Marker genes tree

Numerical ecology analysis of microbiota by metagenomic sequencing, currently depend on the availability of DNA sequences of microbial genomes in the public databases. Often this approach leads to biased interpretation because the majority of the microbial community has no reference genome. To overcome this methodological obstacle, the MetaHIT consortium presented a new method that utilizes the presence of universally conserved in all identifiable bacteria in the microbial metagenome genes (known also as house-keeping genes1) This new method2 has allowed to capture in silico twice as species and a practical example has allowed to describe that species richness was lower in ulcerative colitis patients compared to healthy individuals. This species richness decrease in particular patients was mainly due to the depletion of non-isolated bacteria belonging to Clostridiales. Based on this promising method a new software had been implemented3.

  1. Ciccarelli et al., Science, 2006 

  2. Shinichi Sunagawa, Daniel R Mende, Georg Zeller, Fernando Izquierdo-Carrasco, Simon A Berger, Jens Roat Kultima, Luis Pedro Coelho, Manimozhiyan Arumugam, Julien Tap, Henrik Bjørn Nielsen, Simon Rasmussen, Søren Brunak, Oluf Pedersen, Francisco Guarner, Willem M de Vos, Jun Wang, Junhua Li, Joël Doré, S Dusko Ehrlich, Alexandros Stamatakis & Peer Bork. Metagenomic species profiling using universal phylogenetic marker genes; Nature Methods.2013 

  3. FetchMG: Taxonomic profiling using mOTUs