When someone talks about “the microbiome,” they’re likely referring to the microorganisms that live in our gut. But in fact, the human body is home to a number of different microbiomes. We find unique and important colonies in places like the mouth, vagina, skin and lungs. In pregnant women, even the placenta has a microbiome, expanding our understanding of how an infant’s microbiomes are formed.
The gut microbiome - the most “popular” biome of the moment - is a complex ecosystem of bacteria and fungi. Some of these microorganisms are critical for our health and survival, while others are pathogenic and cause issues.
Still, others are helpful in certain quantities but are opportunistic little buggers that can become pathogenic when given the chance to take hold. I’m looking at you, Candida.
BIOHM’s leading research of the microbiome and mycobiome
When I started researching microbiomes decades ago, I was looking primarily at bacteria. It wasn’t until 2010, when my team and I identified a native fungal community in the mouth, that we started to turn our attention to the fungus among us. (#dadjoke)
I coined this new frontier the “mycobiome” and began uncovering its role in our health and disease.
As an extension of my research, I also launched the BIOHM Gut Report, a gut mapping tool that shows people the contents of their gut and makes recommendations on how to better balance the microbiome for optimal health.
Though it’s common for people to have different microbiotic makeups and still remain healthy, there are a few commonalities that we’ve witnessed at BIOHM as we’ve mapped thousands of client's gut reports.
With the BIOHM Gut Report, we look at six main bacterial phyla - Bacteroidetes, Firmicutes, Actinobacteria, Proteobacteria, Fusobacteria, Euryarchaeota and Verrucomicrobia - and one major fungal phylum, Ascomycota.
While there are many more strains, we’ve found studying these gives us the clearest picture of what’s going on in the gut and around the body.
Common bacterial strains in the gut microbiome
You may have heard about Lactobacillus or Bifidobacterium, as they’re the most commonly added strains in commercial yogurt. Turns out, that’s for a good reason. As part of the Firmicutes and Actinobactera families, these two strains are heavy hitters that have very important jobs.
Lactobacillus is anti-inflammatory and anti-carcinogenic. It also inhibits pathogenic bacteria by producing anti-microbial substances, while Bifidobacterium helps to improve the gut mucosal barrier (goodbye, leaky gut!) and increases anti-inflammatory processes.
When we see a low level of Lactobacillus or Bifidobacterium in a report, there’s a good chance the person has some systemic inflammation going on. A low number of these strains also indicates low diversity in the gut, a significant finding, as a high level of diversity generally equates to better health.
In healthy guts, we also see a positive correlation between higher levels of Bacteroidetes in relation to lower levels of Firmicutes. High amounts of Firmicutes indicates obesity, while decreased levels of Bacteroidetes are associated with irritable bowel disease.
When Firmicutes and Bacteroidetes are challenged with antibiotics, the pathogen C. diff (a strain of Firmicutes) can take hold causing severe diarrhea and abdominal pain. Increased levels of C. diff also increase the risk of IBS and colorectal cancer.
Interestingly, Lactobacillus is also a strain of Firmicutes, which illustrates how “good” and “bad” can exist within the same phylum. It really is all about balance.
One of the biggest red flags we see is a high level of Proteobacteria, including strains like E. coli. Elevated Proteobacteria levels are a sign of imbalance and a marker for gut dysbiosis and potential disease. Unfortunately, we see a large number of people with high levels of Proteobacteria.
How do you know if your gut is normal?
Even without getting your microbiome mapped, your body speaks to you in the language of symptoms, so tuning in to what it’s saying can give you clues to whether or not your gut bugs are living in harmony.
If you’re dealing with any type of regularly occurring abdominal discomfort, diarrhea, constipation or smelly gas, that’s a warning sign that something is off. In a healthy gut, these things should happen infrequently.
Carrying excess weight, surgery and pregnancy can also all mess with your microbiome, as can stress and lack of regular exercise. What you eat obviously plays a big role, too. Eating a traditionally Western diet high in processed carbs and sugar, and low in good fats and fiber, contributes to an imbalance and paves the way for pathogenic strains to take hold.
Overall, there are some general guidelines that nearly everyone can benefit from. To balance your gut microbiome:
- Stop smoking
- Eliminate artificial sweeteners
- Avoid antibiotics, except in the case of emergency
- Increase your daily intake of plant-based foods
- Add a quality fish oil supplement
- Get good quality sleep
- Incorporate movement and exercise at least three times a week
- Maintain a healthy body weight
- Add a pre- and probiotic that includes both bacterial and fungal strains
- Eat naturally probiotic foods like fermented sauerkraut, kimchi, kombucha, natto and yogurt
At BIOHM, I continue to publish new research and am constantly learning more about the important roles the microbiome plays, including how it affects our mental health. Today, we know that a diverse set of bacteria and fungi, in proportionate numbers to one another, is one of the best ways to stave off uncomfortable symptoms and chronic disease.
To find out what’s living in your gut microbiome, check out our Gut Report. When you send in a sample, our certified nutritionist will give you a set of customized recommendations to optimize and diversify your gut flora.