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The Best Probiotics: Understanding the Microbiome

 

For millions of years, our ancestors hunted and gathered fresh 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 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 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.

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 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 probiotics 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 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

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  

New research has found that gut flora plays a role in expressing genes for myelin construction and formation for never fibers. Gut bacteria may have an influence on the body’s use of vitamin B6, which in turn has profound effects on the health of nerve and muscle cells. Microbes may have an influence on autoimmune diseases and therefore play a role in disorders like multiple sclerosis.

I have had a few clients that have had elevated B6 levels on blood tests that couldn’t be explained. Both had very poor gut health and numerous rounds of antibiotics. If gut flora wasn’t there to utilize the B6, then it is conceivable that B6 would elevate. Combine this with low GABA and high glutamate, and it explains neuropathy after rounds of antibiotics.

Type 2 Diabetes

Indolepropionic acid is produced by bacteria in the gut and helps the pancreas produce insulin. People who eat more prebiotic fiber-rich food and less saturated fat encourage production of indolepropionic acid. Researchers discovered the important role the acid plays in diabetes when they assessed 200 people who were all overweight and were not processing glucose well. The major difference was that those who remained diabetes-free had high levels of indolepropionic acid in their gut.

Mental Health

According to an article in Scientific American, “when Pettersson’s team performed a comprehensive gene expression analysis of five different brain regions, they found nearly 40 genes that were affected by the presence of gut bacteria. Not only were these primitive microbes able to influence signaling between nerve cells while sequestered far away in the gut, they had the astonishing ability to influence whether brain cells turn on or off specific genes.”

Bifidobacterium is capable of secreting large amounts of GABA, an inhibitory neurotransmitter to glutamine and glutamate, controlling an imbalance found in numerous mental health issues. The Stanley Foundation Neuropathology Consortium found that levels of glutamate were elevated in individuals with Bi-Polar and Major Depressive disorder compared to controls. Another study shows that lactobacillus influenced GABA levels in certain brain regions, leading to lowered stress hormones, anxiety and depression. Could bacteria and GABA be one of the keys to the underlining cause of numerous mental disorders? Or better labeled, bacterial deficiencies?

You can read more about this fascinating topic in the article Mental Health Begins in the Gut, Not the Brain.

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.

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

8. Lactobacillus delbrueckii: This species has the strongest antioxidant activity.

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 and is highly sensitive to glyphosate (GMO corn and soy). It plays a major role in carbohydrate metabolism in the colon.

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

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 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

A good probiotic product should be diverse with the most studied strains, alive, resistant to low pH/acids and thereby persisting in the intestine and able to adhere to the gut epithelium and have a high probiotic count. How many cheap probiotic products are dead upon delivery due to poor production and storage? You do get what you pay for with probiotics.

1. VSL#3 (112.5 billion, 8 strains)

VSL#3 is the gold standard of probiotics. It requires refrigeration and incorporates multiple levels of protection for the bacteria. VSL#3 has been the main probiotic used in our clinical practice for numerous years for digestive disorders. VSL#3 capsules are about 10 times more potent than the average probiotic. One study found that probiotic therapy using a mixture of probiotics (VSL#3) was shown to increase the total number of intestinal bacteria and to restore the diversity of the bacterial microbiota in patients.

Streptococcus thermophilus
Bifidobacterium breve
Bifidobacterium longum
Bifidobacterium infantis
Lactobacillus acidophilus
Lactobacillus plantarum
Lactobacillus paracasei
Lactobacillus delbrueckii subsp. bulgaricus

2. Bio-Kult (Minimum 2 billion live microorganisms per capsule, equivalent to 10 billion live microorganisms per gram, 14 strains)

BioKult became a popular probiotic due to its use by Dr. Campbell-McBride, author of Gut and Psychology Syndrome.

Bacillus subtilis PXN 21
Bifidobacterium bifidum PXN 23
Bifidobacterium breve PXN 25
Bifidobacterium infantis PXN 27
Bifidobacterium longum PXN 30
Lactobacillus acidophilus PXN 35
Lactobacillus delbrueckii ssp. bulgaricus PXN 39
Lactobacillus casei PXN 37
Lactobacillus plantarum PXN 47
Lactobacillus rhamnosus PXN 54
Lactobacillus helveticus PXN 45
Lactobacillus salivarius PXN 57
Lactococcus lactis ssp. lactis PXN 63
Streptococcus thermophilus PXN 66

“Each strain is microencapsulated and freeze dried individually which affords their protection through the low acidity of the stomach and allows storage of the finished product under normal room temperature. All Bio-Kult products are guaranteed at the end of the shelf life and undergo full pharmaceutical stability testing in humidity and temperature controlled facilities.”

3. Garden of Life Fitbiotic (14 strains, 50 billion live organisms)

This formula is the only one on the list that contains Lactobaccilus gasseri, the bacterial strain associated with weight loss. It also includes prebiotic fiber.

Lactobacillus gasseri
Lactobacillus acidophilus
Lactobacillus rhamnosus
Lactobacillus brevis
Lactobacillus casei
Lactobacillus paracasei
Lactobacillus plantarum
Lactobacillus salivarius
Lactobacillus bulgaricus
Bifidobacterium lactic
Bifidobacterium bifidum
Bifidobacterium breve
Bifidobacterium infatis
Bifidobacterium longum

4. Probiota Sensitive (25 billion in a prebiotic base per capsule, 12 strains, dairy and soy free, shelf stable)

This formula does not require formulation and claims shelf stability for two months in warm temperatures.

