Archaea as emerging organisms in complex human microbiomes
Section snippets
Archaea as extremophile organisms
In the late 1970s, several research groups unexpectedly discovered prokaryotes living in hot springs, submarine volcanic habitats, salt lakes and saline, acidic and alkaline water. These unusual organisms were named Archaea because the extreme environments in which they were found were thought to be the most primitive on Earth [1]. 16S rDNA sequence-based analysis indicated that Archaea form a separate group of prokaryotes that represent one of the elementary domains of life [2], [3]. This was
Archaea as non-extremophile organisms
Further research illustrated that the word Archaea was misleading, as the organisms were found in various non-extreme environments including oceans, oil wells, sewage and soils where they play major roles in recycling elements such as carbon, nitrogen and sulfur [8]. Methanogenic Archaea that produce methane under anaerobic conditions have been found in various anaerobic microniches formed from oxygen elimination by facultative anaerobes [9] and in peat soil and the rhizospheric soil of rice
Archaea as human inhabitants
More than 40 years ago, it was observed that humans expire methane. This observation led Nottingham and Hungate to isolate previously non-identified methanogenic Archaea from human feces using a non-selective medium and an anaerobic atmosphere composed of 80% H2 and 20% CO2 [30]. Miller and collaborators further isolated Methanobrevibacter smithii from human stool specimens from four healthy adults using anaerobic cultures enriched with the same H2–CO2 anaerobic atmosphere pressurized to 2 bar
Human Archaea as fastidious anaerobes
The only Archaea that have been isolated from humans are strict anaerobes. These organisms require a specific atmosphere similar to the anaerobic chamber developed by Edwards and Mc Bride, composed of 80% H2 and 20% CO2 with an optimal pressure of 2 bar [56]. Isolation of methanogenic Archaea from complex specimens such as stool, dental plaque and environmental samples was performed using the roll-tube technique according to Hungate [57]. Media and conditions for culturing M. smithii, M.
Archaeal carriage and human health
The environment is a likely source of human methanogenic Archaea, but their precise ecological niches and the routes of acquisition for humans remain unknown. Several studies have attempted to detect the presence of methanogenic Archaea in the intestinal tract of children. Methanogenic Archaea were not detected in children under 27 months, but it has been shown that carriage increases with age up to 60% in 5-year-old Italian children [69]. Carriage was not associated with any particular diet.
Perspectives
Recent molecular studies indicated that human Archaea constitute an expanding world partially mirroring the human environment. Using methods for the analysis of Archaea DNA such as single cell sequencing and ultra deep methagenomic sequencing in animal and human microbiomes will provide new insights into the diversity of host-associated Archaea. These new data may prompt further efforts to isolate and culture new Archaea, including non-methanogen Archaea, from complex human microbiomes in order
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