July 29, 2017

Your Gut Microbiome – How It Really Looks and How It Works

How your Gut Microbiome really looks and works

Before we start, here’s a quick refresher:

Eukaryote: a generally multicellular organism, like humans, animals and plants that are hosts for microbiomes

Prokaryote: simpler, one-celled bodies like bacteria that preceded eukaryotes in evolution, and make up microbiomes

Human gut microbiome: a collection of microorganisms, mainly bacteria, that live in the human digestive tract. It’s comprised of powerful diverse bacterial colonies that work together in a unified community (consortia). The microbiome acts like a cohesive organ in partnership with the human body.

Human gut microbiome structure: The gut microbiome exists in a biofilm that coats the entire length of every intestine. The biofilm is made up of intestine-secreted mucosa, the microbiome (bacteria and other microorganisms) and various bits of circulating information like DNA, proteins and other microbiome-synthesized biologically active compounds that are exchanged between bacterial colonies.

Human gut microbiome function: The gut microbiome does at least 5 important things for its host human:

  1. Supports host health & increases host vitality by optimizing life processes, efficiently digesting food and synthesizing vitamins and bioactive compounds. Through human cell communication, the microbiome can influence organ and body function and either prevent or provoke disease.
  1. Upholds host integration into food chains & ecosystem by influencing food preference and behavior
  1. Protects its host human from aggressive foreign prokaryotic attacks and pathogenic invasion
  1. Breaks down its host body and returns component parts back into the biosphere’s circulation when the human begins to become terminally sick or die
  1. Facilitates the horizontal exchange of genes between different unrelated species in an ecosystem

Why is the Microbiome Important Now?

The microbiome and its importance as we understand it now is very different compared to just a decade ago. Then, bacteria in the gut wasn’t a particularly riveting topic unless they were actively causing disease, and the link between bacteria, digestion and human health wasn’t actively explored.

Microbiome health recently skyrocketed in popularity as our collective microbiome health began to fail and microbiome-characterizing technology became available. Scientists are now finally understanding how truly vital the microorganisms in our gut are to almost every human body function.

And it makes sense – thanks largely to our gut microbiome, we are more bacteria than we are human. For every human cell, our bodies contain 10 bacterial cells. For every human gene, our bodies contain 100 bacterial genes. Our large intestine, which contains our gut microbiome, weighs more than our heart and brain combined.

How Your Microbiome is Like a Fortune 500 Company

The microbiome’s bacteria aren’t randomly floating in your intestines.

Individual bacteria of the same species are organized into tightly-knit, smart communities called colonies. Imagine the individual bacteria as keys that comprise a keyboard (the keyboard species), and others are wire bacteria that comprise the circuit of a computer (circuit species). Out of context, an individual key or a wire can’t do much, but together, multiple keys or wires can be used to transmit complex information. The whole is greater than the sum of its parts. Bacterial colonies are smarter and stronger than an individual bacterium (Fig. 1).

Bacterial colonies are further organized into consortia, or complex communities of different species working, communicating and living together. A consortium is like a computer – it’s component parts communicate with each other in a unified system to create, transport and store complex information. Bacterial consortiums living in our microbiome perform the same types of tasks. They also communicate on multiple levels: an individual bacterium communicates with other bacterium within its species-specific colony and the colonies communicate with each other to form a consortium (Fig. 1).  

Even further, the consortia communicate with each other too, making up a localized area of the gut microbiome. The small intestine microbiome differs from the large intestine microbiome, as they are comprised of differently tasked small intestine consortia and large intestine consortia. This is analogous to the many computers that form a network within a large company in which constant, multi-level information is exchanged non-stop to follow a mission/vision greater than any one computer, or its component parts, can achieve (Fig. 1).

Figure 1. The different hierarchies of the human gut microbiome: individual bacterium, bacterial colony, bacteria consortium, localized microbiome.

