The Forgotten Microbes: Exploring the Role of Archaea in the Human Body.

For decades, medical research has focused on the bacterial and eukaryotic culprits behind human disease—over 1,500 bacterial species and hundreds of fungi, protists, and helminths are known offenders. Yet one domain of life remains conspicuously underrepresented in medical literature: archaea. First distinguished as a separate domain in 1977, archaea were initially misidentified as bacteria due to their similar appearance. But researchers like Magdalena Kowalewicz-Kulbat, a microbiologist at the University of Lodz, emphasize that archaea are fundamentally different from bacteria. "We now have growing evidence that the domain archaea belong to is entirely distinct," she explained.

Traditionally associated with extreme habitats—boiling geysers, salt flats, and hydrothermal vents—archaea are also present in more familiar environments such as oceans, soils, and the microbiomes of animals, including humans. Although no known pathogenic archaeon has been identified to date, this absence may reflect the limited scope of current research rather than a true lack of disease-causing potential.

One of the primary reasons archaea have been overlooked is methodological. Microbiology has long relied on tools optimized for bacteria, introducing a sampling bias. When scientists culture microbes from human samples like stool, they often use media that favors bacterial growth, potentially excluding archaea. Furthermore, many archaea reproduce slowly or require oxygen-free environments, demanding specialized anaerobic chambers for cultivation. “Some archaeal species take weeks to grow—or even longer,” noted Kowalewicz-Kulbat.

The challenge extends to DNA sequencing. Most commercial DNA extraction kits use lysozyme, an enzyme that targets bacterial cell walls but is ineffective against the pseudopeptidoglycan found in many archaeal species. Even when alternative enzymes succeed in extracting archaeal DNA, their lower abundance relative to bacteria means archaeal sequences often go unnoticed in metagenomic analyses. Additionally, the scientific community has only collected a limited number of reference genomes for archaea, reducing the likelihood of matching sequences during analysis.

Despite these hurdles, researchers have identified archaea across multiple human body sites—the mouth, skin, lungs, and especially the gut. Among the most studied are methanogens, archaea that produce methane and are present in roughly half of all humans. According to Guillaume Borrel of the Pasteur Institute, their presence can even be detected via breath tests. “Typically, if there are more than a million methanogens in the gut, they produce enough methane to be measured in the breath,” he said.

In addition to methanogens, scientists have recently discovered halophilic—or salt-loving—archaea in the gut, a surprising find given their usual preference for high-salt environments. “It was unexpected that gut-dwelling halophilic archaea could thrive under such conditions,” said Kowalewicz-Kulbat.

Still, the diversity of archaea in the human microbiome is limited. Borrel noted that researchers have documented about 30 gut methanogen species—far fewer than the over 1,000 bacterial species found in the intestines. Archaea also account for a much smaller share of the microbiome, comprising just 0.1 to 1 percent in the gut and around 1 percent on the skin, where they may influence skin acidity and dryness.

Interestingly, archaea may contribute positively to human health. Kowalewicz-Kulbat's team recently isolated a new species of halophilic archaea—Halorhabdus rudnickae—from a Polish salt mine. Given that people bathe in nearby salt lakes, she speculated the organism could enter the human body and interact with the immune system. In lab experiments, her team showed that both H. rudnickae and a related species, Natrinema salaciae, could activate human immune cells, especially triggering anti-inflammatory pathways. This suggests a potential therapeutic role for halophilic archaea in modulating immune responses.

Methanogens might also offer benefits. Some can metabolize trimethylamine, a compound linked to heart disease when it converts to trimethylamine oxide in the body. By breaking it down into methane, these archaea may help prevent cardiovascular issues—a finding compelling enough for Borrel to file a patent for their use as dietary supplements.

Yet the possibility of harmful archaea hasn’t been ruled out. For instance, Methanobrevibacter smithii has been identified in the vaginal microbiomes of women with vaginosis, while Methanobrevibacter oralis has appeared in periodontal disease lesions but not in healthy tissue. Other studies have connected archaea to brain abscesses, inflammatory bowel disease, and pneumonia. While not proven to be direct pathogens, these microbes could support disease by fostering harmful bacterial growth.

Ultimately, archaea remain a largely uncharted component of the human microbiome. As research tools evolve, scientists may uncover new insights into whether these ancient organisms are benign passengers, health allies—or silent accomplices in disease.

Source:https://www.the-scientist.com/archaea-inhabit-our-microbiome-but-what-are-they-doing-there-72935

This is non-financial/medical advice and made using AI so could be wrong.