Compilation of small ribosomal subunit RNA structures€¦ · TAXONOMIC CLASSIFICATION OF SPECIES For the Eukarya, the taxonomic classification of the species listed in Table 1 is

© 1993 Oxford University Press Nucleic Acids Research, 1993, Vol. 21, No. 13 3025-3049

Compilation of small ribosomal subunit RNA structures

Jean-Marc Neefs, Yves Van de Peer, Peter De Rijk, Sabine Chapelle and Rupert De Wachter*Departement Biochemie, Universiteit Antwerpen (UIA), Universiteitsplein 1, B-2610 Antwerp, Belgium

ABSTRACT

The database on small ribosomal subunit RNA structurecontained 1804 nucleotlde sequences on April 23,1993. This number comprises 365 eukaryotlc, 65archaeal, 1260 bacterial, 30 plastldial, and 84mttocnondrial sequences. These are .stored In the formof an alignment in order to facilitate the use of thedatabase as input for comparative studies on higher-order structure and for reconstruction of phylogenetlctrees. The elements of the postulated secondarystructure for each molecule are Indicated by specialsymbols. The database Is available on-line directly fromthe authors by ftp and can also be obtained from theEMBL nucleotlde sequence library by electronic mall,ftp, and on CD ROM disk.

CONTENTS OF THE DATABASE

The database on small ribosomal subunit RNA (furtherabbreviated as SSU rRNA) currently contains 1804 nucleotidesequences, stored in the form of an alignment and containing thepostulated secondary structure pattern in encoded form. Thisnumber comprises 365 eukaryotic cytoplasmic, 65 archaeal, 1260bacterial, 30 plastidial, and 84 mitochondrial SSU rRNAs. Partialsequences are included if the combined length of the sequencedsegments corresponds to homologous segments in Escherichiacoli SSU rRNA amounting to at least 70% of the chain lengthof the latter molecule.

Previous compilations (1-5) included a table listing for eachentry the species name, further specifications such as the strain,variety, or tissue used for isolation of the gene, taxonomicposition of the species, length and completeness of the sequence,and accession number in nucleotide sequence libraries. Completeliterature references were also included for each entry. Becausethe number of available structures has nearly doubled sincepublication of the preceding compilation (5), such a table andthe accompanying references would now require an estimated20 pages just to cover the additional structures entered in thedatabase during the last year. Table 1 has therefore been restrictedto a list of the names of species for which the SSU rRNA structureis recorded in the database. However, this list covers all thestructures now filed, not just those added since the precedingcompilation. Instructions for obtaining the complete tableincluding further specifications and literature references,separately or together with the structural data, are given below.

TAXONOMIC CLASSIFICATION OF SPECIES

For the Eukarya, the taxonomic classification of the species listedin Table 1 is according to Brusca and Brusca (6) for the Animalia,according to Cronquist (7) for the higher plants, according toAinsworth et al. (8) for the higher fungi, and according to Corliss(9) for the remaining eukaryotes.

For the Bacteria and the Archaea, the classification followedis based on the phylogeny described by Woese and coworkers(10—12). However, the assignment of a species to one of thetaxa distinguished by these authors is often problematic. To ourknowledge there does not exist a list assigning each bacterial orarchaeal species to one of the divisions or subdivisions that theydistinguish. Moreover, many sequences now become availablethrough deposition in one of the nucleotide sequence libraries,which in many cases is not (yet) accompanied by publication ina journal. The bacterial and archaeal SSU rRNA sequencesdeposited in these libraries are accompanied by a taxonomicdescription which does not correspond to that of Woese et al.(10-12) but is based on Bergey's Manual of SystematicBacteriology (13). Even the sequences described in the literatureare not always accompanied by an assignment of the species toone of the taxa distinguished by Woese and coworkers. In orderto obtain a more or less consistent classification, we havetherefore constructed an evolutionary tree from the alignmentof all archaeal, bacterial, and plastidial SSU rRNA sequences,1355 in total. The method followed for constructing the tree hasbeen described in detail elsewhere (14). In short, a dissimilaritymatrix was computed, corrected for multiple mutation (15), anda tree derived by neighbour-joining (16). The outline of theresulting tree is shown in Fig. 1. Most of the clusters visible inthe tree correspond to the archaeal and bacterial divisions andsubdivisions distinguished by Woese and coworkers (10-12).However, in the bacterial subtree, the genera Fibrobacter andFusobacterium do not integrate in any of the clusters. They aretherefore listed separately in Table 1.

It should be noted that the evolutionary distances between thebranching points leading to the clusters visible in the tree of Fig. 1are very small, especially for the major clusters of the Bacteria.Trees such as this one were constructed periodically as the SSUrRNA sequence alignment grew in size. Although the clustersindicated in Fig. 1 were reproducibly formed, the branching orderof these clusters was not constant but changed as a function ofthe composition of the sequence collection. However, the treecan serve to assign bacterial species to a given division orsubdivision because, although the relative position of the clusters

• To whom correspondence should be addressed

3026 Nucleic Acids Research, 1993, Vol. 21, No. 13

is variable, the appurtenance of each bacterial species to aparticular cluster is stable.

In Table 1, for the Bacteria, no hierarchical distinction is madebetween divisions (e.g. the spirochetes) and subdivisions (e.g.the a, /3, y, 6, and e subdivisions of the division Proteobacteria).This is because the subdivisions do not always form together amonophyletic cluster. As an example, in the tree of Fig. 1, theProteobacteria e group is separated from the monophyletic clusterformed by me Proteobacteria a, /3, y and 5 groups. As for thedivision of Gram positive bacteria and relatives, its twosubdivisions of high and low GC contents almost never formtogether a monophyletic cluster in the trees that we obtain. Forme Archaea, on the contrary, a distinction is made between thedivisions Crenarchaeota and Euryarchaeota (12). The latterdivision is subdivided into 8 subdivisions. Of these, theMethanobacteriales, Methanococcales, Thermococcales andMethanopyrales correspond to lineages distinguished by Olsenand Woese (12). The Methanomicrobiales group of the latterauthors comprises the Methanomicrobium group, theHalobacteria, and Archaeoglobus fulgidus in the tree of Fig. 1.

SECONDARY STRUCTURE MODELProkaryotic and eukaryotic models, nucleotide variabilityFig. 2 shows the prokaryotic secondary structure model,applicable to SSU rRNAs from archaea, bacteria, plastids, andmitochondria. The model of Fig. 3 applies to eukaryoticcytoplasmic SSU rRNAs. In contrast to the corresponding figuresin the preceding compilation (5), the models shown in Fig. 2and 3 do not simply distinguish between conserved and variableareas, but give a more detailed description of the variability ofeach site. The latter is defined as the ratio of the substitution rateat die considered site to me average substitution rate for the entiremolecule. The quantitative derivation of the variability of eachsite from the sequence alignment is described in detail elsewhere(17). Sites that are absolutely conserved, and those that areoccupied only in a limited number of SSU rRNAs, are indicatedby special symbols. The remaining ones were partitioned intofive equally large categories of increasing variability. In Fig. 2and 3, such sites are represented by dots with a diametercommensurate with their variability. Variable areas previouslydistinguished on a more intuitive basis and indicated on thegeneral secondary structure models of the preceding compilation(5) are still shown on Figg. 2 and 3 as VI to V9.

Helix numbering system and changes made to the modelsHelices are given a different number if separated by amultibranched loop (e.g. helices 9 and 10), by a pseudoknot loop(e.g. helices 1 and 2), or by a single stranded area that does notform a loop (e.g. helices 2 and 32). A single number is attributedto 50 'universal' helices, which are present in all hitherto knownSSU rRNAs from Archaea, Bacteria and plastids. They are alsopresent in all known eukaryotic SSU rRNAs except in those ofMicrosporidia, where some of these helices are missing. Thenumber of universal helices has risen from 48 in the precedingcompilation (5) to 50 because the tertiary interaction describedby Woese and Gutell (18) has been taken into account. Thisinteraction effectively transforms the helix previously numbered19 into three helices now numbered 19 to 21.