Lactobacillus rhamnosus
Bifidobacterium bifidum
Lactobacillus acidophilus
Lactobacillus casei
Lactobacillus plantarum
Lactobacillus salivarius
Bifidobacterium longum
Streptococcus thermophilus
Lactobacillus bulgaricus
Lactobacillus paracasei
Bifidobacterium lactis
Bifidobacterium breve

24 Responses to The Best Probiotics: Understanding the Microbiome

  • Thank you for your very generous and informative article – indeed unravelling the mystery of being healthy. Thank you. Fiona

    • Hi Fiona,

      Thanks for the feedback and glad you found it informative. This article was a few months in the making, so I’m happy to finally share the research.

  • Hi Alex, what a coincidence, I was just breaking my head looking for a good probiotic formulation and received your newsletter with this great article. Thank you so much.

    Felipe

  • Hey Alex,
    I love the article amazing as always I have a question what do you think of the Garden of Life Dr. Formulated probiotics? I’m also wondering if the VSL#3 is ok to take for daily use or is it best to use if you have a condition where you need a very strong probiotic?

    • Hi Jeff,

      Thanks for the feedback. Many of Garden of Life’s formulations look well formulated, but I haven’t been that impressed in terms of results from clients using it compared to VSL#3. That said, perhaps Garden of Life’s line is okay for those in generally good health. Yes, VSL#3 can be used for daily use and the dosage ranges based on your needs. I have kept it on hand when a stomach flu is going around or in case of food poisoning. I did just add the Garden of Life Fitbiotic to the list because it contains lactobaccilus gasseri for weight loss, and I was having trouble finding a good product that contains it.

  • Ok thanks sounds good I was using the Garden of Life probiotics I’m going to try the VSL#3 thanks for all the information.

  • What about soil-based organisms, like prescript-assist?

  • Wonderful article! Thank you!

  • Hello Alex – GutPro looks like a great probiotic. Please check it out and see if it is worthy on the list. They have a few different products (Primal, Infant, Yeastbiotic etc.). I found it on Corganics webpage. Also, what is your view on supplementing with digestive enzymes. There seems to be less discussion about enzymes, relative to pre and probotics. Thx.

    • Hi Marty,

      Yes, their products look well thought out and formulated. Good find on another probiotic that contains L. gasseri. I also noticed they share my opinion on soil-based strains that haven’t been studied and how long to use them. They only include two strains that have research in the Primal Soil product and recommend to only use it for less than 3 months.

      • Regarding enzymes, they are helpful for those with digestive issues and low stomach acid (along with betaine/HCL). Digestive enzymes become more necessary as you get older, especially after 70. If you have a good percentage of raw food and fermented food in your diet, you are sparing your own digestive enzymes. Fermented foods and drinks provide both probiotics and live enzymes, making them ideal. There is a book called Enzyme Nutrition by Dr. Howell, and his theory was that aging was strongly related to your enzyme bank and how much you draw from it. So he was a major proponent of taking digestive enzymes with meals to spare your own.

    • Hi John,

      I think Friendly Force looks like a solid formula. I haven’t seen the research behind marshmallow root protecting probiotics but would be interested in reading it.

  • is VSL#3 suitable for seniors? what is your opinion on Dr. Axe probiotics?

    • Hi Nina,

      Yes, VSL#3 is suitable for seniors.

      I think his probiotic products look well-formulated. I know he focuses a lot on gut health, so I’m sure he put a lot of research into it.

  • HI Allex, I understand some probiotic bugs can actually cause inflamation, and some don’

    Hi Allex, I understand that some probiotic bugs can cause inflammation, and some don’t. Please tell us the ones that don’t. I’m fighting hives, candia Thanks !!!

    • Hi Larry,

      Great question and one that is a little complicated to answer. I don’t think the research has really been able to pinpoint a full understanding of this yet. Right now we have theories and one of the theories is that certain strains increase histamines (Lactobacillus casei, Lactobacillus delbrueckii, Lactobacillus bulgaricus, bacilli bacteria, acetic bacteria and yeast in fruit wines) while others reduce histamines (B. infantis, L. plantarum, B. longum, staphylococcus carnosus FS19, Bacillus amyloliquefaciens FS05, Lactobacillus sakei, and Vergibacillus sp.SK33). L. reuteri is an unusual one because it is able to convert L-histidine into histamine but this actually suppresses pro-inflammatory TNF-alpha production.

      Interesting enough, fermented foods rich in diversified probiotics are higher in histamines. Ultimately, I think that it is the underlying alteration of the digestive system like leaky gut or SIBO and the immune system along with genetic differences in histamine genes like DAO and HMNT (and receptors) that determine histamine overload because the diversity of the strains should produce a neutral response. I think there may also be a dysregulated hormone connection because DHEA plays a role in improving the resistance to viral, bacterial and parasitic infections. It appears some people with very sensitive guts respond better to using only specific histamine reducing strains on their own in the beginning to help balance the population.

  • Hi, what do you think about Renew Health, probiotics? Targeted for specific condition and regular ones?

    • Hi Dylan,

      I haven’t tried this one myself or with clients, but I’ve heard positive things. I like that they use clinically documented strains. Five billion is the minimum needed that research has been shown to be effective. As soon as I get more feedback, I will consider adding it to the best list.

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