How Healthy Gut Bacteria Prime the Immune System for Immediate and Longterm Protection

microbiome immunity

Isn’t it unnerving to know that we are host to trillions of bacteria – especially in the gut?

Arguably, we are more bacteria than we are humans.

If you look at the totality of human genes versus the number of genes harbored by the bacteria in our bellies – it’s not even close.

While debate tells us that human genes range from 22,000 to 30,000, the collection of bacterial genes in the gut is over 2,000,000 (1). 

This is a 100-fold difference.

Genes determine function – and when you look at the totality of human biology – 90% or more of biological functions are encoded by the genes found in our friendly microbes.

Human genes take a backseat when it comes to responding to the environment and communicating important messages across the body.

It’s all about the friendly microbes!

If health is your goal, start by keeping our trillions of “mini-bosses” happy and healthy.

While the gut is known as the place where nutrients are absorbed and wastes removed, it is also the home to up to 70% of all immune cells in the body.

Mother nature decided that the internal tube that connects us to the outside world would be an essential part of our immunity – and that it would also be home to the vast majority of healthy microbes in the gut.

A healthy immune system requires a healthy balance of good bacteria in the gut.

When you study the body you’ll find that nature decided to place a lot of microbes at the interface of the “outside” and “inside” worlds.

Nature must have found bacteria useful in protecting us from harm from the outside world…

You’ll find groups of friendly microbes on the skin and gut, but also in areas like the lungs, mouth, and reproductive organs.

We’ve learned that these microbes know how to cross-talk with one another too in a number of ways.

So yes, a healthy gut helps create healthy lungs, healthy reproductive function, healthy detoxification, and a positive mood just to name a few areas. The health of one area promotes health in the others.

If you want to balance inflammation, maintain a healthy and balanced immune system. And, if you want to balance the immune system – you’ll want to promote healthy and diverse bacteria in the gut.

Here are some of the top ways that a healthy gut microbiome – the total number and diversity of microbes in the gut – helps maintain a strong, resilient immune system:

1.) Gut-Immune Crosstalk – Microbial “Gossip”

microbiome communication

The first point worth repeating is that groups of bacteria are able to communicate with one another directly and indirectly.

When bacteria help to train an immune cell – that immune cell travels around in the bloodstream – reaching areas of the body outside of the gut.

When bacteria are unhealthy, absent, or overgrown –  the level of toxins and wastes in our system increases in all areas of the body, not just the gut.

It turns out microbes are gossip addicts too. ..

They “hear” and “spread” the juicy details from the grapevine directly through nanotube “phone line” connections between microbes or through the electrical environment of an entire colony.

Microbes gossip with the purpose to nurture and protect.

One of the coolest examples of cross-talk is called “quorum sensing” where bacteria can sense changes in the environment and almost immediately turn on or off genes in response. With the change in gene function – they start producing different metabolites in response.

For instance – they might start producing prebiotic compounds in response to lower levels of their own colony or to promote other beneficial strains of bacteria. 

Conversely, they might start producing natural antibiotic compounds in response to higher levels of unwanted bacteria!

The Bacillus subtilis organism found in Spore Probiotics – Soil-Based Microbiome Support, SporeBoost IG, Megasporebiotic, HU58, and, RestorFlora have been studied for this unique and interesting behavior (2).

2.) Diverse Exposures are Important – the “Grocery Clerk”

immune protection

Many of the interfaces that separate the potentially harmful outside world and the internal world of the body are lined with bacteria. Bacteria will “see” an outside agent and communicate its findings instantaneously.

Bacteria are known to “sample” the outside environment and through their internal machinery – provide necessary components of a properly trained immune cell  – so if the body is exposed to the agent again – it’s ready to mount an immediate response not just swiftly, but also correctly!

Our little microbial buddies are like grocery clerks scanning barcodes at the checkout aisle – if something is not in the system – they’ll work to enter it in the system so we’re ready again – or they help throw out things that didn’t belong in the cart in the first place.