Helices specific to me prokaryotic model (Fig. 2) are givencomposite numbers of the form Pa-b, where a is the number of

the preceding universal helix and b sequentially numbers allhelices inserted between universal helices a and a + 1 . Helicesspecific to the eukaryotic model (Fig. 3) are similarly numberedEa-b . In Figg. 2 and 3, not all eukaryote- and prokaryote-specific helices that are encountered in various species areindicated, because these models in fact have the shape of theEscherichia colt and Saccharomyces cerevisiae SSU rRNAsecondary structure models, respectively. As an example, inDrosophila melanogaster SSU rRNA, the loop separating helicesE23-2 and E23-5 is a multifurcation bearing two more helicesnumbered E23-3 and E23-4 (5). These and other supernumeraryhelices that are present in a minority of SSU rRNAs are notindicated in Figg. 2 and 3, one of die reasons being that thevariability of the sites composing such helices cannot be computedin a dependable manner. However, in Table 2 the presence orabsence of eukaryote specific helices in SSU rRNAs of differenttaxa is summarized.

Mitochondrial SSU rRNAs, mough mey can be described bydie prokaryotic model, show extreme variability in length,ranging from about 600 nucleotides in flagellates to about 2000nucleotides in plants. This coincides with die absence of severaluniversal helices in the smaller molecules and widi the presenceof extra helices of the P-series in the larger ones. A tentativehelix occupancy table for mitochondrial SSU rRNAs andexamples of secondary structure models can be found in aprevious compilation (4). The alignment of, and transpositionof secondary structure models to, mitochondrial SSU rRNAs isless dependable than for other SSU rRNAs, not only becauseof the variability in length, but also because some of themitochondrial sequences are very monotonous due to their highAU contents.

Examples of secondary structure modelsFigg. 4 to 7 are examples of secondary structure models appliedto specific SSU rRNA sequences. Fig. 4 represents the SSUrRNA of die bacterium Escherichia coli, whereas die SSU rRNAof me halophilic archaebacterium Halobacterium halobium isshown in Fig. 5. The eukarya are represented by me structureof SSU rRNAs of the red alga Palmaria palmata in Fig. 6, andof the polymastigote Giardia duodenalis in Fig. 7. The lattermodel is shown as an example of a molecule possessing arestricted number of helices in variable areas V2 (helices 9 to11) and V4 (helices E23-n). Finally, an example of a model foran animal mitochondrial SSU rRNA is shown in Fig. 8.

COMPLETENESS, ACCURACY, AND AVAILABILITY OFTHE DATA

SSU rRNA sequences deposited in the GenBank and EMBLnucleotide sequence libraries are obtained weekly from the EMBLfile server by electronic mail. By means of an appropriate setof programs, each new sequence is aligned with die most closelyrelated one already present in me alignment, the secondarystructure pattern is transposed to the newly aligned sequence,and die complementarity of die postulated secondary structureelements is checked. Manual corrections are made if necessaryby means of a specially developed editor. Finally, me newlyaligned sequence is automatically compared with the originalrecord in order to eliminate any errors that might have beenintroduced during editing of the alignment.

Nucleic Acids Research, 1993, Vol. 21, No. 13 3027

Files containing all the SSU rRNA sequences present in ourdatabase are available in the following three formats.

1) The sequences, listed one by one, written continuouslywithout the gaps needed for alignment and withoutindication of secondary structure elements.

2) The sequences, listed one by one, but with nucleotidesymbols interspersed with the gaps necessary for alignment.In this file, each sequence covers 4807 positions, whichis the present length of the complete alignment of alleukaryotic, archaeal, bacterial, and organellar sequences.

3) The sequences, listed in the form of an alignment withindication of the secondary elements. The alignment isdivided into 49 pages each comprising 100 positionscontaining a nucleotide or a gap. These positions alternatewith an equal number of positions that are either blank orcontain a symbol indicating the beginning or end of asecondary structure element. The secondary structure modeladopted for each SSU rRNA sequence, is completely definedin this file.

In addition, there are files containing a taxonomic list of speciesfor which the SSU rRNA sequence is known, plus further dataas listed in Table 1 of the previous compilation (5) and literaturereferences, and a file containing general documentation on thedatabase.

These files will be made available through 'anonymous ftp'on host uiam3.uia.ac.be (143.169.8.1). The files, as well as laterupdates, will also be made available to the EMBL nucleotidesequence library at Heidelberg for distribution on their file serverand on their CD-ROM disk. Due to the increasing volume ofthe database, copying it onto diskettes is getting cumbersome.However, researchers who do not have access to theaforementioned distribution channels can address requests forobtaining specific parts of the database on magnetic media to theauthors in writing or by sending an electronic mail message [email protected] or to [email protected].

ACKNOWLEDGEMENTSOur research is supported by the BRIDGE programme of theCommission of European Communities (contract BIOT-CT91-0294), by the Programme on Interuniversity Poles ofAttraction of the Office for Science Policy Programming of theBelgian State (contract 23), and by the Fund for CollectiveFundamental Research. P.De Rijk is research assistant of theNational Fund for Scientific Research.

REFERENCES1. Huysmans.E., De Wachter.R. (1986), Nucleic Adds Res. 14, r73 - r l l7 .2. Dams.E., Hendriks.L., Van de Peer.Y., NeefsJ.M., Smits.G.,

VandenbempU., De Wachter.R. (1988), Nucleic Adds Res. 16, r87-rl73.3. NeefeJ.-M., Van de Peer,Y., Hendriks.L., De Wachter.R. (1990), Nucleic

Adds Res. 18, 2237-2317.4. NeefeJ.-M., Van de Peer.Y., De Ryk,P., Goris A , De Wachter.R. (1991),

Nucleic Acids Res. 19, 1987-2015.5. De Rijk.P., NeefsJ.-M., Van de Pecr.Y., De Wachter.R. (1992), Nucleic

Adds Res. 20, 2075-2089.6. Brusca.R.C, Brusca.G.J. (1990), Invertebrates, Sinauer Associates, Inc.,

Sunderland.7. Cronquist.A. (1971), Introductary Botany, Harper & Row, New York.8. Ainsworth.G.C, Sparrow.F.K., Sussman.A.S. (1973), The Fungi: an

Advanced Treatise, Academic Press, New York, Vol. 4A.9. Corliss J.O. (1984), BioSystems 17, 8-126.

10. Woese.C.R. (1987), Micmbiol Rev. 51, 221-271.11. Woese.C.R. (1991), in Selander, R.K., Clark.A.G., Whittam.T.S. (eds.),

Evolution at the Molecular Level. Sinauer Associates, Inc., Sunderland, pp.1-24.

12. Olsen.G.J., Woese.C.R. (1993), FASEB. J. 7, 113 — 123.13. HolU.G. (1984, 1986, 1989) Bergey's Manual of Systematic Bacteriology,

Williams & Wukins, Baltimore, Vol. 1 - 4 .14. Van de Peer.Y., NeefsJ.-M., De Wachter.R. (1990), J. MoL EvoL 30,

463-476.15. Jukes.T.H., Cantor.C.R. (1969) in Munro.H.N. (ed.). Mammalian Protein

Metabolism. Academic Press, New York, pp. 21-132.16. Saitou.N., Nei.M. (1987), MoL BioL EvoL 4, 406-425.17. Van de Peer.Y., NeefeJ.-M., De Rijk.P., De Wachter.R. (1993), J. MoL

EvoL, in press.18. Woese.C.R., GuteU.R.R. (1989), Proc. NatL Acad. Sd. USA 86,

3119-3122.

Table 1. List of species for which the SSU rRNA structure is recorded in the database*.

