Decoding archaea: The often forgotten third domain of life

Microbes have been known to humankind for centuries. Yet, astoundingly, a significant population of an entire microbial domain of life remained mysteriously undiscovered until the late 20th century. Nearly 50 years after categorizing archaea as a separate domain (Figure 1) by noted American microbiologist Carl Woese, they are still among the least understood organisms. The mystery of the archaean domain could be attributed to the initial misclassification of some archaean species as bacteria, mainly due to their visual resemblance and lack of nuclei and other cell organelles. Only after genetic analysis of some of the then-known archaean species, did the significant differences between the genetic makeup of bacteria and archaea come to light. Notably, the archaean membrane composition, lack of peptidoglycan cell wall, and mechanism of processing genetic information (DNA replication, RNA transcription, protein translation, presence of histone proteins) resemble those in eucaryotes. The overlap with both the existing domains (bacteria and eucarya) justify the placement of the archaean domain in between the other two domains, supporting the possible course of their evolution.

Though archaea were initially believed to be extremophiles inhabiting ecosystems of high temperatures, salinity, acidity, and alkalinity, it is known today that they live almost everywhere, including in mesic environments and the bodies of other organisms. Of course, humans are no exception to this. Archaea, alongside various groups of microbes, have been residents of the human skin, respiratory tract, urogenital tract, mouth, and gut for thousands of years (Figure 2). The evidence of the presence of microbes in a healthy human gut emerged as early as the 1880s, with the discovery of organisms like E. coli in the guts of healthy children. However, archaea were discovered to inhabit the human gut only three decades ago. Reports of archaeal abundance in the human gut exhibited a varied range (0.1–21.3%). Even though archaea constitute a significant portion of the microbial population in our body, their roles and importance are still not well-understood.

The first-known archaea in the human gut were methanogens—methane-producing anaerobic microbes. More than 90% of human-gut archaea are methanogens, predominantly Methanobrevibacter and Methanosphaera. Methanogens maintain gut balance by utilizing the potentially harmful end-products of bacterial fermentation, such as hydrogen, acetates, methanol, and methyl sulfide during methanogenesis, and are assumed to contribute positively to gut health. Studies have revealed the presence of methanogenic archaea in the colostrum and breastmilk of healthy, lactating mothers, facilitating the transfer of these essential microbes to the infant’s gut.

Inflammatory bowel disease (IBD) is a complicated condition associated with inflammation throughout the intestinal mucosa. Studies demonstrate a positive correlation between the incidence of IBD and the presence of many microorganisms. However, patients with IBD show a significant decrease in the gut archaeal population as compared to healthy patients. Though the mechanism of pathogenesis in IBD is not clearly understood, the negative correlation between archaeal population size and the occurrence of IBD points towards the positive roles potentially pursued by these gut archaea.

Another interesting discovery is the ability of methanogens to utilize trimethylamine (TMA) as a substrate for methanogenesis. TMA is an intestinal bacterial metabolite and an abnormal level of TMA is significantly correlated with an increased risk of cardiovascular diseases (CVDs). TMA can also induce oxidative stress, a root cause of numerous chronic health conditions including diabetes and cancer. Recent research also hints at the possibility of methanogens degrading a precursor of trimethylamine N-oxide (TMAO). Along with the risk of CVDs, TMAO is known to increase inflammation, impair cholesterol metabolism, and induce thrombosis. The possibility of methanogens metabolizing TMA and degrading TMAO in the intestine greatly reduces the risk of infiltration of these compounds into the bloodstream. These observations can potentially explain improved gut health in subjects with gut-methanogens. In recent developments, it was also observed that a certain class of archaea (anaerobic methane-oxidizing archaea or ANME) can oxidize methane to carbon dioxide and play a critical role in maintaining the carbon cycle. Reports also indicate a potential role of archaea in stimulating our immune response.

Yet, archaeal presence is not always linked to great gut health. An increase in archaeal population in the gut has been shown to coincide with gut dysbiosis, an imbalance in the microbial inhabitants of the gut. Dysbiosis is an important factor linked to pathologies of the human digestive tract and is associated with a number of health conditions such as irritable bowel syndrome, constipation, obesity, diverticulitis, and colorectal cancer. Pathological conditions related to archaeal dysbiosis are not limited to the gut. Methanogenic archaea also inhabit the oral cavity and an increase in the oral archaeal population may cause periodontal dysbiosis, leading to periodontitis, peri-implantitis, and gingivitis. Similar to the gut, methanogens of the oral cavity consume hydrogen produced by fermentation in the oral cavity. The evidence for the existence of archaea in the periodontal pockets and subgingival plaques has been abundant. Studies have also shown correlations between methanogens and other pathologies. Patients with a greater volume of methanogens in their gut were found to have poorer glycaemic control and increased HbA1c counts. Methanogens, especially Methanobrevibacter smithii, have also been linked to urinary tract infections, vaginal dysbiosis, and vaginosis, with M. smithii detected in ~90% of the patients in some studies. Methanogens have also been detected in the pus specimens of refractory sinusitis and brain and muscle abscesses.

However, all these data only point towards the presence of archaeans in pathological sites. No direct evidence has been obtained establishing the pathogenic nature of archaea to these diseases. The mechanisms of pathogenesis are still uncertain and further studies are underway to understand the role of archaea in causing or enhancing diseases. The correlational evidence in pathology, along with their positive roles in the gut, also suggests that archaea possibly induce diseases not by their nature, but by opportunity. Their highly intricate associations with the other microorganisms and subtle roles in maintaining overall health indicate that other pathological conditions of the host could also play a role in turning seemingly harmless archaea into opportunistic pathogens. The current developments, aided by German bacteriologist Robert Koch’s Germ Theory, indicate that archaea are perhaps not pathogenic in nature and cannot cause diseases. But is it really the case? Over the past few years, microbiologists have been framing several theories to answer this question.