Now, the mass of prokaryotes and eukaryotes comprise almost equal living parts of the biosphere. Although we may not notice it, we eukaryotes live within a prokaryotic environment, and every eukaryote is surrounded by a friendly prokaryotic community that forms its specific microbiota. This specific microbiota, or microbiome, plays a vital role in a eukaryote’s life on an individual and species-wide scale.

Communication: Bacterial Email and Conference Calls

On every level, bacteria communicate with each other using various methods including DNA, proteins and other microbiome-synthesized biologically active compounds. Like a Fortune 500 company uses email, phone, Slack, or other internal communication methods, bacteria use informational packages to talk as well.

For a company to run well, it also must communicate with members outside of itself, like customers and partners. The gut microbiome does too – the friendly microorganisms that have evolved alongside humans during evolution have developed the ability to communicate with our body’s cells. This forms a symbiotic partnership between the gut microbiome and the cells within our digestive system. Each supports the health of the other in a mutually beneficial relationship – like a successful business partnership.

Unfriendly bacteria do not have the same goal as friendly microorganisms as they do not support human health. Their goal is to use the gut environment merely as a growth medium as they have not evolved the ability to communicate with friendly gut bacteria or human cells. It’s like a bad business partnership – the “partner” uses the company for their own gain, but gives nothing back.

Quick digestion refresher:

Role of microbiome in digestion & absorption: the microbiome plays a vital role in nutrient breakdown and absorption as it is part of the biofilm layer that separates digesting food from the human body during the entirety of the digestive and absorption process.

Small Intestine: the organ, following the stomach, in which most food nutrient absorption occurs. The small intestine microbiome (microorganisms cells) is mostly comprised of aerobic bacteria that separate digesting/absorbing food (chyme) from the small intestine’s villi (human cells).

Villi: small finger-like projections lining the inside of the small intestine that increase the surface area for nutrient absorption. The small intestine villi are what the biofilm layer, containing the microbiome, directly sits on. The entire surface area of the villi cover the area the size of a tennis court!

Large Intestine: the organ, following the stomach and small intestine, in which most bacterial-human interaction and activity occurs. The large intestine microbiome is mostly comprised of anaerobic or facultative aerobic bacteria that are tightly integrated in a complex community of microorganisms that work closely in symbiosis with human cells to regulate the human body.

What Does It Look Like?

Figure 2 A shows a cross-section of digestion in the small intestine. Bacteria consortium and mucous forms a biofilm that exists between the chyme and the villi through which nutrient absorption occurs. Food and digestive enzymes form the entering chyme, which can proceed one of three ways: bypassing the microorganisms and enter straight through the villi, entering only into the microorganism colonies without making it to the villi, and entering the microorganism colonies for partial digestion and subsequent procession to the villi. The microorganism consortium also synthesizes new bioactive compounds for direct absorption by the villi. Some colonies are located on the villi and can directly interact with human body cells and regulate immune, hormonal and nervous systems. These colonies can either block or activate food allergic reactions.
Figure 2 B shows a cross-section of the large intestine. Feces passing through consist of 50% bacterial colonies, which are multiplied in the outer mucosal layer and exit on fecal mass. About 30% of feces consist of undigested foods and the remaining 20% is water, toxins, and other secreted toxic compounds. The crypts contain bacterial colonies that are tightly integrated with human body cells. They can influence the function of multiple systems like hormonal, nervous and immune systems and can synthesize metabolites and vitamins that the human body cannot synthesize itself or were not received with food. The outer mucosa layer changes constantly, but the inner mucosa layer colonies are permanent and remain within a human from a very young age. They provide the specificity of the human microbiome and influence diet preference and disease outlook.

