The human microbiome is a hot topic
Microbiome. Gut bacteria. Probiotics. These are hot topics in science, medicine and nutrition. We are full of microbes that do essential things for us.
Our microbes affect our immunity, gut health, inflammation, and weight. Personally I recovered from my autoimmune disease by bio-hacking my microbes. I had tenacious parasitic amebas to get rid of. I also had small intestine bacterial overgrowth (SIBO).
In this post I’ll explain more about the human microbiome and ways to improve it.
What are microbes?
Microscopic critters are the oldest forms of life on earth. They are so tiny that millions can fit into the eye of a needle. They are everywhere! Literally, everywhere. They include bacteria, archaea, fungi, amoebas, algae, protozoa, and arguably viruses.
There are more microbes on one of your hands
than there are people in the world!
That shows how ridiculously vast their numbers are. You have seven pounds of microbes in your intestinal tract (your “gut flora”). Microbes exist in your nose, sinus cavities, mouth, urinary tract, vagina, and all over your skin. Each of these areas have different species.
Microbes are “smart” in terms of survival. They quickly adapt in response to changing environments.
What does microBIOME mean?
Each colony of microbes carries its own DNA, it’s own genome. Your microbiome is the DNA of all of your microbes. Every person has a unique microbiome, like a thumbprint.
Our microbiome communicates with our own DNA (genome). So….
Our microbiome is called our second genome.
We evolved with microbes, in symbiotic, mutually beneficial relationships, since the beginning of our existence. Our microbes do many jobs for us that we can’t do ourselves. They are our little invisible worker minions.
For example, most of our bacteria reside in our digestive tract. Here they ferment fiber and make byproducts that are essential for us. These include vitamins, anti-inflammatory molecules, and chemicals that regulate our metabolism and immune system.
In turn, we feed them and give them a good home. We want these beneficial relationships; we could not exist without them. I like to think of our beneficial bacteria as our microscopic superheroes. You never see them but they are constantly doing great things for us!
Our microbiome is related to………everything!
For almost every disease or condition, scientific research shows a correlation to our microbiome. Most of this research is from 2012 to now. It includes links to:
- Anxiety * , Depression *
- Arthritis and Joint Pain * *
- Autoimmunity * * * * , Inflammation * * * *
- Gluten Intolerance *
- Hormones *
- Obesity and Type 2 Diabetes. * *
- Thyroid *
What exactly is our GUT microbiome?
Our gut flora lines our whole digestive tract, mouth to anus. Think of this tract as a tube that is open to the outside environment. When anything enters this tube, it encounters your microbial colonies throughout. There is only so much space for microbes to colonize. The ones that do colonize establish themselves by building sticky complexes of sugars and protein called biofilms. They fight to defend their space against new microbes coming in.
About 200 species of microbes exist in our mouths. Our stomach is mostly sterile because it is so acidic. The microbes in our small intestine start low in number and increase in number and species further down the tract. Ninety percent of our microbes flourish in our large intestine, or colon. Here there are over 30 different genera (genus) and over 500 different species. This is where most of the action takes place.
What do our gut microbes do for us?
- Synthesize vitamins, especially K2 and the B vitamins folate, biotin and B12.
- Ferment indigestible fiber to make short chain fatty acids (SCFAs). SCFAs provide energy for the large intestine. One of these SCFAs is called butyrate, which has potent anti-inflammatory actions.
- Provide 50% of our stool bulk.
- Break down toxic chemicals for excretion.
- Help convert thyroid hormone T4 into its active form T3.
- Provide a protective barrier between your gut contents and its inner mucosal layer.
- Prevent pathogenic microbes from multiplying.
Why is our gut microbiome so important to our immune system?
Microbes and their biofilms line your entire GI tract. Beneath is a mucous layer secreted by your digestive lining. This inner mucus layer contains 70% of your entire body’s immune cells. It’s known as your “gut immune system.”
Your microbes and gut immune cells deal with a steady stream of guests that pass through. Some are welcome, such as additional beneficial microbes, food particles, medicine, and nutrients. There are also unwanted guests, such as environmental toxins, viruses, endotoxins (byproducts of metabolism from the liver), and pathogenic microbes.
Your microbes help your immune cells identify and tag the “good” from the “bad.” This regulates your entire immune system.
The “good” guys help your immune system. The “bad” ones can throw off your immune system, and create inflammation, allergies, and autoimmunity. Other microbes simply pass through, without benefit or harm. For your immune system to function well, you need the right microbes, the right quantity and diversity, and in the right place.
What’s this about diversity?
The general theory is that more diversity in our microbial species is better. More species make a greater variety of beneficial byproducts to handle the tasks at hand.
The species lactobacillus and bifidus are the most well-known. However, while lacto and bifido species can help you as they travel through your GI tract, they do not colonize. They are beneficial, yet transient. They are wanted guests, but they don’t move in. These species can’t move in, because they are aerobic (need oxygen). The species that colonize are anaerobic (can live without oxygen).
We share bacterial species with humans around the globe. These species also show up in fossilized stool from thousands of years ago. These “ancestral” species cannot be taken in a pill or cultured in a food. Rather, they are anaerobic and can only be cultivated through feeding and growing them inside your gut. They need to be fed.