If they’re unhealthy, understaffed, or overworked – your immune clerks start getting sloppy – allowing things in the bag that shouldn’t be there – or reading the codes incorrectly.

The clerks can also become lazy. If they’re constantly scanning the same things over and over again – they start checking their phone, they take longer breaks off the job, and they’re slower to process the load of items they already have. 

Now, the clerks can become overworked too…if you don’t have enough clerks or aren’t providing them with the tools to do their jobs – they’re having to call in a manager over and over again to price-check an item or figure out why something’s not scanning correctly into their system.

There are only so many managers to go around. The line can get long and the items become impatient or “leak” through security such as the case with “leaky gut”!

In order to stay strong and smart, the body needs diverse exposures so that it’s less likely to be confused with a future danger.

Diversity in your diet and diverse exposures to people and places gives your immune system (via your microbes) the information to train immune cells so they’re ready against a wide range of dangers.

Not providing the raw materials from the diet and environment for the workers to do their job, the immune response either weakens or becomes irritable and overactive.

Social interactions with friends and family allow us to share each other’s immunity – and the connection itself has its own immune benefits from mental ease of feeling connected and supported.

When the immune system is able to routinely scan new information – it’s not only better able to respond to the environment, but also less likely to overreact to food proteins, pollens, molds, and other allergens.

If you lock avoid interaction and eat the same boring foods over and over again, your immune system gets bored too and is more likely to make mistakes.

Getting Dirty for Immune Health

Did you know that kids who grow up on farms or with pets have less incidence of immune problems? (3; 4)

It’s important to keep throwing diverse messages at the body in the form of food, dirt, and other people – so we have a full catalog of coded information to work with – so we’re fully equipped when a dangerous bug or virus tries to get inside and wreak havoc.

Diverse foods provide diverse starches, polyphenols (types of antioxidants/extracts from food), and other compounds that feed and maintain a broader array of bacteria. 

In return, our friendly inhabitants produce a wider array of metabolites that help us respond more efficiently to a wider range of circumstances and threats.

What goes around comes around. You scratch their backs, they’ll scratch yours.

If we eat the same thing for lunch every day; and fail to eat a lot of vegetables, and other prebiotic foods; and, if we work and live indoors and are not getting out in our environments regularly by gardening, hiking, or spending time in our community – We are not giving our friendly microbes enough information to “sample” and prep our immune responses appropriately.

Luckily, the solution is built into the understanding. 

Get outdoors, eat diverse foods, hang out with family, friends, try gardening, and be socially active in your community, and try different colors and varieties of the foods you already enjoy. 

When all else fails, supplement with greens, prebiotics, probiotics, and more when you’re not finding what you need locally. You can do so to further strengthen the areas in which you are doing well too.

3.) Bacteria are Tiny Production Facilities that Make Numerous Compounds Used by Humans

things bacteria make

Bacteria help us metabolize our food and turn it into usable compounds. 

The fancy word for these compounds is “metabolites”. The total of all metabolites present in the body at any given time is the “metabolome”. 

The greater number and diversity of compounds in the body at any time give it the ability to respond quickly and accurately to a wide range of threats and circumstances – yet another reason why a diverse microbiome is essential for health.

90% of all metabolites in the bloodstream at any given time are produced by bacteria!

Are you motivated yet to take good care of your gut microbes?

Metabolites are the hormones, the on/off switches, the dial turners, and the light signals that control and modulate the physiological functions of the body. 90% of them come from our internal microbes.

The microbial outputs are seemingly endless, and the more diversity you have, the more outputs they can produce in response to everchanging circumstances.

