Inventory of archaea in the human intestine

Kiel University professor Ruth Schmitz-Street, along with her international colleagues, have now described a hitherto insufficiently described human gut ‘footprint’. Credit: Keele University

All multicellular organisms contain an unimaginably large number of microorganisms in and on their bodies. The microbiome, that is, the sum of these microbes, forms a symbiotic functional unit with the host organism. From supporting the absorption of nutrients to protecting against pathogens, microorganisms perform vital tasks of the host. Conversely, disturbances of the microbiome can cause various serious diseases, including inflammatory bowel disease.

In recent years, scientists have made a large number of studies of the microbiome. In it, they studied the links between the composition and function of the body’s microbiome and disease progression. Most of this work has focused primarily on bacteria, whose different types dominate the microbiome in number. One particular group of microorganisms has not yet received much attention: the archaea. Although they make an average of “only” 1.2 percent of the total gut microbiome, archaea have broad regulatory effects on the microbiome, as shown in previous studies.

An international research team with the participation of the University of Kiel, the Medical University of Graz, Austria, and other international partner institutions from the United Kingdom and France, provided a characterization of the human intestine that has not yet been adequately characterized on the basis of comprehensive genome data from large sets of different global sites. With this inventory, researchers led by Professor Ruth Schmitz-Street of Microbiology at Kiel University and her colleague from Graz, Professor Christine Moisel Ischinger, want to expand knowledge about this type of microorganism. In the process, they were able to identify the hitherto unknown primitive species. The scientists recently published the results of their research in the scientific journal Nature Microbiology.

Much more diverse than previously known

The new analysis provides the first comprehensive description of the human impacts. The research team used data sources from several existing microbiome studies, each of which includes the complete genetic information of individual intestinal microbial colonization of the test subjects. “First of all, we were able to show that the human footprint is much more diverse than previously known and that it has a basic composition of roughly the same species in most people regardless of external factors such as geography, gender or age,” confirms Dr. Schmitz-Street Working Group. “In addition to the many newly discovered species, we were also able to identify previously unknown types of viruses that can infect archaea,” Shaibani continues.

In addition to just grouping the species, the research team also looked for links with patterns already known in the genetic information of the archaea. To do so, they examined more than 28,000 purported protein clusters, which point to important associations between primitive colonization in the gut and sociodemographic characteristics of the human host. “The occurrence of certain species and the proteins they produce can be used to draw conclusions about age groups or lifestyles, for example,” explains Shaibani, who performed bioinformatic analyzes with co-first author Dr. Alexander Mahnert. “At present, however, such meaningful associations cannot be reliably read regarding disease patterns associated with potential effects,” Shaibani continues.

Another important discovery was the division of the previously known species Methanobrevibacter smithii into two groups at the species level based on genetic information. M. smithii and its new “sister” Methanobrevibacter intestini are highly prevalent in many people. The interaction between these two closely related species and of importance to human health still needs to be resolved.

To date, the association of these methane-forming archaea with diseases, such as colon cancer or inflammatory bowel disease, has not been resolved, possibly due to the inaccuracy of species resolution to date. Certainly, these methanogens are able to support the activity of pathogenic bacteria, for example by consuming inhibitory metabolic products. The research now published expands the understanding of human effects and provides a comprehensive genome and proteomic index for future analyses.

The first steps of an archaeological job description

In general, science is still only initially in determining the full diversity of archaea. “The archaea’s catalog of 1.8 million proteins can be used in the future as a unique source for developing new research questions,” stresses Schmitz-Street, who is particularly active with colleagues in Graz, in developing primitive research. “These future approaches include, for example, studying the physiology and metabolism of newly identified archaea or the nature of their communication with the human host,” continues Schmitz-Street. In order to be able to study the functional aspects of archaea in the future, it is necessary to develop new analytical methods, as they are currently designed primarily for bacterial species, as well as for the targeted cultivation of archaea from the human intestine. “Overall, our work contributes significantly to understanding the human microbiome as a complex, multi-layered network of bacteria, archaea, fungi, and viruses,” Moissl-Eichinger summarizes. On this basis, the researchers hope to decipher the effects of archaea on human physiology and possibly their involvement in disease development step-by-step in future in-depth work.

Scientists investigate the role of archaea in the human microbiome

more information:
Cynthia Maria Chibani et al, A catalog of 1,167 genomes from the human gut trace, Nature Microbiology (2021). DOI: 10.1038 / s41564-021-01020-9

Provided by Keele University

the quote: Inventory of Archaea in the Human Intestine (2022, Jan 11) Retrieved Jan 12, 2022 from

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