For millions of years, our ancestors ingested the best probiotic and prebiotic supplements through hunting and gathering, including fresh unwashed food from the ground and trees. It is only under a microscope that we have become aware of the billions of microorganisms that also occupy these foods and then our guts.

When the agricultural age arrived, we discovered new ways of harnessing this invisible world of bacteria through the fermentation of dairy, vegetables, and grains that also provided a long shelf life without refrigeration.

Now enter the modern age, where the war on germs has led to the rise of extreme sanitation of our hands, refrigeration of our food, and washing of our fruits and vegetables. Let’s not be mistaken, good sanitation has helped prevent the plagues of our past. Like every case of extremes, we are now seeing the effects of taking sanitation too far when we look at our microbiome.

The Two Worlds of the Best Probiotics and Prebiotics

The word “probiotics” is derived from Latin and Greek, and literally means “for life.” The way we get probiotics is from the dirt, unwashed food and fermented foods and drinks. The bacteria in the dirt are different than the bacteria in fermented food.

We have put a lot of focus and research on the probiotic strains including lactobacilli and bifidobacterium, but have neglected many of those found in dirt. These are the ones we are exposed to as children when we stick our hands in the dirt and then our mouths.

Many people also haven’t heard of prebiotics. Prebiotics have been found to alter the neuroendocrine response, decreasing anxiety, and depression. Prebiotics are the fiber component of plants that help feed the probiotics and help them colonize.

Certain people have a lower prebiotic production in their body due to the FUT2 gene found in the Nutrition Genome Report, and therefore require more of these foods to help colonization. This is especially true when multiple rounds of antibiotics have been used. Therefore, prebiotics and probiotics are necessary for a happy, diverse microbiome.

Tiger Nuts (dehydrated root vegetables) are a food that have made a come back to the market from the Paleolithic age, a prebiotic that companies claim comprised 80% of our pre-human ancestors’ diet about two million years ago. Dandelion greens, kiwi, garlic, leeks, radicchio, garlic, artichokes, bananas, yacon syrup, asparagus, pistachios and chicory root are all examples of prebiotics.

The Microbiome Project

Along with genetics, our gut microbiome is going to become one of the major medical revolutions in the understanding of our bodies and disease. We are made up of ten trillion human cells, but there are a hundred trillion microbial cells in and on your body. That means that the microbes are really the ones running the show.

We only share approximately 10% of the microbes with each other. Combined with genetics, it is this percentage that we see the difference in weight, allergies, asthma, inflammatory bowel disease, multiple sclerosis, anxiety, depression, arthritis, autism and more.

It is in the diet and enzymatic activity that may positively influence these microbes, and our genes show how susceptible we are. But as I’ve explained through Nutrition Genome, genes are fixed but the epigenome is flexible.

Seventy to eighty percent of your immune system is made up of the beneficial bacteria living in your gut. Establishment of normal gut flora in the first 20 days of life plays a crucial role in appropriate maturation of a baby’s immune system. Hence, babies who develop abnormal gut flora and bad bacteria are left with compromised immune systems and allergies rise.

We know that low-diversity microbiomes have been associated with those in hospitals and with worse health outcomes. We may find out that centenarians (those living over 100) have an extremely diverse and healthy microbiome, or perhaps there are “longevity strains” that are found in higher amounts in these individuals.

The Health Spectrum of the Microbiome: What are the Benefits of Probiotics?

I wrote an article titled Mental Health Starts in the Gut, Not the Brain. As you will see, we are just beginning to see how significant our bacterial populations are with our health.

Grains

According to microbiome researcher Jeff Leach “Whole grain consumption seems to be associated with high levels of a type of bacteria called prevotella. Prevotella has been associated with inflammation in HIV patients and it’s been associated with rheumatoid arthritis. We don’t know why that is, so the jury’s still out on whole grains.”

Food Allergies

The peanut allergy rise has currently been blamed on the “hygiene theory.” Basically, we are too clean and too quick to use antibiotics. Our immune system is not given a chance to be exercised and made stronger and therefore overreacts.

More specifically, evidence points towards poor gut flora as being the cause. One study in the Journal of Immunology found that an extract taken from E. Coli – which is a bacteria in our gut and becomes a problem when not kept in check – broke down the peanut proteins where the enzymes failed, and practically eliminated the allergenic response. I imagine it is the collective work of many different strains of bacteria that eliminate this response altogether.

About 35% of children with moderate to severe atopic dermatitis have skin symptoms provoked by food hypersensitivity.