Your entire microbiome lives within a biofilm that coats the entirety of your intestines. This biofilm includes a mixture of both human and bacterial components:

  • Intestine-secreted mucosa (the medium, provided by the human body)
  • The microbiome (bacteria and other microorganisms)
  • Various bits of circulating information like DNA and proteins (like bacterial emails and texts)
  • Other microbiome-synthesized biologically active compounds (both bacterial and human)

Of course, during transit on/in food and feces, microorganisms exist outside of the biofilm, but their permanent home is within its favorable mucosal environment.

Each component part plays a vital role in digestive and overall human health, but the biofilm as a whole is incredibly important.

Your Microbiome Influences What You Want to Eat, and Even How those Calories are Processed

Let’s break down how each component of the biofilm makes you who you are.

– Intestinal Mucosa: Your body secretes mucosa for several purposes: to protect your digestive system from digesting itself, to aid in peristalsis (as a lubricant for moving things along), and it provides an ideal medium for the microorganisms of your microbiome. The human-secreted mucosal environment is very similar in composition to the matter that bacterial colonies create for themselves to live in.– The Microbiome (bacteria and microorganisms)The bacteria in your microbiome aren’t accidental. Humans have evolved in tandem with bacteria for millennia. In fact, prokaryotes (which include bacteria) existed far before any of us eukaryotes (which include animals and plants) evolved. We developed within their systems, and they still run the show, even if we can’t always see them. During eukaryotic evolution in the prokaryotic environment, humans developed friendly relationships with certain bacteria, and now we need them in our gut microbiomes to survive. This relationship means the bacteria within us have evolved the ability to communicate directly with our human cells including nervous, endocrine, hormonal and immune system cells that exist inside our digestive systems. This is especially important because the microbiome bacteria communicate with our cells and influence us in many ways, including stimulating us to eat certain foods that bacteria themselves need to be healthy. When your gut microbiome is full of diverse, evolutionarily-supported friendly bacteria, they “order” food that supports their own growth AND the health of your digestive system because friendly bacteria consider the human cells they interact with as part of their consortia. They need everyone to win to be healthy. If your gut microbiome is full of unfriendly bacteria that the human body has not evolved to need, they use your microbiome environment as a growth medium, and do not include human cells in their consortia because they don’t care about the well-being of any cells but their own. They “order” food that is healthy for them, but may not be healthy for you, like sugar-heavy or empty carb loaded food.– Various bits of circulating information like DNA and proteinsLike bacterial emails and texts, these microbiome-synthesized biologically active compounds are what bacteria and microorganisms use to communicate between themselves and with the cells of the human body.

You may ask – what are friendly bacteria? Are they different from person to person? What determines which bacteria I need? How does my microbiome influence my diet – what is a good diet for me and for my microbiome? Interestingly, this answer is already inside you.

Your Ideal Diet is Already Within You, Literally

It’s in your genes! The way that your ancestors have evolved determines what is genetically programmed within you today, including how your body adapted to process different foods, which foods your genes “prefer,” and which bacteria support that diet.

Civilizations that evolved closer to the poles are more heavily meat-based, and communities that evolved closer to the equator are more plant-based. Why? Animals are the main food source closer to the poles where plants don’t grow. Plants are the main food source closer to the equator where they grow best (think ice-fishing in Alaska vs the abundant jungles of India). Therefore, if your ancestors survived off mainly fish and blubber where plants barely grew, your body is adapted for this diet and you can easily consume meat-heavy foods without developing adverse side-effects. The environment your body creates for your microbiome is welcoming to the bacteria that come with these foods. If you’re a mainly carnivore by genetic makeup and you switch to a vegan diet, it will take time for your body and microbiome to adapt to this type of food because it is not your default genetic state. If you transfer from a genetically-carnivorous diet to a self-imposed-herbivorous diet, you may experience side-effects like increased risk for cellulite, diabetes, alcoholism and others as that diet is perpendicular to the evolved diet of generations before you. The same goes the other way – if you’re genetically more vegan and you eat a typical Western diet of burgers and meat-laden meals, you could easily develop cardiovascular and heart-related problems.