EUKARYAANIMALIA

CHORDATAVERTEBRATA

MAMMALIAHomo sapiens 1Homo sapiens 2Homo sapiens 3Mus musculusOryctolagus cuniculusRattus norvegicus 1Rattus norvegicus 2

AVESGallus gallusTurdus migratorius

REPTILIAAlligator mississippiensisHeterodon platyrhinosPseudemys scriptaSceloporus undulatus

AMPHIBIAAmbystoma mexicanumAmphiuma tridactylumBufo vaUkcps

Discoglossus pktusEleutberodactylus cuneatusGastrophryne carolinensisGrandisonia alternansHyla cinereaIchthyophis bannanicusNesomantis thomassetiPkthodon yonhalosseeScaphiopus holbrookiSiren intermediaTyphlonectes natansXenopus borealisXeoopus laevis

OSTEICHTYESFundutus heteroclitus

Sebastolobus aMvelis

CHONDRICHTYESEchinorhinus cookeiRhinobatos lentigmosusSqualuS ftranthias

AGNATHAEptatretus stoutiLampetra aepyptera


Table 1. continued

Myxine glutinosaPetromyzon marinus

UROCHORDATAHerdmania momusStyda plicata

CEPHALOCHORDATABranchiostoma floridae

CHAETOGNATHASagitta elegans

ARTHROPODAINSECTA

Acyrtbosiphon pisumAedes albopictusDrosophila melanogasterTenebrio molitor

CHEUCERATAAmblyomma americanumEurypelma californica

MALACOSTRACAArgulus nobilisArtemia salinaCallinectes sapidusOedignathus isennisPalaemonetes ltadialrmsi*Penaeus aztecusProcambarus leonensisRaninoides kmisianensisStenopus hispidus

PENTASTOMIDAPorocephalus crotali

NEMATODASECERNENTEA

Caenorhabditis elegansHaemonchus contortusHaemonchus placeiHaemonchus similisStrongylokles stereora] is

PLATYHELMENTHESTREMATODA

Opisthorchis viverriniSchistosoma haematobiumSchistosoma japonicumSchistosoma mansoni 1Schistosoma mansoni 2Schistosoma spindale

TURBELLARIABothromesostoma personatumCrenobia alpinaDendrocoelum lacteumDugesia mediterranea

MOLLUSCABIVALVIA

Crassostrea virginicaPlacopecten magellanicus

GASTROPODALimicolaria kambeul

POLYPLACOPHORAAcanthopIeuTa japonica

ACANTHOCEPHALAARCHIACANTHOCEPHALA

Moliniibrmis moliniformis

CNTOARIAANTHOZOA

Anemonia sulcata

PLANTAEMAGNOUOPHYTA

LIUOPSIDAOiyza sativaZea mays

MAGNOUOPSTOAAlnus glutinosaArabidopsis th l'3"^Bucldeya distichophylJaBuxus sempervirensClematis rehderianaConius floridaComus racemosaDendrophthora domingensisEuonymusFragariaGlycine maxHedera helixHydrocotyle sibthorpioidesLycopersicon esculentumMacadamia teraifoliaNyssa sylvaticaPboradeDdron serotinumSchoepfia areoariaSioapis alba 1Sinapis alba 2

PESOPHYTACYCADOPSTOA

Podocarpus fakatusPodocarpus beokelliiZamia pumila

FUNGIZYGOMYCOTINA

Endogone pisiformisGigaspora margaritaGlomus intraradkesMucor racemosus

ASCOMYCOTINAHEMIASCOMYCETES

Ctndida albicans 1Candida albicans 2Candida glabrata 1Candida glabrata 2PpnHirig parapsilosisCandida tropicalis 1Candida tropicalis 2Candida viswanathhClavispora lusitaniae 1Clavispora lusitaniae 2Debaryomyces hansenii 1Debaryomyces hansenii 2Dekkera bruxdlensisDipodascus albidusEndomyces fibuligerGalactomyces geotrichumHanseniaspora uvarumIssatchenlcia orientalis 1Issatchenkia orientalis 2Kluyveromyces lactis 1Kluyveromyces lactis 2Kluyveromyces polysporusMetschnScowia bicuspidataPichia angustaPichia anomalaPichia membranaefaciensSaccharomyces cerevisiaeSaccharomveodes ludwigii


Saccharotnycopsis capsularisToruLaspora delbrueclriiWaltomyccs lipofcrYamadazyma guflHeiiuuudiiYarrowia lipolyticaZygosaccharomyces rouxii

EUASCOMYCETESAscospfaaera apis 1Ascosphaera apis 2Aspergillus fumigatus 1Aspergillus fumigatus 2AspagQlus fumigatus 3Aureobasidium pullulansByssochlamys niveaChactomium ^lntumCoccidioides immMs 1Coccidioidcs immiti* 2Emmonsiella capsulataEremascus albusExophiala dermatidis 1Exophiala dermatidis 2Exophiala dennatidis 3CHomerella cingulataHypomyccs chrysospennusLeucostoma persooniiMonascus purpureusNeurospora crassaOpfaiostoma schenclriiOphiostoma stenocerasOphiostoma ulmiPcnicilium notatumPodospora anscrinaPseudallescheria boydiiSclerotinia sclerotiorumSordaria fimkolaTalaromyccs flavusTaphrina defonnansThermoascus crustaceusTrichophyton rubnun

UNCERTAIN AFFILIATIONPneumocystis cariniiSchizosaccharomyccs pombe 1Schizosaccharomyces pombe 2

BASIDIOMYCOTINAUSTOMYCETES

Leucosporidium scottiiRhodosporidium toruloides 1Rhodosporidhim toruloides 2Sporobolomyccs roseusUstilago maydis

TRUE BASIDIOMYCETESAthelia bombacinaBoletus satanasBulleromyces albusCoprinus cinereusCronartium ribkolaFilobasklklla neoformans 1Filobasidiella neoformans 2Filobasidiella neoformans 3Microascus CUTOSUSSpongipellis unicolorThanatepbonis praticolaTrichosporon cutaneumXerocomus chryseoteron

PROTISTAASSEMBLAGE CHLOROBIONTS

CHLOROPHYTA

Asteromonas gracilisCharacium hindakiiCharacium perforalumCharacium saccatum

Characium vacuolatumChlamydontoBas FemhardtiiChlorefla ellipsoideaChlorella fuscaChloreHa kessleriChlorella lobopboraChlorella tninutissiniaChloitHa prototbecoidesChlorella saccharophilaChlorella sorokmianaChlorella vulgarisChlorococcopsis minutaColeochaete scutataColeochaete oibkularisDunaliella parvaDunalidla saUnaFriedmannia israclieosisHydrodictyon reticulatumKlebsormidium flaccidumNanochloium eucaryotumNeochloris aquaticaNeochloris vigeoisParietochloris pseudoalveolarisPediastrum duplexPrototheca wkkerhamiiProto«heca zopfiiScenedesmus obliquusSpermatozopsis similisTetrasdmis striataTrcbouxia impressaTrebouxia magnaTrebouxia asymmetricaVolvox caiteri

CHAROPHYTAChlorokybus atmophyticusNitella sp.

ASSEMBLAGE CHROMOBIONTSCHRYSOPHYTA

Hibberdia magnaMallomonas papillosaMallomonas striataOchromonas dankaSynura spinosa

DINOPHYTAAlexandrium tamarense•Emilinnin huxleyi 1Emuiania huxleyi 2Symbiodinium microadriaticumSymbiodinium pilosumSymbiodinium sp.Tribonema aequale

PHAEOPHYTACostaria costataPucus gardneriBacillaria paxilliferCylindrocheca closteriumNannochloropsis salinaNhzschia apkulataRhizosolenia setigeraSkeletonetna costatumStephanopyxis broschii

ASSEMBLAGE CILIATESCmOPHORA

Blepharisma amcricanumColpidium campylumColpoda infktaEuplotes Rfdkiilft 11*1

Glaucoma chattoniMetopus palaeformisOnychodromus quadricomutusOpisthonecta hameguyiOxytricha granulifera


Table 1. continued

Oxytricha novaParamecium tetraureliaStylonychia pustulataTetrahymena australisTetrahymeoa borcalisTetrahymena canadensisTetrahymena capricomisTetrahymena hegewischiTetrahymena hyperangularisTetrahymena malaccensisTetrahymena nanneyiTetrahymena patulaTetrahymena pigmentosaTetrahymena pyriformisTetrahymena thermophila 1Tetrahymena thermophila 2Tetrahymena tropkalis

ASSEMBLAGE CRYFTOMONADSCRYPTOPHYTA

Cryptomonas phi 1Cryptomonas phi 2Pyrenomonas salina 1Pyrenomonas salina 2

ASSEMBLAGE DEVOFLAGELLATESPERIDINEA

Crypthecodinium cohniiCryptosporidium muris 1Cryptosporidium muris 2Cryptosporidium parvum 1Cryptosporidium parvum 2Prorocentrum mkans

