Archaeome: Emerging Player In Health And Disease

Archaea are the dark matter of the microbiome. Despite thriving in our guts, skin and respiratory tracts, these microbes are among the least understood organisms in and on the human body. The reasons why are largely methodological-analytical tools used to study the microbiome aren’t great at capturing these not-quite-bacterial, not-quite-eukaryotic microbes. But technology is improving, and with it, associations between the archaeome and human health and disease are coming into focus.

Getting to Know Archaea

According to Christine Moissl-Eichinger, Ph.D., a professor for interactive microbiome research at the Medical University of Graz who studies archaea, if there’s 1 thing to remember about the microbes, it is this: “They are not bacteria-they have different molecular structures, [physiological] setups and evolutionary backgrounds.”

Once upon a time, however, scientists did think archaea were bacteria. This initial misclassification was understandable. Many archaea look like bacteria and similarly lack a nucleus and organelles. But they don’t have lipopolysaccharide (LPS) or peptidoglycan-2 very bacterial characteristics-and, based on genetic data, are evolutionary distinct from the microbes.

Genetically speaking, archaea are more closely related to eukaryotes. Some archaeal qualities, such as their membrane composition and methods for processing genetic information, align with their eukaryotic brethren. But then there are ways archaea are not like eukaryotes at all. The microbes are ultimately a mishmash of bacterial and eukaryotic physiologies with a few distinguishing traits (e.g., a unique flagellum) tossed into the mix.

They are also epic-archaea are largely known for their ability to survive extreme environments, from salt lakes to volcanic landscapes. Moissl-Eichinger highlighted that these hard-core microbes play important roles in biochemical cycling and climate change. There are species, though, that settle down in habitats with less overt hostility. The human body is one of those places.

The Under-Studied ‘Ome

Of all the microbes that call humans home, archaea have gotten the least attention. Analyses have largely centered on the big, easier-to-study bacterial fraction of the community. However, the collection of archaea associated with the body (the archaeome) is not to be overlooked. These organisms are all over the body-on the skin, in the urogenital and respiratory tracts and, most abundantly, in the gut, where they make up roughly 1.2% of the microbiota. Most research so far has focused on the latter community.

Scientists are beginning to understand the breadth of archaeal diversity encompassed by the human gut archaeome, learning that the presence and abundance of certain species is linked to where someone lives, their ethnicity, diet and age. Most gut archaea are methanogens-species that metabolize various compounds (H2, CO2) and belch out methane, which is released in breath and flatus. Measuring levels of methane in someone’s breath can give a rough estimate of methanogen abundance/methanogenic activity in their gut.

For Moissl-Eichinger, this coincides with an interesting observation. “One of the intriguing points is that there are actually 2 different [types] of individuals that exist with respect to archaea,” she said. “[Some people] in the population exhale substantial amounts of methane, and they have a [unique] setup up of the entire microbiome. On the other side are people who have 1000-fold less methanogens in their gut, and they have different metabolites and microbiome composition.”

Indeed, methanogens are active participants in the gut microbial community. For example, bacterial metabolism produces H2, a key archaeal growth substrate. By consuming the gas, methanogens, in turn, influence the growth and metabolic end products of their bacterial “partners” which contributes to host phenotype and processes (e.g., body weight and immune system function).

While bacterial-archaeal hydrogen transfer is an oft-cited interaction, it is certainly not the only one. “This is just a glimpse of how things work,” Moissl-Eichinger said, emphasizing that most of the ways archaea interact with other microbes, and even each other, have yet to be deciphered. “I think there is a huge network of communication. We assume this for bacteria, but we have not considered it for archaea.”

Tangled in this network are also interactions between archaea and their hosts. Archaea come decked out with features that facilitate within-host survival, like adhesins and the ability to form biofilms. As is true for the microbiome writ large, the relationship between archaea and host takes on a sort of push-pull dynamic: the host has strategies to control archaeal growth, while archaea have strategies to persist in the presence of those control measures. The way these host-archaeal connections play out, along with outcomes of bacteria-archaeal relationships, have emerging associations with human health-and lack thereof.

Health, Disease and the Archaea of it All

Changes in archaeal community composition throughout the body have been associated with diseases like inflammatory bowel disease (IBD), colorectal cancer (CRC), periodontitis and vaginosis, among others. Scientists don’t know if or how archaea explicitly cause such conditions (which came first, the altered archaeal community or the disease that altered the community?). But there are examples with sturdier ties to the organisms. For instance, methane production by archaea slows down intestinal transit, which leads to constipation, a condition associated with irritable bowel syndrome. On the other hand, in some cases, the enigmatic organisms might even mitigate disease. Methanogens degrade a precursor of trimethylamine N-oxide (TMAO) that is produced by gut bacteria. When released into the circulatory system, TMAO is associated with atherosclerosis (buildup of plaque in the arteries)-degradation of the precursor throws a wrench in this process.

