In a remarkable breakthrough that peels back another layer of the human microbiome’s complexity, a team of international microbiologists has uncovered two previously unknown archaeal inhabitants of the gut: a novel species named Methanobrevibacter intestini and a unique variant of Methanobrevibacter smithii dubbed GRAZ-2. Led by researchers from the Medical University of Graz (Austria), the DSMZ-German Collection of Microorganisms and Cell Cultures (Germany), and the University of Illinois (U.S.), this research marks a pivotal step in understanding an often-overlooked realm of our microbial ecosystem—the “archaeome.”
Published in the International Journal of Systematic and Evolutionary Microbiology, the study not only expands our taxonomy of human-associated microbes but also reframes our understanding of gut function, microbial metabolism, and potential disease mechanisms.
The Forgotten Domain: What Makes Archaea Unique?
Archaea are neither bacteria nor eukaryotes (organisms with nuclei like humans, plants, and fungi), but a third fundamental branch on the tree of life. While under a microscope they might resemble bacteria, their cellular machinery, genetic makeup, and membrane structures diverge profoundly.
First discovered in extreme environments—boiling hot springs, hypersaline lakes, deep-sea hydrothermal vents—archaea have a well-earned reputation as “extremophiles.” But over the past two decades, researchers have realized that these organisms also live inside us, particularly in our gastrointestinal tract, quietly performing vital roles in digestion and metabolism.
Among them, methanogens—archaea that produce methane—are of particular interest. Using simple substrates such as hydrogen and carbon dioxide, they synthesize methane through specialized pathways. In doing so, they help manage the balance of microbial gases and indirectly influence the behavior of other gut microbes.
However, archaea’s extreme sensitivity to oxygen and the challenges involved in cultivating them have long stymied research. Until now.
The Discovery: Methanobrevibacter intestini and GRAZ-2
Through a blend of pioneering anaerobic cultivation techniques, high-resolution electron microscopy, and state-of-the-art genomic sequencing, the team managed to isolate two novel methanogenic strains from the human gut.
1. Methanobrevibacter intestini (strain WWM1085
This newly identified species stands out both genetically and functionally from any known relatives. Strictly anaerobic, M. intestini thrives only in oxygen-free conditions—similar to the gut environment—and is capable of producing not just methane, but also unusually large quantities of succinic acid.
Succinic acid is no ordinary metabolic byproduct. It plays roles in the inflammatory cascade of the immune system and has been linked to a range of chronic conditions, including inflammatory bowel disease and even metabolic syndrome. That M. intestini contributes such significant amounts suggests that this archaeon could be quietly shaping inflammatory pathways in the gut.
2. GRAZ-2 – A Novel Variant of Methanobrevibacter smithii
The second discovery, GRAZ-2, is a variant of the already known Methanobrevibacter smithii—the most common archaeon in the human gut. But GRAZ-2 behaves in a distinctly different way. It produces formic acid, a volatile molecule capable of influencing the metabolic networks of nearby bacteria.
Formic acid is not just a chemical curiosity—it may disrupt microbial balance, acting either as a signaling molecule or an antimicrobial agent. This opens intriguing questions about how archaea modulate microbial competition and communication within the gut.
A New Frontier: The Human Archaeome
This research shines a bright spotlight on a realm of the human microbiome that has long been shrouded in obscurity—the archaeome. While the last two decades have seen explosive interest in gut bacteria, archaea have remained on the sidelines. But that is changing.
“Archaea have long been overlooked,” says Christine Moissl-Eichinger, Professor of Interactive Microbiome Research at the Medical University of Graz. “They may play a significant role in gut function, microbial gas metabolism and possibly even the development or progression of certain diseases.”
Unlike bacteria, archaea do not cause infections or disease in the traditional sense. Instead, they act as subtle conductors of microbial chemistry, orchestrating the flow of gases, acids, and other small molecules that underpin digestion and immunity. They may not be directly pathogenic, but their influence could be profound.
Why Now? The Challenges of Archaeal Research
Studying archaea is not for the faint of heart. They are notoriously fastidious, often refusing to grow outside their strict anaerobic niches. Their slow growth rates, sensitivity to temperature and oxygen, and unusual nutrient requirements make them a nightmare for traditional microbiology labs.
But the team at Graz and its international collaborators overcame these hurdles using advanced anaerobic chambers, specialized culture media, and prolonged incubation protocols. The strains were then studied using transmission electron microscopy—offering a rare look at their cell morphology—and whole-genome sequencing, which confirmed their novelty.
“This discovery was only possible thanks to a combination of modern tools and classical microbiological methods,” says Viktoria Weinberger, the study’s lead author. “We can only conduct specific mechanistic investigations with cultivated strains. That’s the only way to understand their role in health and disease.”
Health Implications: From Gas to Disease?
The implications of this work go beyond taxonomy or microbiological curiosity. Archaea may influence everything from digestion and immune modulation to metabolic health and chronic inflammation.
Succinic acid, for instance, is already known to act as a signaling molecule in immune cells. Elevated levels have been observed in conditions such as Crohn’s disease, asthma, and obesity. Could M. intestini be a silent contributor? Or perhaps a missing piece of the puzzle?
Formic acid, produced by GRAZ-2, may also play a regulatory role in microbial ecosystems. It’s known to inhibit certain bacterial species while enhancing the growth of others. If archaea like GRAZ-2 subtly engineer the microbial network through acid production, they could indirectly affect everything from nutrient absorption to mood—via the gut-brain axis.
This hints at a paradigm shift: archaea may not be passengers in the microbial universe, but architects of ecosystem dynamics within the human body.
Toward Microbiome Medicine: The Road Ahead
The discovery of Methanobrevibacter intestini and GRAZ-2 opens exciting doors to personalized medicine. As our understanding of the microbiome grows deeper, the potential to manipulate it to treat disease becomes more tangible.
Could we someday transplant beneficial archaea as part of targeted microbiome therapies? Could archaeal markers help us diagnose inflammatory or metabolic disorders before symptoms even arise? These questions were unthinkable a decade ago—but are now within scientific reach.
Moreover, with synthetic biology, it may even be possible to engineer archaeal strains with enhanced or novel capabilities—creating “designer microbiomes” tailored to individual needs.
Yet, as with all scientific advances, caution is key. The archaeome is still in its infancy as a field, and its dynamics within the gut remain largely uncharted. We are only beginning to map this microbial dark matter.
Conclusion: A New Chapter in Human-Microbe Symbiosis
The identification of Methanobrevibacter intestini and the GRAZ-2 strain is more than a discovery—it’s a revelation. It reminds us that the human body is not merely a host to bacteria but a superorganism shaped by a vast, unseen consortium of life, including the mysterious archaea.
As researchers continue to decode the hidden languages of the microbiome, the once-forgotten archaea are stepping into the light—not as relics of ancient Earth, but as key players in modern human health.
The gut, it seems, has kept some of its deepest secrets locked away in the genomes of archaea. But with each discovery, we move closer to understanding how life truly thrives—on and within us.
The age of the archaeome has begun. And with it, the promise of deeper insight into the most fundamental processes of life.
Reference: Viktoria Weinberger et al, Expanding the cultivable human archaeome: Methanobrevibacter intestini sp. nov. and strain Methanobrevibacter smithii ‘GRAZ-2’ from human faeces, International Journal of Systematic and Evolutionary Microbiology (2025). DOI: 10.1099/ijsem.0.006751