Here are a few examples of how the microbiome influences physiology:

  • Manufacture vitamins like a range of B-vitamins and vitamin K2 – essential cofactors to much of physiology – and supportive of stress balance, energy production, nerve health, and more.
  • Microbes control how much energy you take out of a meal (“energy harvest”) – helping with weight control.
  • They produce short-chain fatty acids (SCFAs) that are used as the fuel for immune cells, intestinal cells, and other healthy bacteria.
  • They produce carotenoids or antioxidant compounds that mop up inflammation and modulate our immune responses. 
  • They help us metabolize hormones like estrogen – keeping hormone ratios in balance. 
  • They produce antimicrobial compounds that ward off unwanted cells like Candida.
  • They produce or highly influence the creation of neurotransmitters like serotonin, dopamine, or GABA that keep us happy, productive, and relaxed.
  • Determine levels of glutathione, the body’s most important antioxidant compound that supports detoxification, immune balance, and neurotransmitter activity.

The new field of “Metabolomics” is one of the most exciting frontiers of immune and gut research for the next decade.

Not only are we getting smarter and evaluating what comprises a healthy microbiome- what compounds are produced – and what ratios of healthy bacteria are important for many areas of physiology – but we can start to develop a metabolic fingerprint.

That fingerprint can guide us on the exact areas to start when it comes to behavior changes, supplement additions, and food composition we want to focus on while we wait for bacteria groups to shift and recover with diet and lifestyle strategies. We are even transplanting gut microbes from one person to another.

To evaluate the microbiome, I use BiomeFx by Microbiome Labs. Personalized microbiome analysis is the best way I know how to evaluate the health and metabolic potential of your specific microbiome. It can help you get the most out of a gut healing protocol. They are also using the same technology to test the vaginal microbiome too.

Outside of testing, the next best way to know the health of your gut is to look at your poop. If your bowel movements are so good you want to call someone about it and brag – then you’re likely working with a healthy microbiome. There will likely always be some optimization and fine-tuning to be made and testing can be valuable in this respect too.

While the testing has improved drastically from the first generation of tests, we’re also learning more as to the roles of different bacteria, how their ratios influence health, and what to do with diet, lifestyle, medicine, or supplementation to improve the functional health of the microbiome.

One example of supplementing directly with a metabolite that helps to jumpstart rebalancing is SCFA’s like butyrate, acetate, and propionate. You can support these with products like Sunbutyrate liquid by Pure Encapsulations, or with polyphenols from plants that convert to fuels like PhytoFlora Microbiome Support.

SCFAs are also commonly produced by healthy bacteria as part of their metabolism. The combination of spore probiotics like Spore Probiotics – Soil-Based Microbiome Support, SporeBoost IG, or Megasporebiotic, and bifidobacteria like  BifidoSpectrum come to mind foremost.

A clinical trial has been conducted using Megasporebiotic and MegaPre, another targeted prebiotic mix, confirming synergistic outcomes for microbial diversity, along with a boost in SCFA production too.

SCFA’s fuel bacterial activity – and are also produced by healthy bacteria in a virtuous cycle – so a healthy gut microbiome balances itself too as long as it’s given the ability to do so as a result of your diet and lifestyle.

As mentioned above polyphenols from berries and herbal extracts are acted upon by bacteria – first, providing a fuel source for certain types of bacteria and second, are metabolized into compounds the body can use (often, a polyphenol itself is not useful until after it is acted on by bacteria in the gut!).

Polyphenols are not only antioxidants and immune modulators – they are direct and indirect prebiotics – feeding healthy bacteria who in return give us metabolites that our body can use and add to the diversity of our “metabolome”.

In later years, you may find researchers switch from talking about the microbiome – to the exciting breadth of discoveries of “metabolome” research.

The next generation of advancements will come about by studying all the rich things that are produced by our in-house microbial factories (the “metabolome”) – how to promote the bacteria that produce certain things – what raw materials are best for promoting certain outcomes, and by supplementing with the end-products themselves when possible.

Microbial genes are often the source for the diverse ability to produce metabolites – when you look at the totality of microbial genes in the body and their potential – the terms is referred to as the “holobiome”.

