Fisherman's Guide To The Microbiome

Congratulations!!! The fact that you are reading this webpage means you have made enough of a connection between your health and your microbiome to be here. Making that connection is a great place to start and hopefully the information in this wiki will help you further understand that relationship.

I am not a fisherman but I do have a useful understanding of how my microbiome works that I equate with fishing. Fishing techniques range from science based as commercial fishing operations are likely to utilize to the fuzzy logic traditional, low-tech artisanal fisherman use based on observations in the field.

This Fisherman's Guide To The Microbiome is at the low-tech end of the scale. It is something anyone can read and understand using just plain common sense.

The Ecosystem

First a brief and factual description of the ecosystem our microbiome is...

According to Harvard Health Online:

About 100 trillion bacteria, both good and bad, live inside your digestive system. Collectively, they're known as the gut microbiota.

In the Encyclopedia of Cell Biology:

The gut microbiome is the collection of microorganisms including bacteria, archaea, viruses, and fungi found within the gut and their overall genetic information. Our gut microbiota has been shown to have broad effects on our health and well-being, impacting our immune system and metabolism, detoxifying various ingested components, and even affecting behavior.

Well put! The Fisherman says that sounds right.

This phrase is very important in the context of the type of Failure Of TGA that I describe in detail in this wiki:

detoxifying various ingested components

The Fisherman says that "various ingested components" means chemical compounds in our food. And "detoxifying" means taking care of the chemical compounds in our food that we are not designed to handle. So in this sense our microbiome acts like a garbage collector. In fact it's a symbiotic relationship: we have something we don't need and don't know what to do with but our microbiome has a use for it and disposes of it.

Our microbiome is like a rubber band and flexes and contracts in response to the input we give it: whatever we swallow. Our bodies never evolved to be 100% capable of processing everything we feed it. That's where our microbiome comes in. Not only do our microbes help us digest things we can't, like oxalate, but they also do things like generate chemicals, enzymes and vitamins that our body uses.

In terms of the numbers of bacterial species, kind of like teams or families, I have read estimates ranging from a few hundred to a few thousand.

Mixed in with our bacterial microbiome is our virome, a collection of viruses that also inhabit our gut. It is estimated there are 140,000 different viruses living there. Unfortunately even less is known about our virome than our microbiome.

For our purposes it is adequate to understand that at our level of operation we are talking about species and strains of bacteria, strains are a subset of species. For an in depth explanation of bacterial taxonomy please check out:

en.wikipedia.org/wiki/Bacterial_taxonomy

For further research:

en.wikipedia.org/wiki/Human_microbiome

en.wikipedia.org/wiki/Virome

FunFact!!!

Metagenomic study of the human microbiome has demonstrated that there are 3.3 million unique genes in human gut, 150 times more genes than our own genome.

Enough numbers and science, suffice to say there are a lot of microbes in us and they have a consequential impact on our health.

The Pipe

Now let's consider a line drawing of me and my gut. My gut is really just a pipe and my microbiome resides there.

me and my gut

While I think of my gut as my insides it's not. It's the outside running through me. In the context of conventional medicine treating my microbiome, this picture illustrates the problem, it's a jurisdictional issue: doctors treat me, that includes all parts of my body in the cube, it doesn't include the outside, that is my jurisdiction and responsibility.

But doctors do require access to my gut for the administration of medicine. Under this arrangement any microbiome dysbiosis caused by the prescribed medication is my responsibility to monitor and repair. That's not right, this needs to change. I'm not equipped to be able to do that. At a minimum a patient needs to understand what expected impact a medicine will have on their microbiome.

Now let's imagine the ecosystem that inhabits this pipe that runs through me. Not a literal image but an imaginary one. Personally I think of my microbiome as a river full of fish, bugs, plants, snakes. The idea of a meandering river lends itself to the imagination of my microbiome but other schemes could work too. Maybe a factory, a forest or even Pokemon characters.

The most important thing to get out of this visual exercise is that you have a living ecosystem in your gut. I think this will help people think of their microbiome as something that needs to be considered, taken care of and nurtured.

The Terrain

Next let's consider the pipe itself. This part is me. It's where my body meets the outside that runs through me. I think of this part as the banks of the river that runs through me, or a beach.

Safe Assumptions

Here are some safe assumptions I can make about my microbiome that I believe are a lot more accurate and reliable than The Great Assumption:

• Everything changes it.

• Everything changes it but some things change it temporarily.

• And some things can change it permanently.