An article published in the journal “Nature Biotechnology” describes the proposal of a new taxonomic classification for bacteria based on their phylogenetic similarities. A team of researchers led by Philip Hugenholtz of the Australian Center for Ecogenomics (ACE) used metagenomics to analyze known bacteria and subsequently group them according to their genetic similarities and differences in 99 phyla. The results of this research are available in the Genome Taxonomy Database (GTDB).
The taxonomic system serves to help researchers – but not only – to understand the relationships among the various organisms. However, in the case of microorganisms there are a number of problems which led to difficulties in their classification with the consequence that it also included errors. Multicellular organisms have been classified until recently on the basis of similarities in their physical characteristics but this approach gives limited results with microbes. Most microbes can’t at least for the moment reproduce in lab and this means that it’s necessary to look for them in their ecosystems, another notable problem.
Today the situation has improved considerably and Philip Hugenholtz’s teams used an approach called metagenomics, where microbes’ genetic samples got taken directly in their environment. In this way, their diversity is maintained, an impossible thing using lab cultivation with its limits. In recent years, this approach allowed to obtain the genomes of thousands of species of bacteria, including a lot unknown until a few years ago, so much that other teams proposed the creation of new phyla and even new superphyla.
Philip Hugenholtz’s team based its classification on 120 genes that have a high conservation rate among bacteria. Dr. Donovan Parks, who led the development of the genetic analysis software for this project, stated that the tree of life obtained by comparing the genomes included allowed to create a standard model that fixed the many classification errors made over time.
The image (courtesy of University of Queensland. All Rights Reserved) shows the new bacteria tree of life with 5 superphyla indicated. The large branch that was only vaguely indicated with the expression “candidate phyla radiation” described in an article published in the journal “Nature Microbiology” in April 2016 was included in a single phylum part of the Patescibacteria superphylum.
Research of this type takes time for other scientists to evaluate and discuss the results obtained and in this case the new taxonomy proposed for bacteria. There’s always room to improve the classification, also because approaches like metagenomics are allowing to find new bacteria. The path seems to be the right one in the sense that researchers used advanced genetic techniques to rationally evaluate the relationships among bacteria. A proper classification will help the studies on them and this is positive thinking about the roles they have in their ecosystems and even in the interactions with humans as both symbionts and pathogens.