The diversity of gut microbes is associated with the diversity of microbial genes, and those genes are responsible for 90% of the metabolites floating around in your body and communicating to cells at any given moment, and we’re just scratching the surface of our understanding.

4.) The Gut as an Immune System Training Facility:

strong immune system

If you took a count of immune cells in our gastrointestinal tract – versus the number of threats they need to protect us against – it would be a losing battle for the immune cells.

Luckily, we do have trillions of healthy bacteria that take up the slack!

The microbiome helps “tag” immune cells with the appropriate bar codes so that they’re better able to respond to threats they otherwise may have yet to interact with individually. Gut microbes also help create the chemical weapons that immune cells equip themselves with against unwanted invaders!

Microbes work with specialized cells in the gut lining, which create the “pattern recognition” templates (bar codes or lock & key identification) that immune cells use to protect us (5).

The gut microbiome is constantly sampling its environment and training immune cells to know what groups of bacteria are “self” and which are threats.

This protects the healthy bugs from our immune system too, despite our gut being lined with lots of bacteria. You wouldn’t want your system to kill every microbe – we need the good guys! (6).

Uniquely, our microbiota can control the immune reaction so that healthy bacteria in the gut are okay and left alone by immune cells – but if the same bacteria were to breach the intestinal walls – we can mount an immune response against it outside of the gut.

This “smart learning” is particularly important in an example of a gut infection where you want to target the bad guy, yet also protect healthy bacteria from the immune reaction.

You can also help by reducing a lot of the noise of an infection – taking supplemental immunoglobulins in the form of IgG to bind up toxins and wastes and help carry them out of the gut. I use IgG-Boost 25000 Immunoglobulin Powder or MegaIgG2000 to support this detoxification when dealing with gut overgrowth or infection.

This “superorganism” training facility helps our system determine our tolerance to outside foods, toxins, metals, or bacterial pathogens – and, when working correctly, protects us from developing immune imbalances and autoimmunity.

Mobilize and Arm Troops Against a Variety of Threats

The microbiome can stimulate the production of neutrophils that directly protect against outside microbes.

Gut microbes also provide immune cells with the chemical weapons (pro-oxidant compounds) used to ward off competing microbiomes.

They can also structurally bolster an area with “defensin” compounds. They stimulate the production and potency of natural killer cells – and help clear away infected body tissues.

Lactobacilli and others can trigger the release of interferon messengers which then attract immune activity to the area. Vitamin A is necessary for this response – which is why I commonly recommend supplementation with Vitamin ADK Complete or Micellized Vitamin A drops as not everyone can make vitamin A very well from plant sources of beta-carotene. ADK Complete is my preferred option as the fat-soluble vitamins work together for bone health and immunity.

Bifidobacteria and prebiotic oligosaccharides are also able to prevent infection by boosting antiviral compounds and boosting mucosal barrier function. I use BifidoSpectrum as a source of bifidobacteria, and for prebiotics, I like FloraStart Fiber, and introduce FloraSpectrum Prebiotic Fiber for variety later on.

Mast cells are a type of immune cell that live in a layer of the intestinal lining. They are a source of histamine, support electrolyte balance, and play roles in blood quality and gut motility.

When microbes are disordered in the gut – mast cells are found less in the gut, yet also increase numbers in the circulation, which may be a mechanism as to how disordered gut health may increase histamine-related allergy symptoms like itchy or puffy eyes, runny nose, and tight airways!

5.) The Microbiome and Energy Production:

microbiome energy

Bacteria in the gut produce energy that helps immune cells develop and function. They also are capable of producing SCFAs that fuel immune activity, feed intestinal cells, and act as fuel for other groups of bacteria.

SCFAs increase and maintain mucus production – boosting the barrier protective functions of the gut.

Friendly bacteria also help extract energy from food efficiently – when ratios of microbial groups are off, one may naturally extract more energy from food than needed and the process becomes sloppier. An obese person’s microbiome is going to extract a lot more calories out of a meal than a non-obese person.