Oral Health and Migraines 

One of the bacteria strains responsible for gum disease and tooth decay is called Streptococcus mutans. This showed up in the beginning of the agricultural age when grain and sugar intake went up. The same is true today when grain and sugar consumption gets too high in our diet.

Before you start swishing mouthwash to kill off Streptococcus mutans, remember the lesson of antibiotics. While killing off the bad, you are also killing off the good. There is a balanced community, and it is better to increase the good guys than to drop a bomb on everyone. Streptococcus salivarius is the strain that prevents cavities and promotes healthy gums.

When you eat nitrates (NO3-) from leafy green vegetables, they are converted to nitrites (1 oxygen is taken away to NO2-) by bacteria in the mouth. Nitrites produce nitric oxide (NO, another oxygen is lost). NO relaxes and dilates blood vessels, improving cardiovascular health and numerous other functions.

Beets are major sources of nitrates, and the reason they have been shown to improve athletic performance and lower blood pressure is due to the production of healthy nitric oxide levels.

However, the types and amounts of nitrate to nitrite conversion bacteria ranges person to person. Research has found that 4 out of 5 people who take nitrate-containing drugs for chest pain or congestive heart failure report severe headaches. Due to relaxing and constricting activity of nitric oxide, this mechanism is of major interest for migraines.

Women experience hormonal migraines right before their period because estrogen and serotonin plummet, causing nitric oxide to constrict. Perhaps we will find out that migraine trigger foods are actually linked to their microbiome population. 

Cardiovascular Health

When the latest study connected L-Carnitine from red meat consumption to higher levels of cardiovascular disease due to TMAO, it had to do with poor gut flora, not L-Carnitine in meat. A similar logic was analyzed with isolated choline and blood clots, omitting the fact the choline is often packaged in food with DHA that naturally thins the blood. TMAO fuels growth of E. Coli and salmonella.

TMAO is a precursor of dimethlynitrosamine, which is linked to liver cirrhosis and heart disease. When certain unfavorable gut bacteria are in higher amounts in the gut (from a poor diet), higher amounts of TMAO are produced.

Increase your good gut flora, omega-3 fatty acids and folate-rich vegetables, and you lower the risk of red meat or choline increasing TMAO.

Nerve Health  

Weight Loss

If you have wondered how lean people are able to pack away the calories without gaining weight, here is your clue. Along with genetics, the microbiome is different. Human studies have found that people who are lean and people who are overweight have different microbiomes.

Those who are obese have more firmicutes and fewer bacteroidetes; the two families of good bacteria.  But just like the powerful effect of epigenetics on the genome, you can improve your microbiome.

When you think about the job of gut bacteria and your digestion, it shouldn’t be a surprise that a more diverse microbiome is going to be more efficient at aiding in the digestion of your food and detoxification of excess fat.

Guess what food was the most associated with weight loss in a New England Journal of Medicine study? Yogurt. Evidence suggests that changes in colonic bacteria might influence weight gain.

The strain of bacteria that has been found in studies to be the most effective for weight loss is Lactobacillus gasseri. In a randomized controlled trial, fermented milk containing Lactobacillus gasseri with 210 healthy Japanese adults with large visceral fat areas.

Abdominal fat when down 8.5%, and BMI, waist and hip circumferences, and body fat mass were also significantly decreased from baseline at week 12. After stopping the probiotic, all the weight came back.

Sleep

Researchers also found that weight gain is lowest among people who sleep 6 to 8 hours a night and is higher among those who sleep less than 6 hours or more than 8 hours. This is an interesting point because good bacteria influence the production of GABA, and GABA is produced in higher amounts during deep sleep.

When GABA is too low, glutamate causes your mind to race at night. Bifidobacterium is the most important for sleep is due to its ability to produce large amounts of GABA.

More Strains and their Function

The majority of the research so far has been done on lactobacillus and bifidobacterium. Other strains like Lactococcus, Enterococcus, Saccharomyces, S. Boulardii and Propionibacterium also have unique health-promoting effects.

What about soil-based probiotics like Prescript-Assist?

It is my understanding that many of these strains haven’t been studied yet besides bacillus. I think our understanding of the microbiome is in its infancy, and we have 8 million bacterial genes to work through compared to 22,000 genes in the human genome.

Another thought I’ve had about these types of soil-based organisms, is how do they change in terms of types and ratios from soil to soil, country to country? In other words, how does each unique human microbiome respond to a standard formula?

Which demographics are going to do well and which ones may have a bad reaction? What are the pros and cons to altering the microbiome with these strains and ratios daily? How long should it be used and should it be rotated?

