Understanding Your Microbiome Fingerprint  – Why it is Important to Introduce Diversity Intelligently

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We each have a unique “fingerprint” to our gut microbiome.

No one person’s bacterial composition is the same as the other.

There are a few groups of bacteria that are more consistently present in a healthy microbiome. These keystone bacteria include groups of bacteria from Bifidobacterium, Akkermansia, and Faecalbacterium bacteria, among others.

I work diligently to help promote these groups of bacteria in my clients.

I would include spore probiotics in the gut because these are necessary for a healthy microbiome – but are not sustained by diet like other probiotics.

Spore probiotics such as those found in Megasporebiotic live in the soil as spores, and when ingested or consumed by humans, they germinate in the small intestine where they live for 7-21 days.

They then turn into spores again and are released back into the environment – waiting to be picked up again by another host.

Because of their life cycle, we need consistent exposure to bacillus microbes to experience their benefits.

Since we’re not playing in the dirt, living in dirt, or eating food off the ground covered in dirt – many of us are deficient. The good news is that I’ve helped thousands of people feel better for the first time with probiotics, by trying out soil-based organisms – specifically Megasporebiotic.

These soil based Bacilli organisms are gut organisms who happen to use the soil as vectors into our body.

We’re not the only ones who benefit from spore organisms in the soil – plants do too.

Enhancing the concentration of spore microbes in the soil will help boost crop yields without reverting to GMO technology or fertilizers.

The bacillus strains interact with the hairy root system of plants to help them utilize nutrients more effectively – similar to how they might interact with the millions of absorptive folds of our intestines. It blows my mind sometimes how beautifully nature tends to repeat herself in biology.

I do consider Lactobacilli as keystone strains in the gut, but I’m careful to introduce them as they are more immune-stimulating and may aggravate histamine intolerance or excess D-lactate which can gunk up metabolism.

They are mostly present in the small intestine, and many are histamine and D-lactate producing.

I like to remind my clients that the small intestine is “small” in cross-sectional diameter, not length.

If small intestinal bacteria are overgrown, the extra gases they produce will have less room to maneuver and can immediately cause bloating, distension and discomfort.

While some Lactobaclli strains may make for exceptions, I wait to introduce this group of bacteria, and start with Bifidobacteria and others first. This minimizes setbacks when first working with clients to fix their guts.

When groups of bacteria are out of balance, we call the state “dysbiosis”. Dysbiosis is often a mix of overgrowth and deficiency. Deficiency in key groups of bacteria or yeast set the stage for healthy and unhealthy bacteria to overgrow; and likewise, overgrowth will crowd out resident microbes.

A gut treatment protocol does not always have to “kill” off groups of bacteria or yeast directly. If you can be selective with how you introduce groups of bacteria – you can avoid many pitfalls.

Adding back healthy microbes in systematic fashion will bring balance to the system and help them crowd out or create an environment unfavorable to overgrowth.

Clinical nutritionists are becoming smarter as to finding the balance of “ridding overgrowth” vs. “adding back diversity” as you may often need to do both at various points in a protocol.

A healthy gut protocol will balance the removal of overgrown organisms – while supporting those that are missing or deficient. A protocol should naturally shift to ways to maintain that diversity – often with prebiotics.

Prebiotics are a unique way to promote microbiome balance. Prebiotics are starches, fibers, and polyphenols from food that directly support the growth of healthy bacteria in the gut.

Probiotics like spore organisms in Megasporebiotic, help us metabolize our food more completely – unlocking metabolites from food that promote diversity of bacteria deeper in the intestines. In this way spore probiotics can also work as prebiotics.

The more diversity loss in the gut – the less metabolites we can derive from our food and the less tolerant we will become to our food and environment.

Prebiotics can be a little non-selective -meaning if the ratios of healthy bacteria are off-kilter, some prebiotics may promote too many bacteria types at once. As a consequence, the ratio of bacterial groups stays out of whack.

Equipped with this knowledge, functional clinicians like myself are developing novel strategies to leverage the benefits of probiotics and prebiotics, without potentiating dysbiosis in the process.

It starts with reconditioning the gut with spore probiotics and Bifidobacteria, and slowly promoting diversity with more complex mixes of probiotics and prebiotics – addressing inflammation, motility and other issues along the way.

The introduction of probiotics and prebiotics is best done in step-wise fashion. Promoting keystone bacteria like Akkermansia, Bifidobacteria, and Faecalbacterium species first, and later adding Lactobacilli and prebiotic diversity as the body tolerates.

This is contrary to most probiotic supplements and foods marketed in your standard grocery store. We are inundated with L. acidophilus and other Lactobacilli strains.

The problem with Lactobacilli overload is two-fold

1.) These sources are unprotected and killed by the stomach acid before making it to the intestines.
2.) Dead probiotic organisms maintain an ability to stimulate the immune system in the intestines – often too much too soon.

Trojan Horse Delivery of Probiotics 

I use Master Supplements TruBifido, Theralac, or Truflora, because the company protects the organisms from the stomach acid with a patented inclusion of an algae-derived ingredient that forms a capsule around the organisms while transiting through the acidic stomach. 

