Complete Genomes Used in the Work Arranged as They Appear in the Figures
| Kingdom | Taxonomical adscription | Species | |||
| Rank 1 | Rank 2 | Rank 3 | |||
| Bacteria | Proteobacteria | Gamma | Enterobacteria | Escherichia coli K12 Escherichia coli O157 Salmonella typhimurium LT2 Salmonella typhi Yersinia pestis | |
| Vibronaceae | Vibrio cholerae | ||||
| Enterobacteria | Buchnera aphidicola | ||||
| Pasteurellaceae | Haemophilus influenzae Pasteurella multicocida | ||||
| Pseudomonadaceae | Pseudomonas aeruginosa | ||||
| Xantomonas | Xilella fastidiosa | ||||
| Alpha | Rhizobiaceae | Rhizobium meliloti Rhizobium loti Agrobacterium tumefaciens | |||
| Caulobacter | Caulobacter crescentus | ||||
| Rickettsiales | Rickettsia prowazekii Rickettsia conorii | ||||
| Beta | Neisseriaceae | Neisseria meningitidis MC58 Neisseria meningitidisZ2491 | |||
| Epsilon | Helicobacter | Helicobacter pylori J99 Helicobacter pylori | |||
| Campylobacter | Campylobacter jejuni | ||||
| Firmicutes | Bacillus/Clostridium | Bacillus/Staphylococcus | Bacillus subtilis Bacillus halodurans Staphylococcus aureus Staphylococcus aureus Mu50 Listeria innocua Listeria monocytogenes | ||
| Streptococcaceae | Streptococcus pyogenes Streptococcus pneumoniae Lactococcus lactis | ||||
| Clostridia | Clostridium acetobitylicum | ||||
| Mollicutes | Ureaplasma parvum Mycoplasma pulmonis Mycoplasma pneumoniae Mycoplasma genitalum | ||||
| Actinobacteria | Actinobacteridae | Mycobacterium tuberculosis Mycobacterium leprae | |||
| Thermus | Deinococcus | Deinococcus radiodurans | |||
| Cyanobacteria | Chroococcales | Synechocystis | Synechocystis sp | ||
| Aquificales | Aquificaceae | Aquifex | Aquifex aeolicus | ||
| Thermotogales | Thermotoga | Thermotoga maritima | |||
| Spirochaetales | Spirochaetaceae | Borrellia | Borrellia burgdorferi | ||
| Treponema | Treponema pallidum | ||||
| Chlamydiales | Chlamydiaceae | Chlamydia pneumoniae Chlamydia muridarum Chlamydia trachomatis | |||
| Archaea | Euryarchaeota | Halobacteriales | Halobacteriaceae | Halobacterium sp | |
| Thermococcales | Thermococcaceae | Pyrococcus horikoshii Pyrococcus abysii | |||
| Thermoplasmales | Thermoplasmaceae | Thermoplasma volcanicum Thermoplasma acidophilum | |||
| Archaeoglobales | Archaeoglobaceae | Archaeglobus fulgidus | |||
| Methanococcales | Methanococcaceae | Methanococcus janascii | |||
| Methanobacteriales | Methanobacteriaceae | Methanobacteria thermoautotrophicum | |||
| Crenarchaeota | Desulfurococcales | Desulfurococcaceae | Aeropyrum pernix | ||
| Sulfolobales | Sulfolobaceae | Sulfolobus solfataricus Sulfolobus tokodaii | |||
[i] References for the genomes can be found in the Web page of genomes at EBI (http://www.ebi.ac.uk/genomes/index.html)