VetBact

Introduction

Bacterial taxonomy means naming and classification into various hierarchical groups with increased containment. I.e. a genus may consist of several different species, a family may consist of several different genera, etc. You can usually recognize the rank by its ending, i.e. if the word ends in e.g. -ales, one knows that it is the order that is intended. However, this has not been consistently implemented for all bacterial species. By the phylogeny of bacteria is meant their natural relationship, i.e. their evolutionary history

Taxonomic division

All living organisms are usually divided into three domains: Eukaryotes (Eukarya), bacteria (Bacteria) and archaea (Archaea). There are also other ways of dividing organisms, such as e.g. in seven different kingdoms: Bacteria (Bacteria), Archaea (Archaea), Protozoa (Protozoa), Chromists (Chromista), Plants (Plantae), Fungi (Fungi) and Animals (Animalia). Some bacterial groups are also divided into subfamilies, suborders and/or subclasses. Today, most scientists (at least bacteriologists) have accepted the division of organisms into three different domains and it was Carl Woese (the father of molecular phylogeny), who introduced this system in 1990 (see ref. 1 below). Now, efforts are being made for the taxonomy of the bacteria to reflect their evolutionary history (phylogeny) and as more knowledge is gained about bacteria and their phylogeny, their taxonomy will be revised.

Phylogeny

The phylogeny of bacteria means their natural relationships, i.e. their evolutionary history. When bacteria began to be divided into different taxonomic categories, the classification was based on a few characteristics (e.g. gram stain, biochemical tests, sporulation ability, pathogenicity, etc.). The more features that were used, the better the division reflected the phylogeny of the bacteria. However, these features provided only blunt tools for studying the phylogeny of bacteria. The real breakthrough came when DNA sequence data was used to study the relatedness of bacteria. It was long standard to base phylogenetic trees on sequence data from 16S rRNA genes. Today, however, it has become so cheap to do whole-genome sequencing of bacteria, so you can instead base your phylogenetic trees on sequence data from large parts of the genome. Then you have access to up to 10,000 times more data compared to sequence data from the 16S rRNA gene alone, since each nucleotide position can be considered a unique and well-defined character.

Phylogenetic trees

Phylogenetic trees (or family trees), based on sequence data, are calculated by using special computer programs, which can handle large amounts of data. In the type of phylogenetic trees shown on VetBact, the horizontal distances are proportional to the sequence differences in the compared genes. Thus the distances between two organisms are shorter, the closer they are related to each other.

Phylum (pl. phyla)

The rules for naming bacteria [International Code of Nomenclature of Prokaryotes (ICNP)] did not previously include the taxonomic category (rank) phylum, but recently (February 2021) the members of the International Committee on Systematics of Prokaryotes (ICSP) have decided that from now on it will be so. It has been decided that all names of phyla should be written in italics (which has been done at VetBact also before) and have the suffix -ota. In addition, the phylum name must be based on a genus, which should constitute the nomenclature type (see ref. 2 below).

It is usually said that the phyla of bacteria form their main lineages of evolution and now there are over 40 described phyla. Eleven of these phyla are represented in VetBact. The largest phylum is Pseudomonadota (formerly Proteobacteria) and it is also the phylum that contains the greatest number of pathogenic bacteria. In VetBact there are currently 92 bacterial species, which belong to the phylum Pseudomonadota.

References

1. Woese CR, Kandler O & Wheelis ML. (1990). Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. PNAS 87(12):4576–4579.

2. Oren A, & Garrity GM (2021). Valid publication of the names of forty-two phyla of prokaryotes. Int. J. Syst. Evol. Microbiol. 71(10):005056.

Updated: 2023-04-17.