ASSEMBLAGE EUGLENOZOAEUGLENOPHYTA

Euglena gracilis

HNE T OPL A ST IDE ABodo H^îarusCrithjdia fasciculataEndotrypanum monterogeiiT i hrnflnifl amazonensisLeiahmania brasiliensis

donovanimajortarcntolae 1

Leishmania tarentolae 2Leptomooas sp.Tritrichomonas foetusTrypanosoma brucciTrypanosoma cruzi 1Trypanosoma cruzi 2

ASSEMBLAGE MASTIGOMYCETESCHYTREDIOMYCOTA

Blastocladiella emersoniiChytridium confervaeNeocallimastix fromalisNeocallimastix joyoniiNeocallimastix sp.Piromonas communisSpizellomyces acuminatusAchlya bisexualisLagemdfum gigqnf^nnPhytophthora megasperma 1Pnytophmora megasperma 2

ASSEMBLAGE MICROSPORIDIAMICROSPORIDIA

Encephalitozoon cunuculiVairimorpha necatru

ASSEMBLAGE POLYMASTIGOTESGiardia ardeaeGiardia intestinalis

Giardia duodenahsGiardia muris

ASSEMBLAGE RHIZOPODSAMOEBOZOA

Acanthamoeba cflffTfllflnii 1Acanthamoeba castellanii 2Acanthamoeba palestinensisEntamoeba histolyticaHartmannella vermiformis 1Hartmannella vermiformis 2Naegleria gruberiParatetramitus jugosusTetramitus rostratusVahlkampfia lobospinosa

EUMYCETOZOADictyostelium discoideurcPhysarum polycephalum

ASSEMBLAGE RHODOPHYTESRHODOPHYTA

Gracilaria lemaneiformisGracilaria tilcvahiaeGracilaria vermcosaGracilariopsis sp.Palmaria paimntn

ASSEMBLAGE SPOROZOAAPICOMPLEXA

Babesia bigemina 1Babesia bigemina 2Babesia bigemina 3Babesia bovisBabesia caballiBabesia equiBabesia rodhainiPlasroodium berghei 1Plasmodkim berghei 2Plasmodium cynomolgi 1Plasmodium cynomolgi 2Plasmodium falciparum 1Plasmodium falciparum 2Plasmodium fragilePlasmodium gallinaceumPlasmodium lophuraePlflsmodiurQ malariaePlasmodium vrvaxSarcocystis murisTheileria annulataTbeileria buffeh'Theileria parvaToxoplasma gondii

ARCHAEA

EURYARCHAEOTAHALOBACTERIA

Halobacterium curirubrumHalobacterium halobiumHalobacterium marismortui 1Halobacterium marismortui 2Halobacterium volcanhHalobacterium sp.Halococcus morrhuae 1 ATCC 17082Halococcus morrhuae 2 NRC 16008, NCMB 746Haloferax mediterranei ATCC 33500Natronobacterium magadii NCMB 2190

METHANOBACTERIALESMethanobacterium bryanliiMelhanobacterium fbnnicicum DSM 1312Methanobacterium thermoautotrophicum 1Methanobacterium thennoautotrophkum 2Methanobacterium thennoformicium 1Methanobacterium thennoformicium 2


Methanobacterium thermoformicium 3Methanobacterium thermofonnicium 4Methaoobacterhnn thennofbrmicium SMediaoobacterium thermofoiinicnim 6Methanobacterium thermofomucium 7Methanobacterium thennoformicium 8MethaDobacterium thermoformicium 9Methanobrevibacter arboriphilusMethanosphaera stadtmaniiMethanothermus fervidus 1Methanotbermus fervidus 2

METHANOCOCCALESMethanococcus igneus DSM 5666Methanococcus jannaschiiMethanococcus thennolithotrophicusMethanococcus voltaeMethanococcus vannielii

METHANOMICROBIUM GROUPMethanocoipusculum parvum DSM 3823Methanogenium cariaci DSM 1497Methanogenium marisnigri DSM 1498Methanogenium organophilum DSM 3596Methanogenium tbermophilum DSM 3915Methanohalophilus mahii DSM 5219Metbanohalophitus Thilmnf.Methanohalophilus sp. 1Methanohalophilus sp. 2 DSM 3243Methanolobus tindarius DSM 2278Methanomicrobiuin mobile DSM 1539Methanoplanus limicola DSM 2279Methanosaeta concilii DSM 3013Methanosaeta thermoacetophila DSM 3870Methanosarciaa acidivorans DSM 2834Methanosarcina barken DSM 1538Methanosarcina frisia DSM 3318Methanosarcina frisiusMethanosarcina thennophila DSM 1825Methanosarcina sp. DSM 4659Methanospirillum hungateiMethanothrix sochngeniiMethylcoccoides methylutens DSM 2657

THERMOCOCCALESTbeimococcus celer DSM 2476

THERMOPLASMAThermoplasma acidoprrilum

ARCHAEOGLOBALESArchaeoglobus fulgkius

METHANOPYRALESMethanopyrus kandleri DSM 6324

CRENARCHAEOTADesuUurococcus mobOisPyrodictium occultum DSM 2709Sulfolobus shibatae DSM 5389Sulfolobus soliataricusThennofihim pendens DSM 2475Thermoproceus tenax

BACTERU

PROTEOBACTERIA ALPHAAfipia clevelandeosisAfipU felis ATCC 53690Agrobacterium tume&ciens DSM 30105Anaplasma margiifflleAncylobacter aquaticus ATCC 25396Azospirillum lipofenimBangasternus onentalis esdosymbiontBartonella bacflliformis 1 ATCC 35685Baitonella bacillifonnis 2 NCTC 12138BaitoneUa bacillifonnis 3 ATCC 35685

Beijerinckia iodkaBlastobacter denitrifkans LMG 8443 (T)Bradyihizobium japonicum LMG 6138 (T)Brucella abortusCaulobacter bacteroidesCaulobecter crescentus 1Caulobacter crescentus 2Caulobacter crescentus 3Caulobacter subvibrioidesCaulobacter sp. 1Caulobacter sp. 2Caulobacter sp. 3Caulobacter sp. 4Caulobacter sp. 5Caulobacter sp. 6Caulobacter sp. 7Caulobacter sp. 8Caulobacter sp. 9Caulobacter sp. 10Cowdria ruminantium 1Cowdria ruminantium 2Ehrltchia canis 1Ehriichia canis 2Ehrlicnia chaftechsisEhriichia equiEhriichia ewingii 1Ehdichia ewingii 2Ehriichia phagocytophila 1Ehriichia phagocytophila 2Ehriichia risticiiEhriichia sennetsu 1Ehriichia sennetsu 2Erythrobacter longus 1Erytnrobacter longus 2Erythrobacter longus 3Erythrobacter sp.Flavobacterium capsulatumFlavobacterium devoransHirschia baltkaHyphomicrobium vulgareHyphomonas jannaschianaHyphomonas sp.Magnetite-containing magnetic vibrioMagnetospirillum gryphiswaldense DSM 6361Magnetospirillum magnetotacticum ATCC 31632Methylobacterium extorquens 1Methylobacterium extorquens 2Methylobacterium organophilumMethylobacterium sp. 1Methylobacterium sp. 2Methylobacterium sp. 3Methylocystis parvusMethylosmus sporiumMethylosinus trichosporiumMethylosinus sp. 1Methylosinus sp. 2Methylosporovibrio methanicusPorphyrobacter neustonemis 1Porphyrobacter neustonensis 2Pseudomonas rfiminiiMRhinocyllus conicus endosymbiontRhodobacter capsulatus 1Rhodobacter capsulatus 2Rhodobacter sphaeroides 1Rhodobacter sphaeroides 2Rhodobacter sphaeroides 3Roodomicrobium vannieliiRhodopseudomonas actdophilaRhodopseudomonas globiformisRhodopseudomonas marinaRhodopseudomonas palustrisRhodospirillum centenumRhodospiriUum fulvumRhodospirillum molischiasumRhodospirillum rubrumRhodospirillum salexigenesRhodospirillum salinarum


Table 1. continued

Rhodospirillum sodomenseRicketuia prowazekii BrienlRickettsia rickettsiiRickettsia typfai WilmingtonRochalimaea americaoaRochalimaea quintana 1Rochalimaea quintana 2Rochalimaea saintelizabethsinaRochalimaea vinsonii 1Rochalimaea vinsonii 2Roseooacter denhrificans 1Roscobacter denitrificans 2Simonsidla nmcUcriSitophilus oryzae endosymbiontWolbachia pipientisZoogloea ramigera

