An essential first step in understanding bacterial phylogeny is to develop objective criteria for defining the major taxonomic groups within Bacteria. At present, Bacteria are divided into approximately 23 main groups or phyla based on their branching patterns in the 16S rRNA trees. Some of these phyla consist of only one or a few species (e.g., Thermomicrobia, Chrysiogenetes, Fibrobacteres, Deferribacters), whereas others such as Proteobacteria, Bacteroidetes, Cyanobacteria, Actinobacteria (high G+C gram-positive) and Firmicutes (low G+C gram-positive) are very large and comprised of thousands of species accounting for more than 90-95% of all known bacteria. Many of these smaller phyla (e.g. Fibrobacteres, Chlorobi) were once classified as parts of larger bacterial groups according to common morphological/physiological characteristics, but were later split apart in light of their branch patterns in 16S trees. In the process, much of the information regarding the interrelationships between these groups was lost, so that their genealogies and branch order remain unresolved. What properties define the rank of phylum or other higher taxa such as Class, Order, or Family have never been clearly defined or agreed upon by the scientific community. Likewise, the question as to what constitutes a subdivision or Class within a phylum remains equally unclear. For example, the Proteobacteria phylum is presently divided into 5 subdivisions or Classes namely the α, β, γ, δ and ε proteobacteria. All of these subdivisions constitute major groupings within Bacteria and most of them are clearly distinguished from each other, and from other bacterial divisions, in both phylogenetic trees and by variety of other means. In the absence of objective criteria for the higher taxonomic ranks, it is unclear why these major bacterial groups are recognized as subdivisions or Classes, whereas many other poorly characterized groups consisting of only a few species are recognized as main phyla of Bacteria. Hence, the taxonomic rankings of different bacterial groups is presently entirely arbitrary and not based upon any sound principles.
The question as to how one should define the highest taxonomic ranks within Bacteria can initially be approached from an idealist point of view. Shown above is a hypothetical tree for Bacterial species. In an ideal classification system, the trunk represents the mainline of descent, with the root representing the common bacterial ancestor. All main branches of the tree originating from the trunk will be recognized as the main groups or phyla of the tree. In an ideal classification system, the order in which these branches have diverged from the trunk (starting from the root) will be known and so the system will be based on relative genealogy. It is important that these phyla (or branches) be clearly distinct from one another based on their positions in the tree.
Also, all organisms that comprise a branch should share certain characteristics which distinguish them from all other organisms on other branches. Smaller branches and twigs which are offshoots of the main branches represent descending orders of taxonomic rank e.g. smaller branches are Classes, Orders and Families, twigs are genera and species (see picture to the left). Organisms on the same smaller branch should have more characteristics in common with each other than they do with organisms on other branches, however they still share a subset of unique characteristics with organisms on other branches of the same main branch.
In the work described here, the definitions of higher taxa that we have adopted follow closely this ideal scheme. All main divisions or phyla consist of groups of species whose branching order from the main line of descent can be clearly established, and which is distinct from all other identified main groups. The division of Bacteria into various main groups or subdivisions in the present scheme is based strictly on a genealogical basis, which is the most logical way of understanding phylogeny . We have thus far been able to identify 11 different main groups (Firmicutes, Actinobacteria, Deinococci-Thermus (Chloroflexi), Cyanobacteria, Spirochetes, Chlamydiae, Fibrobacter - Chlorobi - Bacteroidetes (FCB), Aquificales, ε-Proteobacteria, α-Proteobacteria and β,γ Proteobacteria) on the basis of their branching pattern from the main line of descent (i.e. trunk). Based on the identified multigroup or mainline signatures, it should be possible to place any given species into one of these main groups. The number of main groups that we have identified thus far using the signature sequence approach represents a minimal number. Different distinct groups of species branching in the same position, even though they do not share any unique characteristic in common (viz. Chloroflexi and Deinococci) could presently be regarded as provisional subphyla of a given main phyla. As additional signature sequences or other information that either unite these subphyla or clarify their branching orders become available, these phyla can then be placed in either a single phylum or divided into two distinct phyla. Most main phyla or subphyla are presently also distinguished from other main phyla by distinctive group-specific signatures. Based on these criteria, in our scheme the Proteobacteria phylum has been divided into at least three main phyla, each of which can be clearly distinguished from the other and their relative branching order can be clearly deduced. The δ-proteobacteria are distantly related to α-Proteobacteria, but this relationship needs to be further clearly established. The β,γ-Proteobacteria share many common signatures. Although a few signatures indicate γ-Proteobacteria to be a distinct and later branching group, the relationship between these two subdivisions or subphyla needs to be further studied. The scheme based on signature sequences also indicates that three of the presently recognized main phyla viz. Bacteroidetes (or Cytophaga, Flavobacteria, Bacteroides group), Chlorobi and Fibrobacteres, they all branch reliably in the same position and they share many distinctive signature sequences which unite them into a single phylum. Thus, according to the criteria that we have outlined, these groups should be placed into a single phylum and they should be accorded either a Class or Order rank within this main phylum. The relative branching order of these subgroups within the FCB phylum is also clearly established based on a number of subgroup-specific signature sequences (link).
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