After transit through the stomach to areas of the intestine with a more favorable pH, the algae-derived ingredient  thins out – delivering the organisms unharmed.

Spore organisms like those found in Megasporebiotic, RestorFlora, and HU58 – are naturally protected by the spore itself which is unaffected by stomach acid.

I love spores as they act as probiotics, they act as selective antibiotics that help crowd out harmful yeasts and bacteria, and they help unlock compounds from food that create short-chain fatty acids in the colon, and promote diversity of non-spore probiotics throughout the digestive tract. 

When I first started introducing spore probiotics in my practice – my clients did not want to come off of them – often remarking that the formulation was the first probiotic where they truly noticed a difference from taking it.

When I started using non-spore probiotics with acid-proof delivery – my results improved yet another level. 

Prebiotics do not require spores or special delivery to work appropriately. They travel through the digestive system as though on an assembly line – each area of the gut extracting out different metabolites from the material – giving us a treasure trove of materials – many of which we are unable to produce on our own.

Intelligent Introduction of Probiotics and Prebiotics

While I’ve written on a step-wise approach to introducing probiotics in my Probiotic Blueprint. Prebiotics are also necessary for a healthy gut. They can also be used in step-wise fashion.

Prebiotics are important because not all gut organisms can survive outside of the intestinal environment. Many of these organisms are anaerobic – meaning they can’t survive in oxygen-rich environments. Some areas of the intestines are anaerobic and allow these organisms to thrive.

So while we cannot supplement with these organisms – the anaerobic strains will respond to prebiotic support.

We now know some prebiotics tend to be more precise in the organisms they help grow, while others tend to promote a wide spectrum of microbes. Similar to how I start with more balancing probiotics versus the immune-stimulating varieties, I start with precision prebiotics before moving to less precise prebiotics. In both cases, it is not that some probiotics and prebiotics are “bad” or one is better than another – it simply means they are best tolerated when introduced in a more intelligent order.

I start with MegaPrebiotic – as it is more selective to the keystone organisms.

Starting low at first and working up to one scoop per day. I then switch to a more broad prebiotic like partially hydrolyzed guar gum found in TruFiber.

Then, I will go to more of an inulin or fructooligosaccharide-containing prebiotic that feed a wide range of healthy flora, like that found in Biotagen.

Long-term, I actively rotate prebiotics to keep my system guessing and to promote richer diversity of organisms overall. I personally take Megasporebiotic consistently, and take Theralac in the morning and TruBifido at night.

I rotate the prebiotics MegaPrebiotic, TruFiber, and Biotagen – and introduce them in that specific order when working with clients. Once I go through this progression, I personally will mix and match them, changing them up day by day.

You may find that because of genetics, diet, or personal history – you really respond well to one formula or another. You’re not forced to rotate products – you can periodically introduce other products in addition to the core support you have found helpful.

For me, I’m prone to low Bifidobacteria genetically – so I’m always taking a Bifidobacteria product like TruBifido – and rotating others like Theralac or TruFlora around it.

If at any time a formula is less tolerated, I will take a step back and proceed more carefully before increasing intake level or introducing a new formula.

Accepting Intolerances as part of Your Unique Fingerprint

If having trouble tolerating prebiotics, it’s most often a result of dysbiosis still being present  or that you lack the microbiome “fingerprint” necessary to metabolize certain fibers and starches and it might be more of a long-term food intolerance to stay away from.

It is perfectly okay to be less tolerant of certain legumes, beans, grains, or other food group. It might be something specific to the region you live, or the diet you ate growing up. Just because you’re intolerant to a specific food, does not mean you have drastic gut imbalances that need to be addressed – you might just be naturally lactose intolerant (most people are!). And, bingeing on a lot of high-fiber foods can naturally make anyone a little uncomfortable

This is partly why one type of lentil may give you excess gas and bloating, while another lentil type might be tolerated just fine. The same may be said for black beans or pinto beans.

It may also mean that you might be able to tolerate a few bites of something starchy like hummus, but bingeing on it might start causing gas and discomfort as you overwhelm your body’s ability to metabolize it all.

The body is smart, it’s going to adjust to the food you’re eating. Our nomadic ancestors would naturally not eat the same food over and over again on a consistent basis – their food supply depended on the region they were in at the time – so one area may have been heavy with fish and game, while another area with berries, fruits and plants.

The gut microbiome would naturally shift to tolerate more of these foods. Conventional agriculture did not exist for much time at all over our genetic history. Eating the same foods over and over again is not what our ancestors ate.

Even when agriculture developed and societies were eating a bunch of yams or corn – there were 1000’s of varieties of these plants – not just a handful of over-hybridized varieties like we see in the stores today. 

A narrow diet will eventually lead to nutrient deficiency – but more deeply – a deficiency in the vast array of metabolites that bacteria help release from food. Because the microbiome adapts – it will slowly adapt to a narrow diet and you will become increasingly less tolerant of food.

An intelligent gut protocol does not try to reintroduce everything at once for this reason – it takes a stepwise introduction of probiotics, prebiotics, and dietary sources of prebiotics – coaxing a healthy microbiome back so that it can process a large variety of food once again – and not be as reactive to outside foods (or worse our own tissues as the case of autoimmune disease).

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