Two individuals can respond very differently to the same food, at the same caloric level simply due to differences in bacterial make-up of their guts. One may gain weight, while the other maintains weight with the same food – yet another reason to protect your friendly stow-aways in the gut.

6.) Gut Flora Help Maintain Barrier Walls

gut barrier leaky gut

Healthy microbial activity triggers the cells lining the gut to release natural antimicrobials and cell messengers that maintain a strong barrier against unwanted compounds so they do not find their way into the bloodstream.

They also work to maintain a healthy mucosal layer – the mucus in the gut is a home and cafeteria for healthy bacteria – and a physical barrier to entry from invading agents.

Gaps or holes in this barrier put the gut lining at risk – tears in that gut lining lead to “leaky gut” and the leaking of toxins and unwanted proteins into the bloodstream.

The leaky gut study that put Megasporebiotic on the map was a double randomized clinical trial that looked at markers of leaky gut, inflammation, and metabolism.

Researchers gave students an unhealthy meal that triggered the release of toxins that could be measured in the bloodstream. The students then took spore probiotics for 30 days and they gave them the same triggering meal and measured toxin levels. The toxin absorption was 42% lower in the probiotic group, and 36% higher in the placebo group.

The total toxin load improved by a relative 78% between the treatment group and control – a huge improvement in only 30 days.

The researchers also observed a lowering of triglycerides by 24% in the probiotic group, as well as improvements in inflammatory cell messengers and a key hunger and satiety hormone known as ghrelin.

A full discussion can be found here: The Megasporebiotic Leaky Gut Trial

The study was done with young, healthy students – it’s hypothesized that even more dramatic findings might be found had the study been repeated in older adults and/or those with various health conditions.

7.) Conduct “Neighborhood Watch” and Keep Troops Balanced

gut microbiome immunity

If one group of immune cells becomes more dominant – it can lead to autoimmunity and susceptibility to opportunistic threats. Without balance, the body may be tricked into thinking that it’s still in the “heat of the battle” for days, weeks, or even months at a time.

After ramping up groups of immune cells against a known threat – the immune system also needs to know that the threat is gone and that the system can balance again. At baseline, you want a balance amongst the different subtypes of immune cells so that you’re ready to ramp up one at any given time. Overstimulation is not preferred – just like resting after a workout, you do not want to put the body in a constant state of amped-up immune awareness either.

T-regulatory cells help regulate the balance of immune sub-types – warding off new invaders, sensitivities, allergies, and autoimmune-like reactions.

A weak microbiome leads to imbalances of key groups of immune cells – tilting it in favor of sensitivity and allergy symptoms, and a weakness in responding to microbial invaders – a double whammy of poor function.

Commensal bacteria play important roles in attracting immune cells to a specific area – while also tagging normal inhabitants in the area as friends. They also boost IgA secretion – a primary mucosal defense in the body and the “infantry” responsible for first-level immune protection. They modulate these responses only as necessary and help dampen the responses after the threat has disappeared.

These responses communicate widely across systems.

For instance, lung microbes will “see” a pathogen and will send cell messengers that are then picked up by microbes in the gut – which then work to recruit immune cells to the lungs!

Immune surveillance is also critical for discovering and taking care of rogue, cancerous cells and normal tumor-response systems. Cancer development can be a consequence of disordered and imbalanced immune activity.

Immune imbalance also triggers other chronic diseases through upregulated inflammation and failure to calm down after a trigger (or continued exposure to the trigger). These messengers are behind the development of diabetes, cardiovascular disease, inflammatory bowel disease, kidney disease, arthritis, and autoimmunity.

One’s inflammatory potential can be mediated with the intake of certain fats like fish oil versus inflammatory vegetable oils like those from corn, soybean, safflower, sunflower, and others. Inflammatory potential can also be helped by reducing the absorption of endotoxins in the gut (leaky gut). When I supplement with healthy omega 3’s, I use Omega Complete – EPA, DHA, and DPA Support.

