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We Have Archaea In and On Our Bodies

It turns out that we also have microbes called archaea living in and on our bodies. They are part of our microbiome (community of microbes living in and on us, which also includes bacteria, viruses, and fungi). Archaea constitute a domain or kingdom of single-celled microorganisms. These microbes are prokaryotes, meaning that they have no cell nucleus or any other membrane-bound organelles in their cells. Archaeal cells have unique properties that separate them from bacteria and eukaryotes. Archaea were initially classified as bacteria and thought to only exist in extreme environments (such as hot springs and salt lakes), and given the name archaebacteria, but this classification is now outdated. We now know that archaea live in less extreme places, including oceans, marshlands, animals, and humans.

So little is known about archaea that not even medical schools discuss this topic. This may be due to the fact that we currently don't know of any archaea that are human pathogens (that is, that cause illness) or parasitic. They are generally viewed as mutuals (the relationship is beneficial to both organisms) or commensals (they benefit, but don't help or harm the other organism). Humans appear to have low levels of archaea, and so far they have  been found in the human gut (part of digestion and metabolism), on the skin, and in subgingival dental plaque (and perhaps involved with periodontal disease). But studies rarely look for them. We don't know the importance or roles that they play in our bodies (but there are suspicions), but it turns out that drugs such as statins and the antibiotic metronidazole  are eliminating them.

Note that methanogens are archaea that excrete or produce methane as a metabolic byproduct in anoxic (no oxygen) conditions such as the gut. They help digest our food. The species Methanobrevibacter smithii  has been shown to be present in up to 95.7% of humans studied, and found to be the most abundant methanogen in the human gut, comprising up to as much as 10% of all anaerobes found in a healthy individual's colon. Anaerobes are organisms that require oxygen-free conditions to live. Some of the June 2015 article (by M. N. Lurie-Weinberger and U. Goph) excerpts from PLOS:

Archaea in and on the Human Body: Health Implications and Future Directions

Although they are abundant and even dominant members of animal microbiomes (microbiotas), from sponges and termites to mice and cattle, archaea in our own microbiomes have received much less attention than their bacterial counterparts. The fact that human-associated archaea have been relatively little-studied may be at least partially attributed to the lack of any established archaeal human pathogens. Clinically oriented microbiology courses often do not mention archaea at all, and most medical school and biology students are only aware of archaea as exotic extremophiles that have strange and eukaryotic-like molecular machinery. Since archaea have been known to be associated with the human gut for several decades, one would think that human microbiome studies may unravel new facets of archaea–human interactions... 

The human large intestine (colon), in healthy individuals, has extremely low oxygen concentrations, and over 90% of its microbiota are strict anaerobes. Researchers taking metagenomic fecal microbiota surveys of adult Europeans could assign about 0.8% of the genes in their data set to archaea, and similar numbers (0.2%–0.3%) were reported for Amerindians and Malwaians, while North Americans had much lower fractions (<0.05%). With the exception of a single report indicating the presence of halophilic archaea in biopsies of inflammatory bowel disease patients, archaea that reside in the human colon are nearly always methanogens. Most of these strict anaerobes belong to the order Methanobacteriales... 

Methanobrevibacter (previously called Methanobacterium) was first isolated from human stool as early as 1968, followed nearly 15 years later by the discovery that such fecal isolates belonged to the species Methanobrevibacter smithii. M. smithii has been shown to be present in up to 95.7% of human subjects, and to be the most abundant methanogen in the human gut by several studies, comprising up to as much as 10% of all anaerobes found in a healthy individual's colon. Remarkably, its abundance appears to remain stable over time, even following radical dietary changes, and it is highly heritable ....

Another possible connection between gut methanogens and human health is the strong association between methanogen presence and chronic constipation. Methane was shown to slow intestinal transit time by 59%, and thus may contribute substantially to constipation. However, a shorter intestinal transit time probably selects against the presence of methanogens, since they tend to have generation times that are longer than those of many gut bacteria, even when grown in the most favorable, state-of-the-art culture media...Taken together, these findings indicate that in individuals with already slow intestinal transit, methanogens may bloom and promote further constipation.

Methanogenic Archaea have been reported in subgingival dental plaque as early as 1987. To date, three genera have been successfully isolated from subgingival plaque: Methanobrevibacter  Methanobrevibacter, Methanosphaera (based on weak antigenic similarity), and Methanosarcina ... 

Unlike many antibiotics that do not target archaea (because they do not have a peptidoglycan cell wall and have ribosomes that are more eukaryotic like, metronidazole, which is commonly used to treat periodontitis, is highly effective against M.oralis and, thus, suppression of M. oralis could contribute to its efficacy. Statins... lower blood cholesterol in humans, but they also effectively inhibit archaeal growth because they block the synthesis of their main membrane lipids.

Archaea on the human skin have been discovered only in recent years. 

... archaea are still an under-detected and little-studied part of the human microbiome, and their contributions to human health or disease remain mostly unknown. This knowledge gap should be addressed in the near future to inform clinicians, many of whom are totally unaware of these organisms. While no human clinical study studying the in vivo effects of statins on archaea in our microbiomes has been published, in vitro results strongly suggest that these drugs could inhibit the growth of archaea in the human body... Moreover, in highly competitive niches, such as the colon, even partial growth inhibition may cause extinction. In developed countries, such as the United States, statin use is on the rise, and over a third of people over 65 use these drugs for their cholesterol-lowering effects, unaware that at the same time they are taking a broad-spectrum anti-archaeal agent. At the moment, there is little evidence of whether eradication of human-associated archaea (and potentially their bacterial syntrophs) will be beneficial or harmful for human health, with the possible exception of periodontal disease. Thus, before archaea become part of the "disappearing human microbiota" we should at least know if we are going to miss them when they are gone.