PROTEOBACTERIA BETAAlcaligenes eutrophusAlcaligenes faecalis ATCC 8750 (T)Alcaligenes xylosoxidans ATCC 15173 (T)BordeteUa bronchisepticaChroeDobacterium fluviatile ATCC 33051 (T)Chromobacterium violaceum ATCC 12472 (T)Eikenella corrodens 1 ATCC 23834 (T)Eikenella corrodens 2 FDC 373Eikenella coirodens 3 FDC 558Eikenella corrodens 4 FDC 1073Eikenella sp.Galljonella ferrugineaKingella denitrificans 1 ATCC 33394 (T)Kingella denitrificans 2Kingella Iringae ATCC 23330 (T)Kingella oraleLeptothrix discophoraMethylobacillus flayllnhimMethylobacillus glycogenesMethylomonas methanolicaMethylomonas methylovoraMethylophilus methylotrophusNeisseria flnirrmlisNeisseria cardsNeisseria denitrificans 1 ATCC 14686 (T)Neisseria denitrificans 2Neisseria elongata 1Neisseria elongata 2Neisseria flavescensNeisseria gonorrhoeae 1 NCTC 83785Neisseria gonorrhoeae 2Neisseria macacaNeisseria polysacchareaNkrosococcus mobilisNitrosolobus multifonnis 1Nitrosolobus multifonnis 2Nitrosomonas europaeNhrosomonas europaeaNitrosomonas eutrophaNrtrosovibrio tenuis 1Nitrosovibrio tenuis 2Nhrosovibrio tenuis 3Nitrospira bnensisPseudomonas cepacia ATCC 25416 (T)Pseudomonas testosteroni ATCC 11996Rhodocyclus gelatinosusRhodocyclus purpureusSphaCTOtiluS rintwry:

Spirillum volutans ATCC 19554 (T)Thiobacaius thioparus ATCC 8158Vitreoscflla stercoraria 1Vitreoscilla stercoraria 2Zoogloea ramigera 1Zoogloea ramigera 2Zoogloea ramigera 3

PROTEOBACTERIA GAMMA* b

Acinetobacter calcoaceticusAheromonas vaga ATCC 27119Arhodomonas oleiferhydransBacteroides nodosusBathymodiolus tbennophilus gill symbiontCalyptogena magnifica symbiontCardiobacteriuni hominis ATCC 16826 (T)Chromatium tepidumChromatium vinosum ATCC 17899Codakia orbicularis gill symbiontCoxklla bumetiiEctothiorhodospira halochlorisEctothiorhodospira halophilaEctothiorhodospira shaposhnikoviFlavobacterium halmophilumFlavobacterium hitescensHalomonas elongata ATCC 33173Kingella indologenes ATCC 25869 (T)Lcgiooella bozemanii NCTC 11368 (T)Legionella erythra NCTC 11977 (T)Legionella hackeliae NCTC 11979 (T)Legkraella longbeachae NCTC 11477 (T)Legionella maceachernii NCTC 11982Legionella micdadei NCTC 11371 (T)Legionella pneumophila 1 NCTC 11192 (T)LegkraeUa pneumophila 2 NCTC 11286Legionella pneumophila 3 NCTC 11233 (T)Legionella pneumophila 4 NCTC 11405Legionella pneumophila 5Legionella spiritensis NCTC 11990 (T)Legionella sp.Lucinoma aequizonata gill symbiontMarmooacter hydrocarbonoclasticusMethylococcus capsulatusMethylococcus tuteusMethylomonas albusMethylomonas methanicaMethylomonas rubraMethylomonas sp.Nkrosococcus oceanus 1Nitrosococcus oceanus 2Oceanospirfllum linum ATCC 11336 (T)Pseudomonas aeruginosa 1 ATCC 11996Pseudomonas aeruginosa 2 ATCC 25330Pseudomonas mendocinaRiftia pachyptila trophosome symbiontSolemya reidi symbiontSolemya velum symbiontThiobacillus hydrotbermalisXanthomonas maltophiliaXyldla fastidiosa

PROTEOBACTERIA GAMMAActinobacillus actinomycetemcomitans 1 ATCC 29524Actinobacillus actinomycetemcomitans 2 ATCC 29523Actinobacillus actinomycetemcomitans 3 ATCC 33384 (T)Actinobacillus actinomycetemcomitans 4 FDC Y4Actinobacillus actinomycetemcomitans 5 ATCC 29522Actinobacillus capsulatus 1 NCTC 11408 (T)Actinobacillus capsulatus 2 CCUG 19799Actinobacillus capsulatus 3 CCUG 12396 (T)Actinobacillus equuli NCTC 8529 (T)Actinobacillus hominisActinobacillus lignieresii 1 ATCC 19393 (T)Actinobacillus lignieresii 2 NCTC 4189 (T)Actinobacillus pleuropneumoniae ATCC 27088 (T)Actinobacillus salpingitidisActinobaculus seminis ATCC 15768 (T)Actinobaculus suis ATCC 15557Actinobacillus ureaeAcyrthosyphon pisum symbiont PAcyrthosyphon pisum symbiont S


Aeromonas caviae 1 NCIMB 13016 (T)Aeromonas caviae 2 ATCC 15467Aeromonas eucrenophila NCIMB 74 (T)Aeromonas hydropfaila 1Aeromonas hydrophila 2 ATCC 7966 (T)Aeromonas jandaei ATCC 49568 (T)Aeromonas media ATCC 33907 (T)Aeromonas salmonicida 1 NCIMB 1102 (T)Aeromonas salmonicida 2 NCIMB 1102Aeromonas salmonicida 3 NCIMB 1110Aeromonas schubertii DSM 4882 (T)Aeromonas sobria NCIMB 12065 (T)Aeromonas trota ATCC 49657 (T)Aeromonas veronii NCIMB 13015 (T)Aeromonas sp. ATCC 35941Alteromonas haloplanlads ATCC 14393Arsenophonus nasoniae ATCC 49151 (T)Barophile 1Barophile 2Bisgaard Taxon 2Bisgaard Taxon 3Bisgaard Taxon 5Bisgaard Taxon 6Bisgaard Taxon 7Bisgaard Taxon 8Bisgaard Taxon 9Bisgaard Taxon 13Bisgaard Taxon 14 1Bisgaard Taxon 14 2Buchnera aphidicola 1Buchnera aphidicola 2Buchnera aphidicola 3Buchnera aphidicola 4Buchnera aphidicola 5Buchnera aphidicola 6Buchnera aphidicola 7Buchnera aphidicola 8Buchnera aphidicola 9Buchnera aphidicola 10Citrobacter freundiiCrvptosaras couesi symbiontErwinia carotovoraErwinia herbicolaEscherichia coliEuscelidhis variegatus parasiteHaemophilus aegyptius NCTC 8502 (T)Haemophilus aphrophilus ATCC 33389 (T)Haemophilus ducreyi 1 CIP 542 (T)Haemophilus ducreyi 2 CIP 542 (T)Haemophilus ducreyi 3Haemophilus ducreyi 4 ATCC 27722Haemophilus haemoglobinophilus NCTC 1659 (T)Haemophilus haemolyticus NCTC 10659 (T)Haemophilus influenzae ATCC 33391 (T)Haemophilus paracuniculus ATCC 29986 (T)Haemophilus paragallinarum NCTC 11296 (T)Haeinophilus parahaemolyticus NCTC 8479 (T)Haemophilus parainfluenzae 1 ATCC 7901Haemophilus parainfluenzae 2 ATCC 33392 (T)Haemophilus paraphrophaemolyticus NCTC 10670 (T)Haemophilus paraphrophilus 1 ATCC 29241 (T)Hacmophilus paraphrophilus 2 ATCC 29242Haemophilus parasuis 1 NCTC 4557 (T)Haemophilus parasuis 2Haemophilus segnis ATCC 33393 (T)Haemophilus somnusHaemophilus sp.Haemophirus taxonHafnia alveiMelanocetus johnsoni symbiontPasteurella aerogenes ATCC 27883 (T)Pasteurella anatis ATCC 43329 (T)Pasteurella avium NCTC 11297 (T)Pasteurella bettiPasteureUa canis ATCC 43326 (T)

