New Microbe Discovered in the Human Gut

Archaea Could Play a Previously Underestimated Role in the Microbiome

A new roommate:

Scientists have discovered a previously unknown microbe in our gut. It's not a bacterium, but a species of archaea. The species, dubbed Methanobrevibacter intestini, produces the gas methane – similar to a newly discovered variant of the archaea species Methanobrevibacter smithii. These findings suggest that our intestinal flora is significantly more influenced by archaea than previously thought.

With the previously unknown archaea species Methanobrevibacter intestini, biologists have identified another inhabitant of the human intestine. © Weinberger et al./ Evolutionary Microbiology /CC-by 4.0

Trillions of microbial roommates live in our digestive tract – more than we have cells in our bodies. However, the microbiome of bacteria, viruses, fungi, and archaea, which varies from person to person, is by no means a passive inhabitant; rather, it influences numerous areas of our lives, including our appetite, our food preferences, and even our mood.

New addition to the intestinal archaea community

Researchers led by Viktoria Weinberger from the Medical University of Graz have now discovered another tiny inhabitant of our intestines. It is a previously unknown methane-producing archaea species. The new species, dubbed "Methanobrevibacter intestini," was detected in the stool sample of an American, as the team reports.

Archaea, along with bacteria and eukaryotes, form one of the three domains of life. Although these single-celled organisms look similar to bacteria under the microscope, they differ from them in many fundamental characteristics, such as the structure of their cell membranes and their metabolic pathways. Archaea were first discovered in extreme habitats such as hot springs and salt lakes, but it is now clear that these tiny creatures also feel at home in the human body, especially the intestines.

Scanning electron micrograph of Methanobrevibacter smithii DSM 861 (=PST), Methanobrevibacter smithii DSM 2375 (=ALI), Methanobrevibacter smithii GRAZ-2 and WWM1085. Souce:Expanding the cultivable human archaeome: Methanobrevibacter intestini sp. nov. and strain Methanobrevibacter smithii ‘GRAZ-2’ from human faeces / Published: 16 April 2025 / International Jurnal of Systematic And Evolutionary Microbiology)

An enigmatic piece of the puzzle

"Archaea were overlooked for a long time," explains senior author Christine Moissl-Eichinger. "They could play crucial roles in intestinal function, microbial gas balance, and possibly even in the development or progression of certain diseases." The discovery of Methanobrevibacter intestini thus provides another piece of the puzzle for the functional understanding of the human microbiome.

However, it is still unclear what role this microbe, which is up to 0.54 micrometers long and 0.43 micrometers wide, plays in our intestines. All that is known is that Methanobrevibacter intestini usually occurs in pairs or short chains and thrives at temperatures between 35 and 39 degrees Celsius and a pH of 5.5 to 7.5.

In addition, the newly discovered archaea species produces methane from hydrogen and carbon dioxide, as well as surprisingly large amounts of succinate, the team reports. This metabolite, also known as succinic acid, is associated with, among other things, inflammatory processes in the human body.

Scanning electron micrograph of GRAZ-2 © Weinberger et al./ Evolutionary Microbiology /CC-by 4.0

Another strain discovered

In addition to Methanobrevibacter intestini, Weinberger and her colleagues also discovered a new strain of the already known intestinal archaea species Methanobrevibacter smithii, which they named "GRAZ-2." It was found in the stool sample of a 42-year-old, healthy European woman. Additional studies revealed that GRAZ-2 produces formate, or formic acid, and thus potentially interferes with the energy metabolism of other intestinal inhabitants. However, the effects of this archaea strain on us as hosts are still unknown.

(Evolutionary Microbiology, 2025; doi: 10.1099/ijsem.0.006751)

Source: Medical University of Graz