Laboratory tools for detection of archaea in humans

Abstract

This work represents an update of knowledge regarding the detection methods for human microbiome-associated archaea. Despite the fact that, during the last three decades, only four methanoarchaeal species have been isolated from the human mucosa, including faeces, subgingival plaque, and vaginal mucosa (Methanobrevibacter smithii, Methanosphaera stadtmanae, Methanobrevibacter oralis and, most recently, 'Methanomassiliicoccus luminyensis'), molecular studies, including PCR and metagenomic analyses, have detected DNA sequences indicative of the presence of additional methanoarchaea, as well as non-methanogenic archaea, in the human intestinal tract. Opinion is divided on the roles (if any) of these organisms in human disease, and certainly the data are still unclear. Future research and recently reported data highlighting the antimicrobial susceptibility of the human methanoarchaea could help in the design of selective media to discover additional human mucosa-associated archaea and ascertain their role in human infections involving complex flora.

Biofilm formation of mucosa-associated methanoarchaeal strains

“…In particular, the methanoarchaea Methanobrevibacter smithii and Methanosphaera stadtmanae are known to be part of the human gut microbiota (Miller et al, 1982, 1984; Lovley et al, 1984; Miller and Wolin, 1985; Weaver et al, 1986; Backhed et al, 2005; Eckburg et al, 2005; Levitt et al, 2006; Dridi et al, 2009). Notably, Methanobrevibacter smithii has been shown to inhabit nearly every human individual gut ecosystem, whereas Methanosphaera stadtmanae was found in 30% of individuals (Dridi et al, 2009; Dridi, 2012). Both strains, Methanobrevibacter smithii and Methanosphaera stadtmanae , have been shown to be involved in fermentation processes by converting bacterial fermentation products like hydrogen, organic acids (e.g., formate, acetate), and carbon dioxide, to methane (Miller et al, 1984; Samuel and Gordon, 2006; Samuel et al, 2007).…”

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

“…However, adequate universal primers that amplify both bacterial and archaeal small 16S rRNA genes but not any host rRNA genes were only published in mid-2011 [3], and thus, many studies chose to focus on bacteria alone rather than multiply effort and expense to cover taxa that are considered secondary in importance, if not altogether rare. Here, we provide a brief overview of what is currently known about archaea in and on the human body and their potential effects on human health (for additional reviews on archaea and their potential involvement in human disease, see [4–8]).…”

Archaea as emerging, fastidious members of the human microbiota

“…The window opened for the Archaea to be viewed differently when one organism that forms methane in the mammalian gut, later named Methanobrevibacter smithii , was found to be an archaeon [2]. Methane‐forming archaeons, named methanogens, are now recognized as members of the mammal and human gut microbiota; four such methanogens have been cultured, as reviewed by Bédis Dridi [3]. In fact, methanogens are fastidious organisms; the isolation and culture of the species Methanomassilicoccus luminyensis took more than 1 year [4].…”

“…Methanogens, chiefly M. oralis , are also susceptible to topical compounds used as local treatments for periodontopathy. As reviewed by Dridi [3], as well as Mayer and collaborators [10], non‐methanogenic archaeons, including halophilic archaeons, have been detected by PCR‐based methods in the human gut microbiota,. Interestingly, it has been shown that such organisms could be healthcare‐related organisms delivered with the purgative administered before colonoscopy [11].…”