Gut Health

Why fiber is not needed, the Gut Microbiome and Alpha Diversity

Gut bacteria produce butyrate, a short-chain fatty acid that supports digestive health, helps control inflammation and can prevent leaky gut

The gut microbiome is basically the bacteria in the gut.

The gut lining is made up of epithelial cells. Some foods may be deleterious to the lining. 

Hot peppers, capsicum spices, nightshades and other lectin-containing foods may cause zonulin release causing the gut lining to be fenestrated and open. But what do we need to maintain a good gut lining? Firstly you will require the availability of substrates that are associated with good mitochondrial health. This includes all the B vitamins, coQ10 and especially vitamin B6.

It is advisable to not include vegetables or any high fiber food but if you HAVE to include vegetables they're tolerated better well cooked.

Other Factors

High insulin leads to water retention which in turn results in dysregulation of sodium and uric acid levels.

This high water retention will mean endothelial cells will 'bulge' and decrease the internal circumference of the arteries. This has a deleterious impact on the gut lining.

Definition of a healthy microbiome.

There is no one healthy microbiome. If you're healthy then the microbiome you have is probably a good one!

Why is fiber is promoted as healthy when studies and experience seem to prove otherwise?

Some basics

Butyrate is a short chain fatty acid which the cells in your colon need for energy. It was once thought that you can only produce butyrate from fiber but studies have shown you can make isobutyrate from protein and then bacteria convert it to butyrate. You can also get it from fat and even from bile. So a ketogenic diet with no fiber provides plenty of substrates to run the colon.

A bit more science for those that like it.

Remember you need butyrate producing bacteria in your gut because butyrate is the preferred fuel for the cells that line your gut. 

It was once thought of as the only fuel for gut epithelial cells. But in vitro research has shown this to not be true.

Although it is true that butyrate can be produced from the fermentation of dietary fiber and that it can enter the gut’s epithelial cells and be oxidized in the mitochondria. This is not the optimal nutrient source, due to other factors that cause problems downstream.

A better option is the use of protein fermentation, where you are able to get iso butyrate which has the same signaling function and can be used in epithelial cells, with no sub-optimal downstream effects.

There is also evidence that ketones can enter from the basal lateral side (from the side facing the bloodstream)

This is why fiber was once thought of as the only source able to supply short chain fatty acids but this we now know is not true.

This system happens in the colon mostly. (The small intestine uses mostly glutamine but can use ketones.)

So it is now known that you can use beta hydroxybutyrate, acetoacetate and even long chain fatty acids to fuel the cells of the colon.

So there is no need to get short chain fatty acids exclusively from fiber.

It is all down to substrates that are available. The study referenced below demonstrated that if you blocked short chain fatty acids then long chains will be utilized. Reintroducing both shows short chains are preferred.

Even bile contains some medium and long chain fatty acids (in the form of acyl carnitines) 


The acyl carnitines can be used by epithelial cells in the colon and they increase in circulation during fasting and can be taken from the blood side (the lumen is the interior of the colon and it was once thought energy could only be derived from the lumen side)

"Both long- and short-chain fatty acids are oxidized in the colon, where there is an inverse relationship between the two regulated by the abundance of the SCFA butyrate"

The worst diet combination seems to be low fiber and high sugar but it's not the low fiber as often postulated but it's the high sugar and high seed oil consumption.

A Ketogenic diet which is low sugar, moderate protein and fat can see improvements in gut health with zero fiber. The only clinical study in humans showed the best health outcomes were for those patients on zero fiber.

Gut function more widely

Bilophila is a bacteria that in a carnivore diet increases. It's been shown to degrade TMA (TMA converts to TMAO) to DMA so conversion to TMAO in high levels does not happen.

"Cardiovascular disease (CVD) has been linked to animal-based diets, which are a major source of trimethylamine (TMA), a precursor of the proatherogenic compound trimethylamine-N-oxide (TMAO). Human gut bacteria in the genus Bilophila have genomic signatures for genetic code expansion that could enable them to metabolize both TMA and its precursors without production of TMAO. We uncovered evidence that the Bilophila demethylation pathway is actively transcribed in gut microbiomes and that animal-based diets cause Bilophila to rapidly increase in abundance"

It's important to understand the microbial function rather than its species in many cases to understand what is going on.

It's still in its infancy but understanding gut function has led to some research associating certain conditions with specific gut function issues. For instance some diseases seemed linked to a reduction in bacteria that produce butyrate. In essence the characteristics of the gut function. 

There is also an expansion on enterobacter aca. The caveat here is these studies are from people eating a standard western diet as opposed to studies on hunter gatherers like the Hadza. 

Gut microbiome of the Hadza hunter-gatherers

In animal models using antibiotics or inducing inflammation will see a rise in enterobacter aca. Ones you've probably heard of are e-coli Klebsiella and salmonella but there are many other pathogens.

The butyrate producer, especially in carnivores, is corprocascus (very bile tolerant) amongst others.

A lot of the gut microbes are unknown

When you do metagenomic sequencing (also called shotgun sequencing) is where researchers take a gut DNA sample, grind it all up and sequence it. Then compare it to a database of known microbes. Between 50% upto 70% of the results are unknown. A so-called 'dark matter' in the gut that some researchers believe may even be viruses.

16s sequencing is much less nuanced 

Essentially this is taking poop and studying it. So you'll get everything, viruses, fungi, microbes, bacteria etc.

Using a Ketogenic diet or supplementing with ketone esters led to great beta hydroxybutyrate in the gut lumen and the colon tissues.

It played a potential protective role in th17 cells which are often implicated in autoimmune disorders.

More importantly it maintained the gut mucus layer despite the lack of fermentable carbohydrates.

Alpha diversity

Is the name given to how diverse the gut microbes are. Having higher diversity is thought to indicate better health but eating a diverse range of foods does not necessarily lead to better alpha diversity. In studies even diets of meat, organs and honey can lead to a near 100% top rating in alpha diversity.

What does increase alpha diversity?

This study shows urban Italians on a Paleolithic diet had gut diversity similar to three non-western populations, including the Hadza, whereas the Italian people on a 'mediterranean'  diet did not have anywhere near the diversity.

This is a cross sectional study and keep in mind those choosing a Paleolithic diet might exhibit healthy user bias. Meaning that someone deliberately choosing to eat healthier will also improve other areas of their life to achieve their goals, so you can't 100% attribute improvements to diet alone. All participants were considered 'healthy' with daily contact with nature. The Paleolithic group did not eat bread, grains or processed foods. 

Even sunlight exposure increases alpha and beta diversity

Skin Exposure to Narrow Band Ultraviolet (UVB) Light Modulates the Human Intestinal Microbiome

Gut microbiome response to a modern Paleolithic diet in a Western lifestyle context

In an interventional study increasing fiber intake from 20% to 40% of calories saw no change in microbial status.

Interestingly eating fermentable foods did see a slight change in microbiome species. So drinking pickle juice may be beneficial for some people. Remember those in the study were eating a standard western diet. Fermentation can increase histamines so proceed with caution.

In the study yoghurt seemed beneficial in those that can tolerate whey and casein. Others seemed to be tolerating fermented vegetables in brine. Only those with good alpha diversity did well though. For others autoimmune issues increased, which reflects real world data where patients increase these food items but feel worse. 


Gut Microbiota-Targeted Diets Modulate Human Immune Status

Ketogenic Diets Alter the Gut Microbiome Resulting in Decreased Intestinal Th17 Cells