Elsevier

Anaerobe

Volume 17, Issue 2, April 2011, Pages 56-63
Anaerobe

Archaea as emerging organisms in complex human microbiomes

https://doi.org/10.1016/j.anaerobe.2011.03.001Get rights and content

Abstract

In this work, we review the state of knowledge of Archaea associated with the human microbiome. These prokaryotes, initially discovered in extreme environments, were named Archaea because these environments were thought to be the most primitive on Earth. Further research revealed that this terminology is misleading because these organisms were later found in various non-extreme environments, including the human host. Further examination of the human microbiome has enabled the isolation of three archaeal species, Methanobrevibacter smithii, Methanosphaera stadtmanae and Methanobrevibacter oralis, which are associated with oral, intestinal and vaginal mucosae in humans. Moreover, molecular studies including metagenomic analyses detected DNA sequences indicative of the presence of additional methanogenic and non-methanogenic Archaea in the human intestinal tract. All three culturable Archaea are strict anaerobes, although their potential role in human diseases remains to be established. Future research aims to detect and culture additional human mucosa-associated Archaea and to look for their presence in additional human tissues, to establish their role in human infections involving complex flora.

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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