SIBO and the loss of natural microbes

Bacillus subtilis and the underestimated role of microbial diversity: What Dr. William Davis explains about SIBO and lost microbes 

Introduction

Dr. William Davis has been grappling with a crucial question for many years:
Why does the human microbiome appear more unstable today than in previous generations?

One of his central theses is that our modern lifestyle has led to the near disappearance of certain microorganisms – formerly an everyday part of our environment. One of these microorganisms is Bacillus subtilis , a naturally occurring environmental bacterium that may have been part of the human diet for many millennia.

This blog post summarizes the main ideas of Dr. Davis and places them in an objective context.

The invisible gap: Microbes that were once ubiquitous

For most of human history, humans ingested microorganisms from their environment on a daily basis:

• from earth
• of plant surfaces
• from untreated foods
• from natural water

With industrialization, packaging technology and modern hygiene standards, this changed fundamentally:

• Food is thoroughly washed.
• Surfaces are sterilized
• Products are heat-treated
• Natural germs are largely removed.

Dr. Davis points out that this has led to the loss of microorganisms that, from an evolutionary perspective , have always been part of the human balance . Bacillus subtilis is one of those microbes that were regularly ingested in the past but are now rarely found.

SIBO as an expression of modern microbial changes

A key point in Dr. Davis's analysis concerns SIBO , small intestinal bacterial overgrowth. This condition involves the presence of microorganisms in the small intestine at concentrations that are not normally found there.

His change of perspective is important:

• SIBO is not just an overabundance of certain bacteria.
• SIBO can also be caused by a deficiency of other microorganisms that previously maintained balance.

In other words:
The small intestine can be both overfilled and undersupplied at the same time.

This idea explains why modern microbial changes are often more complex than they initially appear.

Why Bacillus subtilis plays a special role for Dr. Davis

Bacillus subtilis is a naturally occurring environmental microorganism found in soil, plants, and natural surfaces. It used to regularly enter the human body through this means.

Dr. Davis highlights several qualities:

1. Spore formation

Bacillus subtilis forms stable spores that:

• Surviving the heat
• Tolerating drought
• stomach acid survive

This allows these spores to reach areas of the digestive system that are inaccessible to other microorganisms.

2. Activation in the small intestine

There are observations that Bacillus subtilis can germinate from spores in the small intestine.
For Davis, this makes the organism particularly interesting in the context of small intestine processes.

3. Production of bacteriocins

Bacteriocins are peptides that microorganisms use to regulate their environment .
Davis sees this as a possible example of natural microbial control.

4. Biofilm formation

The ability to form structured biofilms suggests that Bacillus subtilis may be part of microbial networks that were more common in the human body in the past.

Bacillus subtilis as a model for microbial balance

Dr. Davis does not use Bacillus subtilis as a therapeutic recommendation.
but as a model to make something fundamental visible:

• Microbes that were once commonplace are now missing.
• The microbiome of modern humans has not only become "different", but often also poorer .
• These changes could explain why imbalances like SIBO are occurring more frequently.

Bacillus subtilis refers to microorganisms that have been part of the environment for many generations – and whose absence raises new questions today.

The key finding: Microbial diversity used to be taken for granted

Dr. Davis emphasizes that it is not the human body that has drastically changed,
but the microbial environment in which we live:

• In the past, people ingested microbes from nature on a daily basis.
• Today we predominantly consume sterile products.

In this context, Davis views Bacillus subtilis as an example of lost diversity – not as a solution, but as an indication of how closely humans were once connected to environmental microbes.

Conclusion

Dr. William Davis's considerations demonstrate how strongly modern lifestyles and diets can influence the microbiome. He uses Bacillus subtilis as a vivid model for microbes that were once a natural part of the environment and that may have played a role in the microbial balance – particularly in the small intestine.

Dr. Davis interprets SIBO not only as an overgrowth of certain microbes, but also as a possible consequence of a decline in natural microbial diversity. The question of which microorganisms we are currently lacking is therefore a central component of understanding modern microbiome research.

Author Andreas Kraus
Owner and Managing Director Professional Lead