How exactly does your microbiome influence what you eat and how it affects you? It directly determines what enters your body and what does not.

Your Biofilm Feeds More than Your Diet Does

A cow eats grass. A cow cannot digest grass – it’s body physically can’t digest it by itself. But how does it survive off a grass diet? A cow has special microorganisms in its digestive system which produce enzymes that can break down the cellulose in grass to make it absorbable by the cow’s body. Essentially, the cow doesn’t eat grass – it eats what its microorganisms process for it to absorb.

The human body is similar. The biofilm containing our gut microbiome acts as a filter for the foods that actually get absorbed by our body.

We are not fueled directly by the nutrients we eat, but by the product of collaboration between our microbiome and the nutrients we eat. Food is a raw material, but what our bodies absorb as nutrients first passes through the “filter” of the microbiome, a membrane that optimizes and changes food before it enters our body cells (similar to how a cow does not eat grass, but eats the product of bacterial digestion in its stomach).

The microbiome optimizes food in the following ways:

  1. The bacteria in the microbiome send signals to your body cells, influencing hormonal, endocrine, immune and nervous systems to impact diet preferences
  2. When food is consumed, some nutrients pass directly through the biofilm and into your small and large intestine body cells
  3. A very large portion of this food does not pass directly to your body cells, but instead is processed by the microorganisms in your microbiome first. The product of their digestion is what enters your body
  4. Some nutrients are absorbed by bacteria and their journey ends there. These nutrients never make it to your body, even though you consumed them
  5. The microorganisms themselves also produce certain bioactive compounds, vitamins and other elements that are absorbed by our bodies. Our microbiome also directly feeds us.
  6. This happens in both the small and the large intestine, but the most important and impactful calibration of the nutrients entering our body and of various body systems happens in the large intestine microbiome. The small intestine microbiome helps calibrate the foods that we’ve eaten, and the large intestine microbiome synthesizes vitamins and bioactive compounds that our bodies need but don’t have. The state of the large intestine microbiome primarily regulates our predisposition to disease, base metabolic level, hormonal balance, autoimmune processes and nervous system regulation.

Our microbiome controls what gets through to our intestinal cells and what doesn’t, influences our food preference, and produces its own elements that our bodies absorb. More importantly, a healthy large intestine microbiome actively prevents disease, and a sick microbiome encourages the onset of disease.

Figure 3: Representation of Healthy versus Unhealthy microbiome

How Do I Change My Microbiome?

A microbiome is a complex, conservative community of tightly-knit bacterial consortia. To increase the chances of successfully adding new friendly members to the microbiome community, new bacteria must arrive in already-formed, robust colonies. Individuals or bacteria groups that aren’t structured have a much harder time integrating and are usually rejected by the existing consortia and pass through.

Therefore, there are really only 2 ways that one can change the constitution of the microbiome:

  1. Eliminate nearly all bacteria using antibiotics and repopulate the digestive tract using fecal matter transplants (this is generally a last resort for life-threatening emergencies performed in a medical setting)
  2. Consistently and sustainably sow friendly microorganism colonies through a diet that contains naturally-formed bacterial colonies. This is how humans have evolved to accept friendly bacteria and remains the most effective, safe and sustainable way to achieve microbiome health.

As you may have figured, probiotic pills do not contain natural colony structures, and many of these bacteria pass straight through because they cannot integrate properly. Probiotic drinks do not contain the necessary prebiotics in their naturally occurring probiotic-prebiotic pairing that our microbiomes expect. Currently, the only food that we know of that contains diverse, colonially organized probiotics, naturally occurring prebiotics, ideal nutrition and short-living bioactive compounds is germinated grain.

To read about how germinated grain contains naturally-formed probiotic and prebiotic complexes, read our grain microbiota article here.

To read about how to use germinated grain as a part of an effective microbiome and health-supportive system, read our comprehensive health article here.

© 2017 Volgin LLC

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