The influence of rickettsiologists on post-modern microbiology

Abstract

Many of the definitions in microbiology are currently false. We have reviewed the great denominations of microbiology and attempted to free microorganisms from the theories of the twentieth century. The presence of compartmentation and a nucleoid in Planctomycetes clearly calls into question the accuracy of the definitions of eukaryotes and prokaryotes. Archaea are viewed as prokaryotes resembling bacteria. However, the name archaea, suggesting an archaic origin of lifestyle, is inconsistent with the lifestyle of this family. Viruses are defined as small, filterable infectious agents, but giant viruses challenge the size criteria used for the definition of a virus. Pathogenicity does not require the acquisition of virulence factors (except for toxins), and in many cases, gene loss is significantly inked to the emergence of virulence. Species classification based on 16S rRNA is useless for taxonomic purposes of human pathogens, as a 2% divergence would classify all Rickettsiae within the same species and would not identify bacteria specialized for mammal infection. The use of metagenomics helps us to understand evolution and physiology by elucidating the structure, function, and interactions of the major microbial communities, but it neglects the minority populations. Finally, Darwin's descent with modification theory, as represented by the tree of life, no longer matches our current genomic knowledge because genomics has revealed the occurrence of de novo-created genes and the mosaic structure of genomes, the Rhizome of life is therefore more appropriate.

Keywords: archaea; bacterial virulence factors; definitions; metagenomics; orphan genes; prokaryotes; tree of life; virus.

Figure 1

Compartmentation in prokaryotes and eukaryotes. Compartmentation of Gemmata obscuriglobus (A) and a eukaryotic cell (B) is comparable.

Figure 2

Time scale of eukaryogenesis and nucleogenesis. Eukaryotes are not the only species with compartmentation. First eukaryotes emerged from an endosymbiotic event. The first nucleus appeared approximately 3 billion years ago in Planctomycetes and Chlamydia. These numbers are approximations (Bromham and Penny, ; Cavalier-Smith, ; Trevors and Abel, 2004).

Figure 3

Motility is not necessarily a virulence factor. (A) Rickettsia conorii is mobile in the cytoplasm and in the nucleus and moves quickly. Actin-based motility is associated with the Sca2 and RickA proteins (represented in red and blue circles respectively). Yellow stars are to demonstrate that the bacterium moves fast in the cytoplasm; dotted lines are to show that the bacterium can be found anywhere in the cytoplasm and even in the nucleus. (B) Rickettsia typhi is also mobile in the cytoplasm, but it moves less quickly than R. conorii. Its mobility is associated with the Sca2 protein. (C) R. prowazekii is completely immobile in the cytoplasm. The Sca2 and RickA proteins are absent.

Figure 4

Phylogenomic tree based on whole gene content (present/absent genes) in pathogenic and non-pathogenic E. coli species and S. dysenteriae. Two clusters are formed: one for pathogenic species (in red), and one for non-pathogenic species (in blue). Pathogenic strains are divided into five groups: EPEC, enteropathogenic; EHEC, enterohemorrhagic; UPEC, uropathogenic; ETEC, enterotoxigenic; EAEC, enteroaggregative.

Figure 5

Each one of the four domains of life, (A) Eukaryotes (in yellow), (B) Archaea (in blue), (C) Viruses (in pink), and (D) Bacteria (in green), is represented as mosaics containing genes from all four domains. Purple squares represent ORFan genes.