Antibiotics are killing our microbial diversity
Antibiotics have done wonders for saving and prolonging lives, but clearly we have overused them. The first time you take antibiotics, you obliterate the precious microbiota that you have cultivated since birth, and it never returns as it was before. You can imagine what multiple doses of antibiotics do.
People think they can prevent this loss by taking tiny doses of lactobacillus and bifidus strains. These strains may help as they travel through, they are transient guests and will not colonize. Plus the tiny amount that comes in probiotic capsules is a bit like spitting in the wind, compared to your 7 pounds of gut bacteria.
Doctors are suggesting probiotic therapy following antibiotic therapy, and this is good start. Research shows that probiotics are far more effective if they are taken during antibiotic therapy, instead of after. They can reduce side effects of antibiotics as well.
Babies, C-Sections, and breastfeeding
Cesarean section births don’t let babies inherit microbes from their mother’s vaginas. Instead they inherit microbes from their mother’s skin, and the hospital, which is a very different biome. Some parents are swabbing their C-section babies with the mother’s vaginal fluid, a technique called “vaginal swabbing.”
Breastfeeding establishes microbes from a special fiber called HMO (Human Milk Oligosaccharide). Breast milk also has live bacteria. Formula companies are substituting GOS (galactose oligosaccharide, derived from cow’s milk) and probiotics. There is no evidence yet as to how this affects babies’ microbiota.
Kiss your dog and put your hands in the dirt
The move from living outdoors to indoors in our evolution drastically cut down our microbial exposure. In cites we don’t often garden, play in healthy dirt, and live with a variety of animals. These contribute to microbial diversity and a better regulated immune system in other cultures. Studies show that children who were brought up on farms with animals have less asthma and allergies. * *
The “hygiene hypothesis” states that a lack of childhood exposure to microbes increases allergic diseases by suppressing the natural development of the immune system.
The “old friends hypothesis” recognizes that missing microbes also affect chronic inflammatory diseases and autoimmune diseases.
The cause for missing microbes is not just due to being clean and out of the dirt, there are other factors involved, like diet.
Modern industrial diets = microbe starvation
Possibly the biggest factor in our loss of diversity is our modern diet and its:
- Lack of “microbial accessible fiber” (MAC). The Sonnenburgs, Stanford gut microbe researchers and authors of The Good Gut coined this term.
- Abundance of simple sugars that feed the wrong microbes, in the wrong places.
Lack of MAC
Traditional cultures and hunter-gatherers eat a lot of MAC, from 30 to 200 grams per day. We Americans typically eat only 10 to 15 grams of fiber on a good day. Our lack of dietary fiber starves our microbiota.
The Sonnenburgs write that more MAC helps weight loss and lowers inflammation.
People in high-fiber consuming societies not only have a much larger variety of bacteria in their microbiota, they have more diversity, and they also have strains that haven’t been observed in Westerners… and much lower rates of inflammatory diseases.
Nurturing our gut bacteria so that they produce the compounds that our bodies need
is one of the most important choices we can make for our health.
– Justin and Erica Sonnenburg,
Too much sugar n’ starch
Our modern Western diet provides excessive and inexpensive simple sugars and starches, 24/7. It is too easy to get food like this. It’s everywhere and we can get it with very little effort. We absorb simple sugars and starches as glucose, or our microbes and yeast ferment them.
Simple sugars and starch never make it down to the large intestine to act as MACS. Instead they get turned into glucose. Excess glucose becomes fat, or feeds microbes in areas we don’t want.
Excessive sugar and starch can also starve bacteria in the colon. People often show up with bacterial overgrowth in the small intestine, and a lack of bacteria in the colon. Not a good clinical picture.
What Can You Do?
Abstain from antibiotics, move into your backyard with some animals, roll around in healthy dirt, stop bathing, and eat roughage? To a certain extent….yes. You can also:
- Minimize added simple sugars and refined starches. Look at labels for sugar content. Refined starches are those made from flour products, such as white bread, most whole grain bread, pastries, cookies, pasta, tortillas, and packaged foods in general.
- Eat resistant starch. This includes beans, tiger nuts, plantains and bananas on the green side, white rice and potatoes that have been cooked then cooled.
- Eat lots of whole plants in the form of vegetables and fruit.
- Swab your C-section baby with mom’s vaginal fluids – there’s a growing movement to do this in hospitals. If you need to use formula, do supplement with GOS and possibly some probiotics. Please consult with a medical provider.
- Stop obsessive hand washing. Yes, it’s a good idea after being in a medical clinic, a crowded grocery store, or a preschool classroom. But after petting the dog or picking a carrot from the organic garden? Don’t bother.
- Don’t use antibacterial cleansers, wipes, washes. Vinegar and soap work well!
- Live with dogs if you don’t live on a farm. Their microbiota will improve yours, and vice versa.
- Use antibiotics sparingly. Try botanical anti-microbials first. They work just as well in many cases, if not better. They don’t have the same scorched earth effect on your microbiota that pharmaceuticals have. Please consult with a medical provider.
For more detailed information about feeding your “good” guys,” see my post Feeding Your Microbiome Superheroes.