I think we are definitely missing soil exposure by not eating directly from the land and getting our hands and feet in the dirt, but I’d like to see more research looking at environmental diversity, individual strain research and human studies before recommending a standardized soil-based organism formula for a wide population of people.

Lactobacillus

Lactobacilli are the dominant bacteria of the oral cavity, gastrointestinal tract and female reproductive and urinary system. This genus of bacteria has been found to improve the nutritional value of food, control gastrointestinal infections, improving digestion of lactose, control serum cholesterol levels, and control some types of cancer.

Lactobacillus is well known for its role in fermentation. You will find it in yogurt, kefir, pickles, cheese, sourdough bread, sauerkraut, kimchi and sour beers. Lactobacillus produces antioxidants, the cancer-preventive peptide lunasin in sourdough bread, and anti-allergenic substances,

One interesting fact is that lactobacillus as a genus can render iron unavailable for pathogenic microorganisms. Therefore, if you have very low iron levels despite iron-rich food and supplementation, you likely have a poor lactobacilli population and pathogenic bacteria are feeding off of iron.

1. Lactobacillus reuteri: L. reuteri produces reuterin (3-hydroxypropionaldehyde), a broad-spectrum antibiotic, active against bacteria, yeast, fungi, protozoa, and viruses. In infants with functional acid reflux, L. reuteri reduced gastric distension and accelerated gastric emptying.

Research found a significant effect of L. reuteri on bone health via decreasing tumor necrosis factor (TNF) levels and reducing bone resorption.

2. Lactobacillus casei MTCC 1423 strain as well and Enterococcus Faecium SF68: Effective in eliminating Giardia infection from mice.

3. Lactobacillus salivarius LS04: Found to reverse atopic dermatitis symptoms in some children.

4. Lactobacillus sakei: This strain is found in kimchi and the alcoholic drink sake. Researchers have found the sinuses of healthy people have higher levels of lactobacillus sakei that seem to help the body naturally ward off sinusitis. In laboratory experiments, inoculating mice with this one bacterium defended them against the condition.

5. Lactobacillus plantarum: A folate producing strain common in fermented vegetables and saliva. It enhances the expression of genes involved in tight junction signaling to improve intestinal barrier function, lowers high LDL cholesterol, lowers breast cancer risk in rats,  influences GABA and serotonin, lowers fibrinogen, and has been found to be effective in abdominal pain and bloating in IBS patients.

6. Lactobacillus gasseri: Improves glucose tolerance, lowers body weight by increasing the carbohydrate burn rate and shortens the duration of a cold.

7. Lactobacillus delbrueckii: This species has the strongest antioxidant activity. High levels of the endotoxin LPS from poor gut bacteria can elevate inflammation and oxidative stress.

Bifidobacterium

Bifidobacteria are generally considered to synthesize folate (all 44 strains), biotin, thiamine, nicotinic acid, pyridoxine (B6), riboflavin (B2), and B12. It produces the majority of GABA, requires iron and prebiotics, and is highly sensitive to glyphosate (GMO corn and soy). According to one study, “among the trillions of microorganisms in the gut, bifidobacteria, which, interestingly, were found through the literature to play a key role not only in regulating gut microbiota function and metabolism, but also in reducing classical risk factors for cardiovascular disease (e.g., obesity, hyperlipidemia, diabetes) by suppressing oxidative stress, improving immunomodulation, and correcting lipid, glucose, and cholesterol metabolism.”

1. Bifidobacterium longum: Mice studies have found that bifidobacterium longum normalizes anxiety-like behavior, hippocampal brain-derived neurotrophic factor (BDNF) and activate the vagal nerve in a colitis model. A rat study found that it reduced the inflammation from gliadin, the gluten protein found in wheat.

In children, it improved the symptoms of allergic rhinitis and allergic asthma and prevented constipation. One study found it shortened the duration of a cold along with lactobacillus gassari and bifidum. Another study showed that longum reduced depression in IBS patients by altering brain activity.

Results from one study using B. longum and B. breve in the presence of prebiotics significantly reduced the growth of C. diff.

2. Bifidobacterium bifidum: Bifidobacterium bifidum is a well-known species that has been shown to improve the immune system and IBS symptoms.

3. Bifidobacterium breve: Lactobacillus casei and Bifidobacterium breve have been found to reduce candida in the oral cavity of the elderly. B. breve has been found to increase mineral solubility, producing the phytase enzyme by bacteria to overcome the effect of mineral blocking phytate, reduces intestinal inflammation, and increases bone mass density.

4. Bifidobacterium lactis: A double-blind, randomized, placebo-controlled trial found that a mixture of Bifidobacterium bifidum, Bifidobacterium lactis and Lactobacillus acidophilus given to women starting at 4-8 wks before delivery and continuing until 6 months after delivery reduced the incidence of eczema.

