play an important role in regulating the immune system. However, they only make up a small percentage of the microbiota.
Butyrate-producing microbes can comprise up to 40% of a healthy gut. Butyrate is a major fuel source for the cells that line our intestine. Without butyrate, the gut barrier can break down causing leaky gut, increased inflammation, and the mounting of an immune response. These microbes feed on fiber, so a processed food diet reduces their numbers. Antibiotics also reduce their numbers greatly. And you cannot take these microbes in probiotic form because they're very difficult to culture. Things that can help increase their numbers include a fiber-rich diet, especially vegetables that contain inulin. Exercise can also increase butyrate.
(Evey: The microbiome consists of those organisms, such as the previous mentioned Lactobacillus,Bifidobacterium and butyrate-producing organisms that promote health, and those that cause illness.)
Gut dysbiosis is the term given to the altered state of the gut microbiome that's usually associated with disease. A common signature of gut dysbiosis is a low number of the butyrate-producing microbes and a high number of inflammatory microbes (Evey: i.e. the when the “bad” bacteria outnumber the “good.”)
But, microbes don't always fall into one category or the other. What's beneficial to one person in one circumstance might be harmful to another.
When it comes to microbial health, it isn't about a single microbe being “good” or “bad”. It's about the whole microbiome ecosystem and whether it is supporting or detracting from health. And each of us has a unique ecosystem.
Probiotics
Strains matter. Different strains can have different effects even on the same disease. Lactobacillus is a genus. Plantarum is a species. 299v is an example of a strain. Most probiotics will only list Lactobacillus plantarum on the label. For this reason, store-bought probiotics are often a shot in the dark rather than a targeted therapeutic.
That said, Dr. Mailing does use probiotics herself and recommends them to her patients. She's just very particular in those recommendations. One clinically tested brand she trusts is Visbiome, formerly called VSL #3. Note: don't buy any probiotic labeled VSL #3 now. The original clinically tested formula is sold under the new name of Visbiome, and a different untested formula is sold under the old name of VSL #3. We know this is confusing! There are lawsuits pending.
Dr. Mailing also trusts the brand Florastor, which contains a unique clinically tested strain of Saccharomyces boulardii (lyo CNCM I-745).
(Evey: Every probiotic strain targets different symptoms. Some might help regulate digestion, others can help heal a leaky gut or strengthen the immune system. Still, others claim to help with weight loss and reduced cancer risk, or regulate mood.)
(I am currently using Megasporebiotic by Microbiome Labs to help regulate my digestion. In the past, I also had success with Jarro-dophilus EPS from Jarrow Formulas (available at health food stores.)
To help you in your search for the correct probiotic Dr. Mailing recommends using Probiotic Advisor, an online database where, for an annual subscription, you can search for clinical trials by condition, to find what strains have been found beneficial for your diagnosis.
Whenever you try a new supplement, consider it a self-experiment. We're all unique. Don't continue taking any supplement that worsens your condition. Also know that supplement needs and responses can change over time, as your health changes.
Microbiome Myths
Myth #1: A high-fat diet is bad for the gut. This is based on research done in mice that thrive on a high-carbohydrate diet and have trouble processing fats. In addition, the diet used in the research was high in refined oils and refined sugars and low in fiber. This is very different from a carefully crafted, nutrient-dense, ketogenic diet.
Myth #2: That you can take a stool test to find out what beneficial microbes are missing and then take probiotics to fill that deficiency. Probiotics don't colonize the gut. They have many other benefits (such as modulating the immune system, impacting gene expression, and influencing motility) but colonization isn't one of them.
Myth #3: That we should take probiotics with antibiotics. Recent research suggests that this can actually delay the return of the normal microbiome, including the return of beneficial butyrate-producing bacteria. More research needs to be done to clarify this topic, but right now Dr. Mailing's recommendation is to supplement with butyrate instead, and Dr. Mailing's preferred brand is ProButyrate. This provides fuel for the cells of the intestinal lining while the microbiome naturally recovers. She also recommends watching diet closely, prioritizing nutrient-dense foods rich in prebiotic fiber (which promote the growth of beneficial bacteria) and avoiding processed foods and refined sugar (which promote the growth of pathogenic bacteria).
Prescription Stool Testing Services
DayTwo – A stool testing service that predicts blood glucose response to foods with nearly twice the accuracy of traditional carbohydrate counting. This is an evidence-based service with peer-reviewed research to prove their results, and it's an excellent resource for diabetics and anyone with blood sugar issues.
Viome, Thryve, and others – These are stool testing services that make blanket probiotic and food recommendations based on microbiome data. These recommendations aren't supported by science. They're partially based on faulty assumptions (like the myth that probiotics can colonize the gut). They also claim knowledge that we don't yet have (the ability to make specific food recommendations based on microbiome testing). Sometimes companies will say they have research but that information is proprietary. This is a red flag because true science is based on peer-reviewed research.
Research in progress: Studying individual responses to prebiotics (the foods that feed bacteria).
This research is not yet complete, but it's an exciting area. Dr. Mailing looks forward to seeing the results in the coming years.
How We Can Support a Healthy Microbiome
Step 1: The same lifestyle practices that support health overall also support a healthy microbiome. Eat a nutrient-dense diet, move every day, get enough sleep, and manage stress. This will do more than any probiotic or prebiotic supplement.
Step 2: If you have all of these lifestyle factors in place and are still experiencing symptoms, consider an evidence-based probiotic, ideally one that has been clinically tested for your condition.
Step 3: If you still have symptoms after implementing steps 1 and 2, sometimes there can be an underlying infection that needs to be treated. Stool testing under the guidance of a functional medicine practitioner can be helpful.
For more information: Dr. Dr. Lucy Mailing's website is Next Gen Medicine. where she shares extensive microbiome information and research. You can support her work through Patreon.
Further Reading:
Welcome to the Microbiome: Getting to Know the Trillions of Bacteria and Other Microbes In, On, and Around You by Rob DeSalle and Susan L. Perkins
Gut: The Inside Story of Our Body's Most Underrated Organ Giulia Enders
The Good Gut, by Justin Sonnenburg and Erica Sonnenburg, PhDs
Clean Gut, Alejandro Junger, MD
