Your Microbiome, Probiotics, Fermented Foods and Some Surprising New Facts – You Really Need to Read This!

Your Microbiome, Probiotics, Fermented Foods and Some Surprising New Facts – You Really Need to Read This! post image

There has been more progress in our understanding of the microbiome and the world of bacteria in the last 3 to 5 years then there has been in all the years preceding. This is due to the new genetic testing that can analyze the DNA of the bacteria. In doing so we have identified over 35,000 species that can potentially inhabit the human gut.

It’s been very difficult to study gut bacteria because most bacteria in the gut are anaerobic – that is, oxygen is toxic to them so they die off as soon as they come out of the gut. But there’s been huge progress in this regard and that has allowed us to understand the importance and significance of gut bacteria to our health.

Microbiome Controls Our Behavior

The Human Microbiome Project discovered that the average human carries about 1000 species of microbes in the gut. However, there are about 35,000 species that could exist within the gut. No two people have the same microbial community – we all have our own gut fingerprint. Your ability to metabolize and absorb foods and medications is controlled by gut bacteria.

Antibiotic treatment is the worst thing to happen your microbiome and is still over-used by the medical community. Studies show that children who have used antibiotics before the age of 4 have much greater risk for autoimmunity, skin problems, asthma, allergies, etc.

How We Get Our Microbiome

We have ten times more bacterial cells than human cells. Some say that we have evolved to house bacteria. The inoculation of the baby’s gut, body and all organs occurs via the mom. Previously it was thought that the uterine environment was sterile.

Not so. Not only does the placenta house bacteria, but there are actually immune cells coming from the mom’s gut that transfer bacteria to the baby through the umbilical cord during the pregnancy.

This prepares the baby for the large inoculation of bacteria that will occur while it travels through the vaginal birth canal.

Typically vaginal bacteria are very different from gut bacteria. However, in readiness for birth, at the end of the first trimester of pregnancy the vaginal bacterial colonies shift to mimic gut bacteria. This supports bacteria that are helpful in digesting milk. Clearly this is to prepare the fetus to have the ability to digest milk.


During birth, the huge inoculation occurs when the baby travels through the birth canal and is covered with all the bacteria. There is also the close skin to skin contact with the mom or caregiver.

Another way the baby develops their microbiome is through breast milk which has 400 – 600 species of beneficial bacteria. Breast milk is high in oligosaccharides (non-digestible sugars) which cannot be digested by the baby. Instead these oligosaccharides are there as a prebiotic to feed the baby’s bacteria.

It takes close to 3 years to develop the microbiota. The diversity in individuals is a co-selection process of tissue compatibility with bacterial strains. This is not totally understood but is the reason for the individual fingerprint we all have.

The environment is also a way to develop the microbiome and playing in the dirt is the best thing for humans – something not many of us do anymore in our modern environments.

C-Section babies are at a 40% greater risk of developing autoimmunity, asthma, allergies and the other chronic conditions that we are now seeing, because they do not have the benefit of the huge inoculation through the birth canal.

A c-section baby who is formula feed additionally increases inflammatory conditions. Put antibiotic use on top of that and the risk goes even higher.

Our children are at great risk.

The diversity of the species creates health — we are learning this from the Human Microbiome Project.

Health Problems Start in the Gut

Every health condition can be traced back to the gut. For example, sinusitis is directly related to gut bacteria. Inflammation in the sinus cavity is due to imbalances in gut bacteria and using antibiotics for the treatment is making it worse. Extra-intestinal problems are also related to the gut such as, arthritis and skin conditions.

Kidney stones occur because of the absence of the bacteria called oxalobacter. This particular bacteria breaks down oxalates in food. If they are not broken down, they form tiny stones in the tubules of the kidneys. If you have ever had kidney stones you will know that it is extraordinarily painful.

Obesity is also due to the bacteria that supports weight gain. Those folks have bacteria that can take more calories from each gram of food than someone who does not. It’s a survival mechanism.

Other studies show that gut bacteria control appetite.

Bacteria also cause cravings that create a real neurological need for sugar. The bacteria can produce neurotransmitters that control appetite and cravings.

Gut Bacteria Give Us Molecules Critical to Our Health

Proteomics is the emerging study of proteins made by gut bacteria. They have identified 1000 of these proteins (and enzymes which are proteins). For example, glutamate dehydrogenase is an important enzyme for metabolism needed to break down glutamate to glutamic acid. We need the bacteria in the gut to make this critical nutrient.

Vitamins K2 is also a critical nutrient that can be made by our gut bacteria. We tend not to get enough K2 from the food but there are certain foods high in vitamin K2.

Gut bacteria are also producing critical nutrients such as carotinoids and anti-oxidants that we get from all the colorful vegetables. However, it is very hard for the body to extract the molecules from the food. There are certain bacteria strains that actually make the anti-oxidants for us.

What Current Research Shows About Probiotic Supplements

Have you ever taken a probiotic and not felt any change? I know I have and I have tried many different products.

It has been taught that the best probiotics are refrigerated because that keeps them alive. However, the human body is 98.6º. If the bacteria can’t survive at room temperature, which is lower, then how will they survive in the body? The answer is that they may be alive in the bottle, but once you swallow them they die. So essentially you are supplementing with dead bacteria – certainly by the time they reach the colon.