PasteureUa dagmatis ATCC 43325 (T)Pasteurella gallinarum NCTC 11188 (T)Pasteurella haemolytica 1 NCTC 10624PasteureUa haemolytica 2 NCTC 9380 (T)Pasteurella langaa ATCC 43328 (T)Pasteurella multocida NCTC 10322 (T)PasteureUa pneumotropica NCTC 8141 (T)Pasteurella stomatis ATCC 43327 (T)PasteureUa t< niHini<;Pasteurella volantium 1 NCTC 4101PasteureUa volanrium 2 NCTC 3438 (T)Pasteurella sp. 1 CCUG 19794PasteureUa sp. 2 CCUG 18782Photobacterium phosphoreumPiscirickettsia salmomsPiesiomonas shigelloides 1Ptesiomonas shigeUoides 2 NCIMB 9242 (T)Proteus vulgaris 1Proteus vulgaris 2Ruminobacter amylophihis DSM 1361 (T)Serratia entomophila ATCC 43705Serratia ficaria ATCC 33105Serratia fonticola ATCC 29844Serratia grimesii ATCC 14460Serratia liquefaciens ATCC 27592Serratia marcescens 1 ATCC 13880Serratia marcescens 2Serratia odorifera ATCC 33077Serratia plymuthica ATCC 183Serratia proteamaculans ATCC 19323Serratia rubidaea ATCC 27593Shophilus zeamais endosymbiont 1Sitophilus zeamais endosymbiont 2Thiomjcrospira sp.Vibrio alginoryticus ATCC 17749 (T)Vibrio anguularum NCMB 6, ATCC 12964 (T)Vibrio campbeEii ATCC 25920 (T)Vibrio diazotrophicus ATCC 33466 (T)Vibrio harveyi 1Vibrio harveyi 2 ATCC 14126 (T)Vibrio boUisae ATCC 33564 (T)Vibrio natriegens ATCC 14048 (T)Vibrio parahaemolyticus 1Vibrio parahaemolyticus 2 ATCC 17802 (T)Vibrio proteolyticus ATCC 15338 (T)Vibrio vulnificus ATCC 27562 (T)Wolbachia perska ATCC VR 331Xenorhabdus nematophilusYersinia enterocolitica

PROTEOBACTERIA DELTAAngkicoccus discifbrmisArchanghim gephyraBdeUovibrio bacteriovorusBdeUovibrio stolpiiCbondromyces apiculatusChondromyces crocatusCystobacter fuscusDesulfobacter curvatus DSM 3379Desulfobacter hydrogenophilus DSM 3380Desulfobacter lactus DSM 3381Desulfobacter postgatei DSM 2034Desulfobacter sp. 1 DSM 2035Desulfobacter sp. 2 DSM 2057Desulfobacterium autotrophicum DSM 3382Desulfobacterium niacini DSM 2650Desulfobacterium vacuolatum DSM 3385Desulfbbulbus propionicus ATCC 33891Desulfobulbus sp. DSM 2058Desulfococcus multivorans ATCC 33890Desulfomonas pigra ATCC 29098Desulfomonile tiedjei ATCC 49306Desulfbsarcina variabilis 1Desulfosarcina variabilis 2 DSM 2060Desulfovibrio africanus


Table 1. continued

Desulfovibrio baarsii DSM 2075Desulfovibrio baculatus DSM 1743Desulfovibrio dcsulfiiricans 1 ATCC 27774Desulfovibrio desulfuricans 2Desulfovibrio desulniricans 3Desulfovibrio gigas ATCC 19364Desulfovibrio longusDesulfovibrio salexigens ATCC 14822Desulfovibrio sapovorans ATCC 33892Desulfovibrio vulgaris DSM 644Desulfovibrio sp.Desulfuromonas acetoxidans DSM 684Magnetotactic bacteriuniMelittangium lichenicolaMyxococcus coralloidesMyxococcus xanthnsNannocystis exedensPolyangium cellulosumStigmatclla aurantiaca

PROTEOBACTERIA EPSILONBacterokles gracilisBacteroides ureolyticusCampylobacter coli 1Campylobacter coli 2Campylobacter coacisus 1Campylobacter concisus 2Campylobacter curvus 1Campylobacter curvus 2Campylobacter fetusCampylobacter fetus subsp. fetus ATCC 27374Campylobacter fetus subsp. venerealis ATCC 19438Campylobacter hyointestinalis 1Campylobacter hyointestinalis 2 ATCC 25317Campylobacter jejuni 1Campylobacter jejuni 2Campylobacter lariCampylobacter mucosalisCampylobacter rectus 1Campylobacter rectus 2Campylobacter showae 1Campylobacter showae 2Campylobacter sputorum 1 LMG 7795Campylobacter sputorum 2Flexispira lappiniHelicobacter acinonyx 1Helicobacter acinonyx 2Helicobacter cinaediHdicobacter felis 1 ATCC 49179Helicobacter felis 2Helicobacter felis 3Helicobacter fennelliaeHelicobacter muridarumHelicobacter mustelae 1 ATCC 43772Helicobacter mustelae 2Helicobacter pyloriHelicobacter sp. 1Helkobacter sp. 2Helicobacter sp. 3Helicobacter sp. 4Helicobacter sp. 5Helicobacter sp. 6Helicobacter sp. 7Helicobacter sp. 8Helicobacter sp. 9Helicobacter sp. 10Helicobacter sp. 11Helicobacter sp. 12Wolinella succinogenes 1 ATCC 29453Wolinella succinogenes 2Wolinella succinogenes 3

PROTEOBACTERIA, UNCERTAIN AFFILIATIONTtuobacilluj thiooxidans DSM 612

GREEN SULFURCblorobium limicolaChlorobium tepidum ATCC 49652Chlorobium vibriofonneClamrochloris sulfurica

FLAVOBACTERIA AND RELATIVESAntarcticum vesiculatumBacteroides distasonisBacteroides fragilis 1 ATCC 25285Bacteroides fragilis 2Bacteroides thetaiotaomicronBacteroides vulgatusCapnocytophaga gingivalisCapnocytophaga ochraceaCapnocytophaga sputigena ATCC 33612Cytophaga Hfpiflfpi*Cytophaga diffiuensCytophaga fermentansCytophaga flevensisCytophaga neparina IFO 12017, ATCC 13125Cytophaga hutchinsoniiCytophaga johnsonae 1Cytophaga johnsonae 2Cytophaga laterculaCytophaga lytica ATCC 23178Cytophaga marinoflavaCytophaga salmonicolorFlavobacterium aquatile ATCC 11947Flavobacterium balustinumFlavobacterium breveFlavobacterium ferrugineum ATCC 13524Flavobacterium gleumFlavobacterium gondwanenseFlavobacterium indologenesFlavobacterium indoltheticumFlavobacterium meningoseptiaimFlavobacterium odoratumFlsvobacterium salegensFlavobacterium spiritivorumFlavobacterium thalpophilumFlflvobacterium uliginosum ATCC 14397Flectobacillus glomeratusHectobaciUus major ATCC 29496Flectobacillus marinus ATCC 43824Flexibacter aggregans 1Flexibacter aggregans 2Flexibacter aurantiacus ATCC 23107Flaubacter canadensis ATCC 29591Flexibacter columnarisFlexibacter elegans 1Flexibacter elegans 2Flexibacter elegans 3Flexibacter elegans 4Flexibacter flexOis ATCC 23079Flexibacter litoralisFlexibacter maritimus 1Flexibacter maritimus 2Flexibacter polymorphusFlexibacter roseolusFlexibacter ruberFlexibacter sancti ATCC 23092Flexibacter tractuosusHaliscomenobacter hydrossisMicroscilla aggregans subsp. catalytkaMicroscilla arenariaMicroscilla furvescensMicroscilla marinaMicroscilla sericeaRunella slimyformis ATCC 29530Saprospira grandisSphingobacter mizutacSpirosoma linguale ATCC 23276Sporocytophaga cauliformis


