Archaea vs. Bacteria: What’s the difference?

This article explains the key differences between archaea and bacteria, including how they’re classified and where they live in the body. It also looks at their role in gut health, especially in conditions like SIBO and IBS.

Written by the Re:Your Gut Team
12 min read, Updated March 2026

Archaea and bacteria are both microscopic organisms in the human microbiome, but they differ in structure, behavior, and how they affect gut health. This article explains those differences, why archaea matter in conditions like SIBO, and how they may influence digestive symptoms and overall balance in the gut.

Archaea vs. Bacteria: What’s the difference?

Key Takeaways

  • Archaea and bacteria are both ancient single-celled microorganisms, but they are distinct groups with different cell wall structures, evolutionary relationships, and metabolic traits.
  • In the gut, bacteria make up most of the microbiome, while archaea are a smaller group that can still play an important role in health and symptoms.
  • SIBO is often linked more to archaea than bacteria, which helps explain why antibiotics may only provide temporary relief.
  • Both archaea and bacteria can be beneficial in the right place, but when they appear where they do not belong, they may contribute to digestive issues and inflammation.
  • The article's main message is that understanding the difference between archaea and bacteria is important for better understanding gut health and SIBO.

If you’ve been following Atrantil or Dr. Brown for a while, you know that we have used the term archaebacteria often in the past. As research continues, we learn more and more about the distinction between different organisms, and as that happens, we like to keep you informed on these subtleties. So today we are going to talk about the difference between bacteria and archaea and what it means for your gut health.

A little bit about microorganisms

With the surge of microbiome research in the last few decades, you’ve probably heard that we have healthy bacteria that help our bodies to do tasks. Microbial cells outnumber the human cells in the body 10:1. So, while there are 10 trillion human cells, there are 100 trillion microbial cells!

However, while bacteria make up the majority of the gut microbiome, they aren’t the only living organisms that live there. You can also find:

  • Fungi
  • Archaea
  • Viruses
  • Protozoa

Each microorganism is slightly different, requiring a different classification. There are healthy strains of each that help our body do what it needs to do. There are also pathogenic strains that can make us sick.

This is why it can sound confusing when your doctor tells you to take probiotics when you have infections. Some strains are meant to work with the human body, while others just use the human body to proliferate, which ends up causing sickness.

On the other hand, some of these microorganisms are healthy when in the colon (where the gut microbiome is), but if they travel elsewhere in the body, they can cause problems — a great example of this is SIBO.

SIBO — small intestine bacterial overgrowth — is a condition in which there are microorganisms in the small intestine. The small intestine should be fairly sterile. When microorganisms end up there, they cause gas, bloating, abdominal pain, and irregular bowel movements.

SIBO is when we often referred to archaebacteria in the past. In reality, they are archaea causing the issues here, not bacteria. So when doctors prescribe SIBO patients with antibiotics they only get temporary relief because bacteria and archaea react differently to antibiotics.

What are archaea?

Archaea are prokaryotes that have been around since the beginning of time. They can be found in extreme environments like hot springs, salt lakes, and submarine volcanic areas. Since they can survive in places that most other microorganisms would not, they are extremely resilient.

In humans, archaea have been found in the gut, vaginal, and oral microbiomes. In these areas, they coexist and do not cause harm or complications.

Archaea only appear to make up around 1-2% of the entire gut microbiome. While this doesn’t seem like much to make a difference, more studies are uncovering their ability to support the functions of our bodies.

The major groups of archaea found within the human microbiome include:

  • Methanobacteriales
  • Methanomassiliicoccales
  • Methanomicrobiales
  • Halobacteriales

What are bacteria?

Bacteria make up the largest group of microorganisms on the planet.

Bacteria are also prokaryotes having no nucleus or organelles. Bacteria make up the largest portion of the human microbiomes. They can be found in the gut, vaginal, oral, and skin microbiomes.

The major groups of bacteria found in the human microbiomes include Firmicutes and Bacteroidetes.

Bacteria can also survive in extreme terrains, but not quite as well as archaea.

What do archaea and bacteria have in common?

Both bacteria and archaea are ancient living organisms. They’re both able to survive and adapt to the changing environment around them. Although we dub some as good and others as bad, they are just species that try to continue evolving to survive — there is no malice behind their actions, just survival.

Both archaea and bacteria are prokaryotes making them single-celled organisms. They both have cell walls and lack a nucleus and other organelles. They have very basic functions.

They both inhabit the human body among other places and often have a symbiotic relationship with the environment around them. Because of their adaptability, they can be hard to remove when they have inhabited an area. They proliferate quickly but need a sustainable environment and food to do so.

What are the differences between bacteria and archaea?

The major differences between bacteria and archaea are:

  • Cell wall composition
  • Evolutionary relationships
  • Metabolism

The bacterial cell wall contains peptidoglycan, while the archaea’s cell wall does not.

Evolutionarily speaking, archaea are closer to eukaryotes (multicellular organisms) than they are to bacteria.

Because of these findings, there is a distinct difference between the two organism,s and they should no longer be joined together as if they are the same type of microorganism.

Isolating these differences allows us to understand their intimate reactions as a microorganism and with their environments around them — specifically within the human body and their relationship to host health.

How do archaea and bacteria affect gut health?

Both are required to sustain the gut microbiome. While they are necessary for a healthy and balanced gut microbiome, they have been found to lead to complications as well.

If they escape their designated areas or are fed things that don’t create a healthy microbiome, they can cause havoc within our bodies.

If archaea or bacteria are found outside of their natural habitat of the microbiomes, they can cause an overreaction of the immune system which can lead to damage of human cells and tissues in the area. If this is an ongoing occurrence it can lead to systemic inflammation, tissue damage, and ultimately disease.

Some conditions related to this include:

  • Inflammatory bowel diseases such as ulcerative colitis (UC)
  • Small intestine bacterial overgrowth (SIBO) — archaea are often the problem in this case because they give off the gasses and can survive in the small bowel where bacteria often can’t
  • Irritable bowel syndrome (IBS)

If you are experiencing SIBO or IBS, you don’t have to worry about figuring out if you have a bacterial or archaeal problem. While there is a difference between them, we have an easy solution to get to the root cause of your symptoms.

Atrantil was found to help the body remove both bacteria and archaea and the gas they give off from the small intestine. The large polyphenols that create Atrantil are one of the few things that can disrupt the cell wall of archaea and shut down their mechanisms.

Atrantil also brings a homeostatic balance to the gut microbiome by nourishing the healthy strains of archaea and bacteria to help them fight off the pathogenic strains. So it can help you whether you experience gastrointestinal issues or not.

Grab your bottle of Atrantil here!

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    Dr. Ken Brown, MD

    Board-Certified Gastroenterologist
    Creator of Atrantil · Host, Gut Check Project

    Dr. Brown has practiced gastroenterology for over 20 years in Plano, TX. He developed Atrantil to bridge the gap between natural and medical science, and educates millions through the Gut Check Project podcast.