Over the years, scientists have formulated several hypotheses and theories behind this unusual behaviour of archaea, with respect to their inability to cause diseases. Gill and Brinkman proposed that the lack of archaeal pathogens is due to mutually exclusive populations of phages and other viruses that infect bacteria and archaea. Cavicchioli et al. analysed the toxins secreted by archaea (archaeocins) that targeted a few other archaea but were not potent against a range of bacteria. Martin proposed that eucaryotes are not a good source of nutrients for archaea as the cofactors utilised by archaea in their biochemical and metabolic pathways are totally different from that in eucarya and bacteria. He predicted, ‘if archaebacterial “pathogens” are found, they will infect other archaebacteria—not eukaryotes’. However, this argument was countered by Cavicchioli and Curmi as archaea can be benefited from the metabolites, amino acids, nucleic acids, and energy sources as well, not just cofactors. Another potential reason behind the non-pathogenic nature of archaea is perhaps the lack of virulent genes in the identified species. Although lateral gene transfer (LGT) can take place between bacteria and archaea, no phages or viruses capable of infecting both archaea and bacteria have been reported so far. Despite these theories individually or collectively supporting the non-pathogenic nature of archaea, there is one particular scenario that cannot be ruled out: what if pathogenic archaea do exist but are yet to be discovered?

Microbes in general can exhibit pathogenic traits. Among the three domains of life, both the other domains (bacteria and eucarya) include a variety of pathogenic organisms (Figure 3). So, why are not archaea? Are they really incapable of causing diseases? Or, are there pathogenic archaea yet to be discovered? Cavicchioli et al. listed a number of pathogenic features possessed by archaea and did not rule out the possibility of discovering disease-causing archaea in the near future. In nature, less than 0.5% of bacteria have been found to be pathogenic. Applying the same ratio to archaea, Gill and Brinkman (2011) expected around 16 of them to be pathogenic. Even though this expected number should be slightly higher now, it is really surprizing that scientists have not been able to conclusively prove the presence of a single pathogenic archaean to date. Moreover, the pathogenic nature of a microbe is usually established by determining the cause of a disease, and not the other way around. The fact that the microbe-induced pathogenic diseases are well-characterized and none of them has identified any archaean species as the root cause further points toward the non-pathogenic nature of archaea.

Despite the obvious morphological resemblance with bacteria, archaea are more closely related to eucaryotes in general—a puzzling observation that baffled scientists for years. Although archaea and bacteria are unicellular and lack cell organelles, archaea are genetically and biochemically more similar to eucaryotes. The mutually inclusive characteristics between archaea and eucarya—similarities in their genetic composition and metabolic pathways including protein synthesis and DNA replication—suggest that archaea and eucaryotes perhaps shared a common ancestor more recently than both of them do with bacteria and are monophyletic in nature.

Recent studies have provided diverse answers to the much-debated question of the origin of the domain eucarya. One of the most radical findings in this regard is the discovery of Asgard archaea (phylum Asgardarchaeota). Keeping the spirit of Norse mythology floating, some of the group members of this phylum have been named Lokiarchaeota, Thorarchaeota, Odinarchaeota, and Heimdallarchaeota after the Gods in Norse mythology. Scientists now believe that the eucarya and archaea perhaps do not share a common ancestor. Rather, a eucaryotic form of life might have originated from the Asgard archaea. Leão et al. recently reported how Asgard archaea could have played a key role in the evolution of modern eucaryotic immune systems. Viperin and argonaute—two key proteins for the eucaryotic defence systems in their fight against viruses, came from Asgard archaea. The findings to date suggest that the domain archaea are not only non-pathogenic but also might have played an integral role in building our immune system.

It is undeniable that archaea have been receiving more attention in the past few decades and scientists are regularly unraveling new morphological and functional insights into archaea. Even then the number of studies on archaea is nowhere close to that on other common microbes such as bacteria or viruses. Some of the most intriguing unanswered questions regarding archaea remain about their pathogenicity, their roles, and their positions in phylogenetic tree. Similar microorganisms have shown pathogenic behaviour, however, not a single archaeon has been conclusively connected to the origin of any diseases. Certain archaea can form symbiotic relationships with other organisms (both bacteria and eucaryots), and at times can be beneficial to humans. However, archaea can worsen a diseased state indirectly and their roles in causing diseases cannot be entirely ruled out. Difficulties in culturing and studying archaea in a microbiology lab pose a practical challenge. Overcoming these challenges and further advancements in molecular biology could potentially lead us to understand the roles of archaea, their evolution, and their potential as pathogenic microbes.

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Vagdevi Rao K C is Research Associate at Prayoga Institute of Education Research (Bengaluru, India), specializing in phytochemistry, microbiology, and plant-based medicines. She completed her Bachelor’s program in chemistry, botany, and zoology and a diploma in medicinal and aromatic plants. Vagdevi then completed M.Sc. in Botany from the University of Mysore (Karnataka). Currently she is working on multiple projects encompassing the fields of microbiology and botany. Email: [email protected].

Subhadip Senapati is a Lead Researcher at Prayoga Institute of Education Research (Bengaluru, India). Upon completing his M.Sc. from Indian Institute of Technology Madras (IITM), he earned his Ph.D. from Arizona State University in 2015 under the guidance of Dr. Stuart Lindsay. Later he pursued postdoctoral training under Dr. Paul S.-H. Park at Case Western Reserve University. At present, he is working on several academic and industrial challenges focused on green chemistry, biochemistry, and nanoscience. Email: [email protected].