It has been shown that there is some benefit to taking dead bacteria cells. There will be some beneficial expression of DNA in the cells or a beneficial change to PH.

In nature these species that are in most probiotics are not designed to be viable outside of the body. Placing various species together and in high numbers will not recreate the original inoculation from the mom. Even the studies of specific species do not answer the question of individual fingerprints and how individual colonies live together.

Can We Get Bacteria From Fermented Foods?

It is commonly thought that eating fermented foods will provide trillions of beneficial bacterial cells. However, when you eat fermented foods, the bacteria that is in the fermented foods is not going into your digestive system.

The benefit is from the actual ferment — the breakdown of the nutrients in the food and the nutrients that are produced as a result of the ferment. These bacterial peptides and peptidoglycans can be very healing for the gut and may support the bacteria that are part of your microbiome.

You may have thought that fermented foods provide the beneficial bacteria, but these bacteria die as they travel through the digestive system and just pass through.

Diversity is the Key

The gut is an ecosystem. We need many different strains of bacteria and we need overlap in what they do for us. In this way, if some strains die off (or are killed by outside factors such as medications) you still have other species that can do the same for you.

Bacterial diversity protects you from pathogenic species that can overtake the microbiome. Additionally, the more diverse, the more functions they can do for you.

How to Grow Your Microbiome

Instead of trying to kill off the bad bacteria, the best approach is to nourish the microbiome and support it in order to increase diversity. When the microbiome is healthy it will naturally suppress the bad bacteria.

Much like a garden, instead of using weed killer, it is more productive to encourage the good organisms in the yard and soil and these will keep out the pests.

Create the environment that favors the growth of good bacteria. Diet is critical. Sugars, processed foods and grains are pro-inflammatory and the pro-inflammatory state encourages bad bacteria (and cancer and other diseases).

Another important action is to improve the PH by eating plant based foods as well as good animal fats, animal proteins and eating a diverse array of foods. Diverse foods will encourage diversity in the bacteria.

Additionally, fermented foods play a huge role here as they give you so many nutrients that are not available through foods. Lastly, get environmental bacteria such as soil based bacteria as these bacteria provide many beneficial functions and nutrients.

Potentially the Best Probiotic

Right here, I want to say that I am not paid to promote this product – I just want to give you the information that I find critically important for anyone on a health journey.

That said, there is a new probiotic on the market called Megaspore. It provides 5 strains of spore forming bacteria that will actually reach the colon and colonize there. These 5 strains support increasing the diversity of the gut and there are many testimonials that all say that this is the first probiotic that someone actually feels has made a difference.

I think you need to get it through a health care practitioner. I just ordered mine.

There is a lower dose product made for commercial use called Peakbiotics which you can probably find in health food stores.

The information for this article was gleaned from an interview with Kiran Krishnan at Primal90. He is a microbiologist (among many other credentials) and his talk was thoroughly fascinating and offers new research and a new understanding for healing the microbiome. He is a principle at Physicians Exclusive the makers of Megaspore.

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Leave a Comment

  • Elizabeth Casey March 4, 2015, 1:04 pm

    Dear Jill, I can’t tell you how much I love, love, love your blog! Today’s post, on the micro biome, just blew me away. (And, yes, it’s true; I have a thing for the little critters.) The amount of research you do is outstanding and then you manage to present reams of important information in a clear, comprehensible style. I could while away an entire morning clicking on more and more of the links you provide. Thanks for the work you do and thanks for sharing it with all of us! Peace, Liz Casey

    • Jill March 4, 2015, 5:01 pm

      Hi Elizabeth,
      Thank you so much for your kind words. I have to give credit to Kiran Krishnan and the folks at Primal90, as the interview with him provided me with this incredible information!

  • Judy M. March 4, 2015, 3:13 pm

    I have always wondered if it would be helpful to open up probiotic capsules and put them in some warm water and introduce them into the colon by means of an enema bag? That way they would not have to pass through the stomach and small intestine?? What do you think?

    • Jill March 4, 2015, 5:00 pm

      Hi Judy,
      I know of some folks who find that probiotic enemas are helpful. However, here again, most probiotics are already dead bacteria and if you have a serious condition I would approach this with caution. That said, fecal microbial transplant is the ultimate probiotic enema.

  • Laura Childs March 5, 2015, 2:19 pm

    Great article! I’m on your email list and I have been listening in to most of the Primal90 session as well. I hadn’t had a chance to listen to Kiran Krishnan’s segment. Thank you for taking the time to write this and share it with us. There is so much interesting information being made available on the microbiome of late. I agree, diversity is vital!

  • Delbert Parkinson December 21, 2015, 8:45 pm

    Awesome job yesterday.
    After working for 62 years in electronics I believe that I have discovered the main cause for most Alzheimer’s, Cancers and other diseases. They are causes by the over-saturating our immune systems with trillions and trillions of pi-bonding electrons in caffeine(10) and benzene (6) that creates the large magnetic current energy fields. These magnetic fields can electronically mutate all of your body’s innate and adaptive immune cells, your brains glial and neurons cells, and the Hydrogen bonding of your DNA. We have over 20 different microscopic analog and digital voltage levels in our body and the strong caffeine and benzene magnetic fields can mutate these small microscopic voltages. Lets talk. Del.