Bacterial Membership of Tryptophan Cohesion Groupsa

Cohesion Group Congruent with 16S rRNA Expectations Intruder Membersb Expected Members Absentc

Lower-gamma Proteobacteria
Actinobacillus actinomycetemcomitans
Buchnera aphidicolad
Blochmannia floridanusd
Erwinia carotovora
Escherichia coli
Haemophilus influenzae
Klebsiella pneumoniae
Pasteurella multocida
Photorhabdus luminescens
Salmonella enterica
Shewanella putrefaciens
Shigella flexneri
Vibrio cholerae
Vibrio parahaemolyticus
Vibrio vulnificus
Yersinia pestis

Corynebacterium diphtheriae (see TrpCG-5)
Corynebacterium glutamicum (see TrpCG-5)
Corynebacterium efficiens (see TrpCG-5)
Helicobacter pylori (see Orphan Group)

Upper-gamma Proteobacteria
Beta Proteobacteria
Acinetobacter sp.
Azotobacter vinelandii*
Bordetella parapertussis
Bordetella pertussis
Burkholderia fungorum
Chromobacterium violaceum
Methylococcus capsulatus
Microbulbifer degradans
Neisseria gonorrhoeae
Neisseria meningitidis
Nitrosomonas europaea
Pseudomonas aeruginosa*
Pseudomonas fluorescens*
Pseudomonas putida*
Pseudomonas syringae*
Psychrobacter sp.
Ralstonia metallidurans
Ralstonia solanacearum
Thiobacillus ferrooxidans
Xanthomonas axonopodis
Xanthomonas campestris
Xylella fastidiosa


Alpha Proteobacteria
Agrobacterium tumefaciens
Bradyrhizobium japonicum
Brucella melitensis
Brucella suis
Caulobacter crescentus
Rhizobium loti
Rhodobacter sphaeroides
Rhodopseudomonas palustris
Sphingomonas aromaticivorans
Sinorhizobium meliloti


Anabaena sp. PCC 7120
Anabaena variabilis ATCC 29413
Crocosphaera watsonii WH 8501
Gloeobacter violaceus PCC 2471
Nostoc punctiforme
Prochlorococcus marinus CCMP1375 (SS120)
Prochlorococcus marinus CCMP1986 (MED4)
Prochlorococcus marinus MIT9313
Synechococcus sp. WH8102
Synechococcus elongatus PCC 7942
Synechocystis sp. PCC 6803
Thermosynechococcus elongatus BP-1
Trichodesmium erythraeum


Bifidobacterium longum
Mycobacterium avium
Mycobacterium bovis
Mycobacterium leprae
Mycobacterium smegmatis
Mycobacterium tuberculosis
Streptomyces avermitilis
Streptomyces coelicolor
Thermomonospora fusca

  Corynebacterium diphtheriae (see TrpCG-1)
Corynebacterium glutamicum (see TrpCG-1)
Corynebacterium efficiens (see TrpCG-1)


Low-GC Gram-positives_1
Bacillus halodurans
Bacillus stearothermophilus
Bacillus subtilis
Oceanobacillus iheyensis


Low-GC Gram-positives_2
Bacillus anthracis
Bacillus cereus
Lactococcus lactis
Listeria innocua
Listeria monocytogenes
Staphylococcus aureus
Staphylococcus epidermidis
Streptococcus gordonii
Streptococcus mutans
Streptococcus pneumoniae

Aquifex aeolicus VF5
Campylobacter jejuni
Chlorobium tepidum
Clostridium acetobutylicum
Cytophaga hutchinsonii ATCC 33406
Dehalococcoides ethenogenes
Desulfitobacterium hafniense DCB-2
Desulfovibrio vulgaris Hildenborough
Deinococcus radiodurans
Geobacter sulfurreducens PCA
Helicobacter hepaticus
Helicobacter pylori (see TrpCG-1)
Thermotoga maritima
Wolinella succinogenes

a Each tryptophan cohesion group (TrpCG) defined by the concatenated tree for Trp proteins (Figure) is congruent with the color-coded subtree section within the 16S rRNA tree (Figure). Organisms that are included in the concatenated tree are indicated in regular type, whereas additional organisms not included in the concatenated tree but that were qualitatively determined to belong to a given TrpCG are indicated in boldface type. 
b Intruder Members are sequences that belong to the cohesion group, but whose presence there (probably, but not necessarily, due to LGT) is incongruent with vertical genealogical expectations, as guided by 16S rRNA trees.
c Expected Members are sequences from organisms whose inclusion in the group would be predicted on the criterion of a vertical genealogy, i.e., matching 16S rRNA subtrees.
d Insect symbionts. 
e The five organisms marked with asterisks(*) form a distinctive subclade that is, in fact, not a “pure” component of TrpCG-2 because of the LGT origins of trpEa and trpEb from TrpCG-3 [Ref].
All members of TrpCG-5 lack trpC and presumably utilize [Ref] a dual-pathway hisA (priA) for this function.

L O S   A L A M O S   N A T I O N A L   L A B O R A T O R Y • Est 1943
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