A growing pool of data also shows that archaea activate human immune cells, and studies in animal models indicate that methane boosts production of anti-inflammatory immune molecules while promoting decreased production of pro-inflammatory ones. Some diseases (e.g., CRC) are associated with decreased methanogen concentrations. Could the reduction in methane production play a role in their progression?

Really, all that researchers can definitively say about archaea is that they are likely doing something in the setting of disease. That “something” is still largely a mystery and varies from 1 disease to the next. Even the associations that exist aren’t always the strongest. “To be honest, a lot of reports out there are based on a few case studies where [the researchers] observed a bloom of methanogens,” Moissl-Eichinger stated. “Others do not have consistent methods or have [few participants],” and few studies account for the 2 populations of methane producers previously mentioned. “If you do not recruit properly, and have a clear mixture of both groups, it will shift your entire results.”

A further complication-some methanogens are clumped into 1 species when they are, in actuality, separate species. Moissl-Eichinger pointed to Methanobrevibacter smithii, a prominent gut archaeon, as an example. “M. smithii is very abundant, but it’s actually 2 species, or even more species. Whenever people talk about M. smithii, you don’t know if they’re talking about a single M. smithii species or a mixture of different species, so you cannot resolve [their findings] properly.” Without clear resolution, comparing studies exploring the intersection between archaea and disease, and diving deeper into the mechanisms underlying those observations, becomes difficult.

Advancing Archaeal Analyses

Which brings us to the crux of the issue: to understand host-dwelling archaea, one must study host-dwelling archaea. And yet, tools for examining the microbiome are not made with archaea in mind. For example, many DNA extraction kits created for bacteria don’t work for archaea. These kits sometimes use lysozyme to break up bacterial cell walls, but that enzyme is useless against archaea. A dearth in databases cataloguing host-associated archaea hasn’t helped matters.

“A lot of bioinformatic tools out there do not see methanogens-or archaea in general-very well, or [they] misclassify them. If you don’t use the right database, you will see [reports of] extremophilic archaea in the gut, which cannot be true. They should not be there. It’s just misclassification,” Moissl-Eichinger explained. Even growing archaea in the lab, a basic steppingstone toward understanding their physiology and behavior, isn’t easy. “There’s only a handful of cultures available now in the culture collections from gut archaea, and these are from the 1980s, so they have not been really touched. They are hard to grow, but we need more cultures. There’s so much diversity out there that we have not understood yet,” she said.

Luckily, progress is being made. Moissl-Eichinger’s lab has focused largely on improving databases, including uncovering and cataloguing over 1000 genomes of gut archaea. They’ve also dived into improving cultivation of the microbes, finding ways to bulk up culture collections by cultivating methanogens from individual hosts.

The goal now is to build on these new data to increase their utility. “The databases are quite fine as we have them,” she said. “The problem now is that more than 50% of all the genes [in archaea] are unknown. We do not know what they are doing [and] which proteins they are coding for. And so, we must do our homework. For instance, we need to have genetic models where we can knock out genes.”

Completing this homework is worthwhile, as the results could someday give rise to a whole new branch of microbe-based therapeutics that leverage archaea and their unique proteins and metabolites; scientists have pointed to archaea as the next generation of probiotics. Moissl-Eichinger acknowledged that while such an idea is “amazing,” it’s currently more pie-in-the-sky than practical. “All the rough work must be done.”

Looking Beyond the Gut

“More work must be done” could be the tagline for the archaeome; the number of questions about it far outnumber the answers. How do archaea interact with the immune system? What is their role in disease? How do they communicate with bacteria or with the host? How is this communication mediated? Where are they located?

The last question ties into an area Moissl-Eichinger thinks deserves attention moving forward. “We need to extend our focus-we’re focusing on the gut because it’s easy to get samples. But we are forgetting about the archaea in other places like the upper gastrointestinal tract or respiratory tract. I do not know many groups who really look at this, but they really are important for [understanding] microbiome networks [throughout the body].”

This reflects the general recognition among scientists that bacteria are only a single piece of the multi-microbial pie that is the broader, body-wide human microbiome. The more they can dig into these other fractions (e.g., viral, fungal, archaeal) the better positioned we will be to grasp why and how they matter for human health.