Weeksella virosaWecksella zoohelcum

CHLAMYDIAEChlamydia pneumoniaeChlamydia psittaciChlamydia tracbomatis

FTBROBACTERFibrobacter intestinales 1Fibrobacter intestinales 2Fibrobacter intestinales 3Fibrobacter intestinales 4Fibrobacter intestinales 5Fibrobacter succinogenes 1Fibrobacter succinogenes 2Fibrobacter succinogenes 3Fibrobacter succinogenes 4Fibrobacter succinogenes 5Fibrobacter succinogenes 6Fibrobacter succinogenes 7Fibrobacter succinogenes 8Fibrobacter succinogenes 9Fibrobacter succinogenes 10

SHROCHETESBorrelia anserina 1Borrelia anserina 2Borrelia burgdorferiBorrelia burgdorferi 1Borrelia burgdorferi 2Borrelia burgdorferi 3Borrelia burgdorferi 4Borrelia burgdorferi,5Borrelia burgdorferi 6Borrelia burgdorferi 7 ATCC 35210 (T)Borrelia burgdorferi 8Borrelia burgdorferi 9Borrelia burgdorferi 10Borrelia burgdorferi 11Borrelia burgdorferi 12Borrelia coriaceae ATCC 43381Borrelia bennsii 1 ATCC 35209Borrelia hermsii 2Borrelia hermsii 3Borrelia bennsii 4Borrelia hermsii 5Borrelia sp.Leptonema illiniLeptospira illiniLeptospira interrogans 1 ATCC 23606Leptospira interrogans 2Leptospira sp.Serpula hyodysenteriae 1 ATCC 27164 (T)Serpula hyodysenteriae 2Serpula hyodysenteriae 3Serpula famocens 1 ATCC 29796 (T)Serpula innocens 2Spircchaeta aurantia ATCC 25082 (T)Spirochaeta bajacalifonriensis ATCC 35968 (T)Spirochaeta halophila ATCC 29478 (T)Spirochaeta isovalericaSpirochaeta litoralis ATCC 27000 (T)Spirochaeta stenostrepta ATCC 25083 (T)Spirochaeta thermophila DSM 6192Spirochaeta zuelzeri ATCC 19044 (T)Spirochaeta sp. 1Spircchaeta sp. 2Treponema bryantii ATCC 33254 (T)Treponema dentkola ATCC 33520Treponema palltrhim 1Treponema pallidum 2Treponema pectinovorum ATCC 33768 (T)Treponema phagedenisTreponema saccharophihim ATCC 43261 (T)Treponema succinifaciens ATCC 33096 (T)

Treponema sp. 1 ATCC 43811Treponema sp. 2Treponema sp. 3Treponema sp. 4

FUSOBACTERIUM AND RELATIVESBacteroides termitidisFusobacterium alocis ATCC 35896 (T)Fusobacterium gonidiafbnnans ATCC 25563 (T)Fusobacterium gonidoformansFusobacterium mortiferum 1Fusobacterium mortiferum 2 ATCC 25557 (T)Fusobacterium necrogenes ATCC 25556 (T)Fusobacterium necrophorum ATCC 25286 (T)Fusobacterium nucleatumFusobacterium nucleatum ssp. animalis NCTC 12276 (T)Fusobacterium nucleatum ssp. fusiformis NCTC 11326 (T)Fusobacterium nucleatum ssp. nucleatum ATCC 25586 (T)Fusobacterium nucleatum ssp. polymorphum ATCC 10953Fusobacterium perfbetensFusobacterium periodonticum ATCC 33693 (T)Fusobacterium russii 1Fusobacterium russii 2 ATCC 25533 (T)Fusobacterium simiae 1Fusobacterium simiae 2 ATCC 33568 (T)Fusobacterium ulcerans NCTC 12111 (T)Fusobacterium varium 1Fusobacterium varium 2 NCTC 10560 (T)Leptotrichia buccalisPropionigenium modestum

CYANOBACTERIAAnabaena sp.Anacystis nidulansCyanobacterium sp.Cyanopbora paradoxa cyanelleMastigocladus laminosusProchlorococcus imrimiiProchloron sp.Prochlorothrix hollandica

GRAM P O S i n V E S AND RELATIVES, LOW G + CAcetomaculum ruminisAcetonema longum DSM 6540 (T)Acholeplasma entomophilum ATCC 43706Acholeplasma laidlawiiAcholeplasma modicum ATCC 29102Acidaminococcus fermentans ATCC 25085Aerococcus urinae NCTC 12142 (T)Aerococcus viridansAlloiococcus otitisAnaeroplasma abactoclasticum ATCC 27879Anaeroplasma bactoclasticum ATCC 27112Anaeroplasma varium ATCC 43167Asteroleplasma anaerobium ATCC 27880Bacillus acidocaldarius 1 ATCC 43034Bacillus acidocaldarius 2 DSM 446 (T)Bacillus acidoterrestris 1 DSM 3922Bacillus acidoterrestris 2 DSM 3923Bacillus alcalophilus DSM 485Bacillus alvei 1 ATCC 6344Bacillus alvei 2 NCDO 1153Bacillus amyloliquefaciens ATCC 23350Bacillus amylolyticus NCIMB 8144Bacillus aneurinolyticus NCIMB 10056Bacillus anthracisBacillus atrophaeus NCIMB 12899Bacillus azotofuans ATCC 35681Bacillus azotoformans ATCC 29788Bacillus badhis NCDO 1760Bacillus benzeovorans NCIMB 12555Bacillus brevis 1 NCIMB 9372Bacillus brevis 2Bacillus cereus 1 NCTC 11143Bacillus cereus 2 NCDO 1771 (T)Bacillus circulans NCDO 1775


Table 1. continued

Bacillus coagulans NCDO 1761Bacillus cycloheptanicus DSM 4006 (T)Bacillus fastidiosus DSM 91Bacillus finnus NCIMB 9366Bacillus globisporus 1 NCIMB 11434BaciUus globisporus 2 ATCC 23301, DSM 4 (T)Bacillus gordonae ATCC 29948Bacillus insolitus DSM 5Bacillus kaustopralus NCIMB 8547Bacillus larvae ATCC 9545Bacillus laterosporus 1 ATCC 6344, DSM 25Bacillus laterosporus 2 NCDO 1763Bacillus lautus NCIMB 12780Bacillus lentimorbus ATCC 14707Bacillus lentus NCDO 1127Bacillus licheniformis NCDO 1772Bacillus macerans 1 ATCC 8244, DSM 24Bacillus macerans 2 NCDO 1764Bacillus macquariensis 1 DSM/ATCC 23464 (T)Bacillus macquariensis 2 NCTC 10419Bacillus maroccanus NCIMB 10500Bacillus medusa NCIMB 10437Bacillus megaterium DSM 32Bacillus mycoides DSM 2048 (T)Bacillus pabuli NCIMB 12781Bacillus pantothenticus NCDO 1765Bacillus pasteurii NCIMB 8841Bacillus polymyxa 1 DSM 36Bacillus polymyxa 2 NCDO 1774BaciUus popilliae ATCC 14706Bacillus psychrophilus 1 ATCC 23304Bacillus psychrophilus 2 ATCC 23304, DSM 3 (T)Bacillus psychrophilus 3 ATCC 23306, DSM 2273Bacillus psychrosaccharolyticus ATCC 23296Bacillus pulvifaciens NCDO 1141Bacillus pumilus NCDO 1766Bacillus simplex DSM 1321Bacillus smithii DSM 4216Bacillus sphaericus NCDO 1767Bacillus stearothermophilus 1Bacillus stearothermophilus 2 NCDO 1768Bacillus subtilis 1Bacillus subtilis 2 NCDO 1769Bacillus thennoglucosadicus ATCC 43742Bacillus thuringiensis NCIMB 9134" (T)Brochomrix campestris ATCC 43754 (T)Brochothrix thennosphacta 1 NCDO 1676 (T)Brocbothrix thennosphacta 2Camobacterium divergens NCDO 2763 (T)Carnobacterium gallinarumCamobacterium mobileCamobacterium piscicola NCDO 2762 (T)Qostridium acetobutylkum NCIMB 8052Clostridium acidiuriciClostridium aminophilumClostridium aminovalericumClostridium aurantibutyricum NCIMB 10659Clostridium barati 1 ATCC 27638Clostridium barati 2 ATCC 43756Clostridium barkenClostridium brijerinclrii 1 DSM 791Clostridium beijerinclrii 2 NCIMB 9362Clostridium botulinum 1Clostridium botulinum 2Clostridium botulinum 3Clostridium botulinum 4 NCTC 10281Clostridium botulinum 5 ATCC 25765Clostridium butyricum 1 ATCC 43755Clostridium butyricum 2 DSM 2478Clostridium butyricum 3 NCIMB 8082Clostridium cadaverisQostridium camisClostridium clostridiiformesClostridium coccoidesClostridium cochlearium

