Additional file 5. The 100 features describing each organism which were used in the search for
the phenotypes predictive of the changes in translation efficiency within COGs. All features are
binary variables, and can be undefined for some organisms. 70 features describing the phylogeny
(left/middle columns) and the 6 features describing genome size and GC content (right column, top)
are included to ensure that correlations detected with the remaining 24 features (phenotypes, right
column) could not be explained by the phylogeny or the genomic size/GC. "#pos" is the number of
organisms marked as positive for the feature, and "#neg" as negative.
domain / phylum /
class
#pos
#neg
domain: Archaea
domain: Bacteria
phylum: Actinobacteria
85
826
97
826
85
813
phylum: Bacteroidetes
phylum: Chlamydiae
phylum: Chlorobi
phylum: Chloroflexi
34
8
10
15
876
902
900
895
order
(taxonomy)
#pos
#neg
Actinomycetales
Alteromonadales
Bacillales
83
28
46
801
856
838
Bacteroidales
Bifidobacteriales
Burkholderiales
Campylobacterales
10
6
47
18
874
878
837
866
genomic features
G+C: above median(>47.5%)
G+C: high(>59.9%)
G+C: low(<37.6%)
Genome size: above
median(>3.2Mb)
Genome size: large(>4.8Mb)
Genome size: small(<2Mb)
23
28
887
882
Chlamydiales
Chlorobiales
8
10
876
874
phenotypes
10
58
900
852
Chroococcales
Clostridiales
20
37
864
847
phylum: Firmicutes
145
765
Desulfovibrionales
8
876
phylum: Proteobacteria
383
527
Enterobacteriales
46
838
phylum: Spirochaetes
phylum: Tenericutes
phylum: Thermotogae
17
28
11
893
882
899
Flavobacteriales
Halobacteriales
Lactobacillales
14
12
36
870
872
848
class: Actinobacteria
97
775
Legionellales
3
881
107
82
10
68
8
10
61
10
33
22
765
790
862
804
864
862
811
862
839
850
Methanococcales
Mycoplasmatales
Neisseriales
Pasteurellales
Prochlorales
Pseudomonadales
Rhizobiales
Rhodobacterales
Rickettsiales
Spirochaetales
9
22
5
10
1
18
47
12
25
17
875
862
879
874
883
866
837
872
859
867
14
858
5
879
152
720
Sulfolobales
Thermoanaerobacterales
20
864
class: Halobacteria
12
860
Thermococcales
8
876
class: Methanococci
9
863
Thermotogales
11
873
14
28
17
23
11
858
844
855
849
861
Thiotrichales
Vibrionales
Xanthomonadales
4
9
8
880
875
876
Gram Stain=positive
Growth in groups
Habitat=aquatic(pos) vs.
terrestrial(neg)
Habitat=free-living(pos) vs.
hostAssociated(neg)
Habitat=multiple(pos) vs.
single(neg)
Halophilic
Motility
Oxygen = aerotolerant (pos) vs.
strictly anaerobic (neg)
Oxygen = facultative aerobe (pos)
vs. strict aerobe (neg)
Psychrophilic
Radioresistance
Shape = coccus (pos) vs. rod (neg)
Thermophilic
Pathogenic in plants
Pathogenic in mammals
Mammalian pathogen = blood
Mammalian pathogen =enteric
Mammalian pathogen = heart
Mammalian pathogen = nervous
system
Mammalian pathogen =
oportunistic/nosocomial
Mammalian pathogen = oral
cavity
Mammalian pathogen =
respiratory
Mammalian pathogen = skin/soft
tissues
phylum: Crenarchaeota
phylum: Cyanobacteria
phylum: DeinococcusThermus
phylum: Euryarchaeota
class: α-proteobacteria
class: Bacilli
class: Bacteroidia
class: β-proteobacteria
class: Chlamydiae
class: Chlorobia
class: Clostridia
class: Deinococci
class: δ-proteobacteria
class: ε-proteobacteria
class: Flavobacteria
class: γ-proteobacteria
class: Methanomicrobia
class: Mollicutes
class: Spirochaetes
class: Thermoprotei
class: Thermotogae
Endospores
#pos
#ne
g
425
235
188
387
576
624
454
226
195
443
671
702
#pos
#ne
g
75
337
216
61
466
228
167
71
238
222
190
40
379
587
140
231
514
214
217
25
16
105
142
23
163
35
31
8
296
760
887
506
643
304
166
128
132
155
17
146
16
147
8
155
43
120
24
139