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Microbiome research: Introducing the archaeome

The microorganisms living in our gastrointestinal tracts are collectively called the gut microbiome, and they have a complex relationship with the human body.

They take energy from our food, break down certain compounds, and release important metabolites, a product of the body’s metabolism.

A change in the healthy balance of these organisms is associated with a range of health problems. These include metabolic disordersTrusted Source, inflammatory and auto-immune diseasesTrusted Source, neurological conditionsTrusted Source, and cancerTrusted Source, among others.

The human microbiome consists of bacteria, archaea, fungi, and viruses. The vast majority of research into the microbiome deals with bacteria.

More recently, the number of studies targeting fungi and viruses in the human microbiome has increased, but relatively little is known about the populations of archaea — collectively called the “archaeome.”

A group of scientists recently analyzed a large dataset of human gut microbiome samples and profiled the archaea that were present. The team’s intriguing findings appear in the journal Nature MicrobiologyTrusted Source.

The results provide more information about our resident archaea and will help researchers discover more about their impact on human health.

Lead authors Dr. Cynthia Maria Chibani, at the University of Kiel, in Germany, and Dr. Alexander Manhert, at the Medical University of Graz, in Austria, spoke with Medical News Today.

They said they were surprised to find so many types of archaea that were new to science — three genera, 15 species, and 52 strains.

“Archaea were usually neglected and understudied because a large number of archaeal species require specialized methods for cell lysis and DNA extraction, and other methodological pitfalls,” they explained.

What are archaea?

Archaea are single-celled organisms that are similar to bacteria, though they have different characteristics.

They can be spherical, rod-shaped, spiral, or rectangular. Beyond the human body, archaea live in extreme habitats. They can survive in very high and low temperatures, as well as in high-pressure, very salty, and very acidic environments.

Although archaea only account for about 1.2% of the entire gut microbiome, scientists believe that they may have considerable regulatory effects in the body.

Discovering new species

The researchers, who are also based at institutions in the United Kingdom and France, gathered data from publicly available genomes.

Their data included samples from people in 24 countries, with a range of demographic characteristics. They included other recent collections of microbiome genomes, as well, from the Unified Human Gastrointestinal Genome collection, National Center for Biotechnology Information, Pathosystems Resource Integration Center, and Integrated Microbial Genomes and Microbiomes.

The results of the analysis showed that the observed percentage of archaea present in the microbiomes was around 1.2%, which corresponds with previous research.

The team determined that most people seem to host populations of archaea that are similar. The species present seem to depend on external factors, such as geography, sex, age, and health status.

The researchers found 1,167 archaeal genomes. These included members of the orders Methanobacteriales (87.15%), Methanomassiliicoccales (12.43%), Methanomicrobiales (0.26%), and Halobacteriales (0.17%).

In their paper, they also suggest that a previously identified species — Methanobrevibacter smithii — should be reclassified as two branches, with one represented by the previously undescribed Candidatus Methanobrevibacter intestini.

Interestingly, the analysis also uncovered 94 viruses that infect archaea.

Ákos Kovács, a professor of bacterial physiology and genetics at the Technical University of Denmark, told MNT:

“This is a fascinating study that extends our knowledge on microbes in the human gut outside of the mostly studied eubacterial kingdom. While archaea are less studied, these microbes have a nonetheless crucial role in the world’s ecosystem, as well as in human health.”

Noting limitations

The researchers explain that because the data is based on samples that were processed to analyze the bacterial component of the microbiome, many archaeal species might have been missing from their analysis. These species may require specialized methods of extraction.

They add that an analysis of stool samples might not represent the complete diversity of species present in the intestines. This is because, for instance, some archaea form biofilms that stick to tissues and may not be present in stool samples.

Next step s

The team hopes that its catalogue might serve as a unique source for future research.

Going forward, scientists might, for example, compare wild archaea with those in humans and animals. They may also investigate how archaea interact with the bacteriome and virome, as well as how the archaeome interacts with its human host.

Dr. Chibani and Dr. Manhert explained to MNT:

“We need more dedicated studies in the human archaeome field. This study was the result of looking into standard bacterial-focused studies. Hence, it will be critical to address the peculiarities of archaea.”

They said that future work should focus on “populations with a traditional lifestyle and a non-Westernized diet” because these groups “often harbor a higher diversity of methanogens in their guts.” Methanogens produce methane and increase the efficiency of digestion.

“We are just beginning to understand the actual biology of archaea in the gastrointestinal tract — how they colonize the gut [and] how they interact with bacteria, viruses, and other members of the microbiome, as well as the human host, its cells, and the gut-brain axis. So we have a lot of new territory to explore.”

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