In-depth studies of microbial communities previously relied on cultivation of the bacteria under lab conditions. However, this culturing is complicated, and in most cases even impossible (1). Within this context, the development of new DNA sequencing technologies has led to a revolution in microbial ecology, as it allows scrutinizing in detail microbial communities without the need of culturing them in the lab. This methodology – called metagenomics – offers a unique approach to identify the potential of microbes surviving in extreme environments, such as the cooling circuits of the BR2 (2, 3) or clay water of the underground waste disposal repository (4). Nowadays the most used strategy is to amplify and sequence one specific phylogenetic marker gene which enables microbiologists to identify the type of bacteria present in the studied community. While powerful, this approach has certain limitations, the most important one that it only enables to give an insight on the taxonomic classification but not on the biological functions that can be performed by the community. Due to a decrease in the sequencing costs, it is now feasible to sequence the complete DNA of a microbial community (i.e. shotgun metagenomics), rather than focusing on a specific marker gene, which will give access to the complete metabolic potential of this community and the biological functions encoded within the bacterial genomes. However, this approach comes with a dramatic increase in the complexity of the data analysis as such requiring the development of new bioinformatics tools.
References: (1) Oliver JD. 2005. The viable but nonculturable state in bacteria. J Microbiol 43 Spec No:93-100. (2) Props R, Kerckhof FM, Rubbens P, De Vrieze J, Hernandez Sanabria E, Waegeman W, Monsieurs P, Hammes F, Boon N. 2016. Absolute quantification of microbial taxon abundances. ISME J doi:10.1038/ismej.2016.117. (3) Props R, Monsieurs P, Mysara M, Clement L, Boon N. 2016. Measuring the biodiversity of microbial communities by flow cytometry. Methods in Ecology and Evolution doi:10.1111/2041-210x.12607. (4) Wouters K, Moors H, Boven P, Leys N. 2013. Evidence and characteristics of a diverse and metabolically active microbial community in deep subsurface clay borehole water. FEMS Microbiol Ecol 86:458-473.