Eating healthy fats and supporting leaky gut work to decrease inflammation promote a robust mucosa, provide a healthy home for wanted bacteria, and discourage unwanted foes from gaining entry or taking up residence

1 in 2 Americans have a chronic disease. 1 in 4 have 2+ chronic diseases! There are a LOT of individuals with imbalanced guts and immune systems.

Chronic inflammation is behind ALL of them – and can be mediated at a baseline with sufficient omega-3 fats and a non-leaky gut. High cholesterol can be a sign of high endotoxins – independent of fat intake in the diet. This is because cholesterol is upregulated, in part, to bind up endotoxins. High cholesterol readings can be a sign that it’s time to address inflammation from the gut.

Chronic inflammation creates “white noise” and normal signals can be missed – and it can be more difficult to respond to new threats.

Learn from Past Invasions

Certain immune cells in the gut produce immunoglobulins (IgG) that provide long-term protection against future assaults. IgGs help confirm good guys versus bad guys at any given snapshot of time or to reflect the immune challenges of a specific environment (drinking the local water on vacation). They also help to physically bind toxins produced by bacteria or that get absorbed through a leaky gut through normal microbial metabolism.

You can supplement with IgGs to support their activities in the gut by taking IgG-Boost 2500 or MegaIgG2000.

Their ability to do so is dependent on good microbial diversity, continued exposure to new microbes, and new foods in the environment.

This is how diets that include a limited number of foods (or eating the same few foods over and over again) – can lead to immune problems such as food sensitivities or allergies. It’s also how social groups confer immunity between each other to help protect against existing or new collective threats.

Exposure to diverse “antigens” in the form of foods and microbes can be considered essential for a healthy functioning immune system. This may also be why, as mentioned earlier, kids who grow up with pets, live on farms, or generally play in the dirt more have lower incidences of sensitivities, allergies, and autoimmune symptoms later in life.

Bacillus subtilis found in the soil for instance, produces a number of antimicrobial compounds and is a component of sporebiotics. We have receptors for B. subtilis in the gut – while it lives in the soil, it is a normal inhabitant of the gut, that uses soil as the vector or delivery system. Interestingly various spore microbes are used to boost nutrient absorption in plants too when added to soil!

When body tissues are injured, the proteins specific to that area are released. Certain types of immune cells grab up these and start targeting our immune cells to get rid of them – to help clear the debris and assist in the healing process. When this gets turned on permanently, however, we get autoimmunity.

The diversity of exposures promotes immune training and prevents microbial “weeds” from growing and immune cells from being confused or overactive.

Just like not going to the gym for a few weeks makes us physically weaker – not having training opportunities for your immune system can also weaken the ability to respond to opportunistic and new threats – and more prone to immune problems following chronic injury to thyroid cells, or brain cells, or muscle and joint cells as a few examples.

When it comes to training, you don’t start training at the starting line on the day of the race. You prepare prior to the event, going for smaller runs, quick bursts, and eventually peaking your performance on the day of the race (or at the acute moment you need to run from danger).

The same goes for your immune system – you don’t want to wait until you have food poisoning, a Clostridium difficile infection or H. pylori overgrowth to start a new training regimen.

Luckily the body is dynamic and gives us many second chances to get it right – but as we age, these chances become less and less.

A healthy, diverse gut microbiome helps recognize unwanted invaders, stimulate the production of protective cells, arm them with weapons needed to do their job, maintain the walls that protect the castle, provide energy/fuel for sustained function, help determine the potency of cells, and target the protective function to where they’re wanted, and away from where they’re unwanted. 

Lastly, they help dampen the response when it is no longer necessary and promote improved pattern recognition for future instances of the same or similar attack.

We’re a “walking, talking rainforest” that needs strong species diversity of microbes to perform at high and balanced functions. It’s not just the species diversity – it’s the genetic diversity and functional capacity to respond to your environment that makes us healthy now and in the future.

Take care of your bugs, and they’ll take care of you.


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