New archaea discovered in the human intestine

Methanobrevibacter intestini expands the known gut microbiome

The human gut microbiome is a fascinating ecosystem – with trillions of microorganisms that have a significant influence on our health. When we think of gut flora, we always think of bacteria, and rarely of yeasts such as Candida sp. But one part of this microcosm has been largely overlooked until now: the archaea. A new study by Weinberger et al. (2025) now brings light into the darkness. It describes for the first time the cultivation and precise characterization of a new archaea species from the human intestine: Methanobrevibacter intestini.

What are archaea – and what are they doing in the gut?

Archaea are unicellular microorganisms that do not belong to bacteria, but form their own domain. However, they are very similar to bacteria and were therefore often referred to as archaebacteria or primordial bacteria. They are extremely adaptable – originally known from hot springs, salt lakes or the deep sea. But they are also at home in our large intestine.

In the human gut, they primarily play a role in methane production. They use hydrogen (H₂) and carbon dioxide (CO₂), which are produced during the bacterial breakdown of e.g. dietary fiber, and produce methane (CH₄) from them. The most important species to date is Methanobrevibacter smithii – it can be detected in almost all people and influences the composition of the intestinal microbiome, gas formation and possibly also bowel habits.

The new player in the intestine: Methanobrevibacter intestine

In the current ^study1, two archaea strains were isolated from human stool samples. One of them was described as a completely new species: Methanobrevibacter intestini. The name literally means “methane producer from the intestine”.

What does this mean for our understanding of the gut microbiome?

The finding that M. intestini differs genetically and functionally from M. smithii has far-reaching implications:

1. Expanding microbial diversity in the gut: Archaea are an integral part of our microbiome, not just “fellow travelers”.
2. Current methods for analyzing the microbiome – especially those that only target the 16S rRNA gene – cannot reliably differentiate between M. intestini and M. smithii. This means that, as with many bacteria, the microbiome analyses often sold for home use cannot provide accurate and diagnostically useful information.
3. Potential links to health and disease: The study shows differences in metabolism, e.g. in formate formation, which could have an influence on flatulence, bowel movements or methane formation in the air we breathe. However, archaea are not known to cause disease, so there is no need to be afraid of them.
4. Our microbiome consists of more than just bacteria. It is an extremely complex system made up of all kinds of creatures whose benefits, significance, damage and interactions we still barely understand. So please be careful with “consultants” who explain to you exactly how it works in the gut… because we don’t really know that yet.

And the second find? Methanobrevibacter smithii “GRAZ-2”

In addition to the new species, another strain of M. smithii was also isolated – from a stool sample in Graz. This strain, called “GRAZ-2”, shows small differences to known isolates, but is not a new species, but a variant of M. smithii.

The “human archaeome” is an underestimated part of the gut microbiome

With the discovery and description of Methanobrevibacter intestini, the study provides an important building block for understanding the human archaeome – i.e. the archaea in the human gut. Such findings are central to future personalized medical microbiome diagnostics, the development of microbiome-based therapies and the targeted modulation of the gut microbiome in functional gastrointestinal diseases. But there is still a long way to go.

Source

1. Weinberger, V. et al. Expanding the cultivable human archaeome: Methanobrevibacter intestini sp. nov. and strain Methanobrevibacter smithii ‘GRAZ-2’ from human faeces . Int. J. Syst. Evol. Microbiol. 75, (2025).