In college students, lactobacillus rhamnosus, Bifidobacterium animalis and B. lactis were found to reduce the severity of upper respiratory infections and missed school days. B. lactis has also been found to be beneficial for constipation in women and children.

How to Choose the Best Probiotic and Prebiotic Supplements

My thoughts on probiotic supplements have evolved. The past approach has been to cram as many strains as possible with billions of bacteria. The more the better, it seemed. Then, strains with numbers behind them became the only strains that should be considered viable due to clinical verification.

Now, I believe the research is going towards understanding individual microbiomes, where strong targeted probiotic supplementation should potentially only be used with clear bacterial deficiencies in certain strains or after antibiotic use. Therefore, I think diversified prebiotic foods and powders are superior for a balanced microbiome. 

One small study even found that probiotic supplements cause confusion, difficulty concentrating and bloating, with the researcher stating another interview “If you are taking gut bacteria that doesn’t jive with your current gut bacteria, then that could definitely cause symptoms.” What this also made me think of is that we all have different requirements and microbiomes, and the future approach needs to take this into account.

Then, we have hunter-gatherer populations like the Hadza who completely lack bifidobacterium, men and women have different microbiomes based on men eating more meat and honey and women more tubers, and a high level of Treponema bacteria, linked systemic lupus and periodontitis, as well as syphilis in Western populations.

Yet, the Hazda do not experience any autoimmune disorders, diabetes or obesity. Their microbiome is more diverse, but different than what we understand to be a “healthy” microbiome. The truth is, we don’t really know what that looks like and it changes person to person, country to country.

A good probiotic supplement should contain studied strains (number after them), be alive, resistant to low pH/acids and thereby persisting in the intestine and able to adhere to the gut epithelium.  How many cheap probiotic products are dead upon delivery due to poor production and storage? 

Probiotic strain-dependent supplements are most likely not necessary if your digestion is healthy and you are eating prebiotic foods, fermented foods and drinking fermented drinks (but careful not to overdo it). Diversified prebiotic fiber – however- has tremendous benefits for everyone and provides a balanced microbiome.

The Best Probiotic/Prebiotic Supplements For Adults

1. Biome Protect by Adapt Naturals (20% off with this link)

This is a new product that I have tested within my own family with tremendous results. If you need to reduce bloating and focus on building a healthy gut barrier while helping re-colonize healthy gut flora, this is your product. Biome Protect is a 4-in-1 blend of prebiotics, probiotics, postbiotics, and polyphenols. What makes this product different is that it focuses on how to create an environment for all the beneficial bacteria to thrive and grow instead of individualized strains that may not survive. This is the future of prebiotic and probiotic supplementation.

• Tributyrin is a highly bioavailable form of butyrate, a short-chain fatty acid that plays a crucial role in gut health
• Bacillus Coagulans is a spore-forming probiotic survives stomach acid to reach the intestines intact
• PreforPro® is a next-generation prebiotic that works at a much lower dose than traditional prebiotics—without the side effects often associated with fiber
• The polyphenol blend – which also encourage healthy probiotic growth – includes pomegranate, grape, cranberry, and blueberry

I am currently searching for more products like this one. If you are aware of one, please let me know. 

The Best Probiotic Supplements for Pregnancy

The research on probiotics during pregnancy has been notoriously conflicting, and there isn’t a formula that can’t accurately be designed just for pregnancy. It depends on the individual’s needs. After reviewing many studies up to 2019 ^{1,2,3,4,5,6,7,8} here are my conclusions:

If you have a healthy digestive system, I see no reason to supplement with probiotics and you should simply concentrate on fermented foods and prebiotics. Probiotic supplementation may actually disturb an already balanced system.

If you are at risk for gestational diabetes, a formula containing Lactobacillus rhamnosus HN001 may reduce the risk.

Those with an autoimmune disorder may benefit from probiotic supplementation and impact the child’s immune system in a positive way.

Lactobacillus rhamnosus GR-1 may prevent preterm birth (caused by preeclampsia, UTI’s, other infections, intrauterine growth restriction or idiopathic spontaneous preterm labor.  This one is likely the best preventative take since antibiotics do not have a good track record for these issues. This can be found in Fem-dophilus by Jarrow.

If dermatitis runs in the family, probiotic supplementation during pregnancy and infancy helps to prevent atopic dermatitis in children, and a formula with both lactobacillus and bifidobacterium intervention has a better effect. In this case, I would recommend Jarro-Dophilus + FOS.