aostridium estertheticum NCIMB 12511Clostridium falls*Clostridium histolytkumClostridium innocuum ATCC 14501Clostridium IduyveriGostridium leptumClostridium limosumGostridium lituseburenseClostridium ljungdahliiGostridium malenomimtumGostridium mflngffiiofiiGostridium mayombeii DSM 6539 (T)Gostridhun novyiGostridium oceanicumGostridium oroticumGostridium paraperfringensGostridium pasteurianumClostridium perfringens 1Gostridium perfringens 2Gostridium piliformeGostridium purinolyticumGostridium quercicolumClostridium ramosum ATCC 25582Clostridium scatologenesClostridium sordelliiClostridium sporogenesGostridium sporosphaeroidesGostridium sticklandii 1Gostridium sticklandii 2Clostridium subterminaleGostridium symbiosumaostridium tetanomorphum NCIMB 11547Gostridium thermaceticumaostridium thcrmoaceticumaostridium tbennoautotrophicum 1aostridium tnermoautotrophkum 2Qostridium mermohydrosulfuricumaostridium thermosaccharolyticumaostridium mermosulfurogenesOostridium tyrobutyricum 1aostridium tyrobutyricum 2Desulfbtomaculum nigrificans NCIMB 8395 (T)Desulfotomaculum orientis NOMB 8382Desulfbtomaculum ruminis NCIMB 8452Enterococcus avium NCDO 2369 (T)Enterococcus casseliflavus NCDO 2376Enterococcus columbae NCIMB 13013Enterococcus disparEttterococcus durans NCDO 596 (T)Enterococcus faecalisEnterococcus faecium NCDO 942 (T)Enterococcus gaUinarum NCDO 2313 (T)Enterococcus hirea NCDO 1258 (T)Enterococcus malodoratus NCDO 846 (T)Enterococcus mundtii NCDO 2375 (T)Enterococcus pseudoavtum NCDO 2138 (T)Enterococcus rafEnosus NCTC 12192 (T)Enterococcus sulfurcus NCDO 2379Epulopischnn sp. 1Epulopiscium sp. 2Erysipelothrix rhusiopathiae ATCC 19414Eubacterium alactolyticum DSM 3980Eubacterium bifbrmeEubacterium limosumEubacterium tenueGemeHa haemolysansHeliobactenum chlorumKurthia zopfiiLactobacillus acetoleransLactobacilhis acidophilus 1 NCDO 1748 (T)Lactobacillus acidophilus 2Lactobacillus agilisLactobacillus alimentariusLactobacillus amylophihisLactobacillus amylovoms


Lactobacillus animalis 1 NCDO 2425 (T)LactobaciUus animalis 2Lactobacillus aviariusLactobacillus bifennentansLactobaciUus brevis 1 NCDO 1749 (T)Lactobacillus brevis 2Lactobacillus buchneri 1 NCDO 110 (T)Lactobacillus buchneri 2Lactobacillus camisLactobacillus casei 1LactobaciUus casei 2 NCDO 161 (T)Lactobacillus casei 3Lactobacillus catenafonne ATCC 25536 (T)Lactobacillus confusus 1 NCDO 5186Lactobacillus confiisus 2 DSM 20196Lactobacillus coiyniformisLactobacillus delbrueckii 1LactobaciUus delbrueclcii 2 NCDO 213LactobaciUus divergensLactobaciUus farciminisLactobaciUus fermentum 1 NCDO 1750 (T)LactobaciUus fermentum 2LactobaciUus fructivoransLactobaciUus fructosus NCDO 2345 (T)LactobaciUus gasseri 1 NCDO 2233 (T)LactobaciUus gasseri 2LactobaciUus halotolerans DSM 20190LactobaciUus belveticus NCDO 2712 (T)LactobaciUus hilgardiiLactobaciUus kandleri 1 NCDO 2753LactobaciUus kandleri 2 DSM 20593LactobaciUus lactisLactobaciUus maliLactobaciUus maltaromicus 1LactobaciUus maltaromicus 2 JCM 1154LactobaciUus minor 1 NCDO 1973LactobaciUus minor 2 DSM 20014LactobaciUus murinusLactobaciUus oris NCDO 2160 (T)LactobaciUus plantarum 1LactobaciUus plantarum 2 NCDO 1752LactobaciUus ruminisLactobaciUus sakeLactobaciUus saUvariusLactobacillus sanfrancisco 1 JCM 5668LactobaciUus sanfrancisco 2LactobaciUus sharpeaeLactobacillus tfaermopbilusLactobacillus vaginalis NCTC 12197LactobaciUus vermiformeLactobaciUus viridescens 1 NCDO 1655LactobaciUus viridescens 2 ATCC 12706LactobaciUus vhulinus ATCC 27783LactobaciUus sp.Lactococcus garviae NCDO 2156Lactococcus lactis 1 ssp. lactis NCDO 2118Lactococcus lactis 2Lactococcus pisciumLactococcus plantarum NCDO 1871Lactococcus raffinolactis NCDO 2112Leuconostoc amelobiosumLeuconostoc camosumLeuconostoc citreum NCDO 1837Leuconostoc cremoris DSM 20346Leucoaostoc faUax DSM 20189Leuconostoc gelidumLeuconostoc lactis 1 DSM 20202Leuconostoc lactis 2 NCDO 533Leuconostoc mesenteroides 1 DSM 20343Leuconostoc mesenteroides 2 NCDO 523Leuconostoc oenos 1 DSM 20252Leuconostoc oenos 2 NCDO 1674Leuconostoc paramesenteroides 1 DSM 20288Leuconostoc paramesenteroides 2 NCDO 803Leuconostoc pseudomesenteroides NCDO 768Listeria grayi CIP 6818 (T)Listeria innocua NCTC 11288 (T)

Listeria ivanovii NCTC 11846 (T)Listeria monocytogenes 1Listeria monocytogenes 2 NCTC 10357 (T)Listeria murrayi NCTC 10812 (T)Listeria sedigeri NCTC 11856 (T)Listeria wekhimeri NCTC 11857 (T)Marinococcus halophilus NCIMB 2178 (T)Megaspbaera elsdeniiMycoplasma agalactiae NCTC 10123Mycoplasma arginini ATCC 23838Mycoplasma arthritidis ATCC 19611Mycoplasma bovigenitalium ATCC 19852Mycoplasma califomkum ATCC 33461Mycoplasma capricolumMycoplasma coragypsumMycoplasma dlychniae ATCC 43707Mycoplasma fermentans ATCC 19989Mycoplasma flocculare ATCC 27716Mycoplasma gaUisepticum 1Mycoplasma gaUisepticum 2Mycoplasma gaUisepticum 3Mycoplasma bominis 1 ATCC 23114Mycoplasma bominis 2Mycoplasma hyopneumoniae ATCC 27719Mycoplasma hyorhinis ATCC 17981Mycoplasma iowae 1 ATCC 33552Mycoplasma iowae 2Mycoplasma-like organism 1Mycoplasma-like organism 2Mycoplasma-like organism 3Mycoplasma lipophilum ATCC 27104Mycoplasma mobile ATCC 43663Mycoplasma muris ATCC 33757Mycoplasma mycoidesMycoplasma neurolyticum ATCC 19988Mycoplasma orale ATCC 23714Mycoplasma pirum ATCC 25960Mycoplasma pneumoniae ATCC 15531Mycoplasma pulmonis ATCC 19612Mycoplasma putrefeciens ATCC 15718Mycoplasma salivarium ATCC 23064Mycoplasma sualvi ATCC 33004Mycoplasma sp. 1Mycoplasma sp. 2Mycoplasma sp. 3 ATCC 49193Mycoplasma sp. 4 ATCC 49191Oenothera hoolceri MLOPectinatus cerevisiiphilus ATCC 29359Pectinatus frisigensis ATCC 33332Pediococcus acidilacticiPediococcus pentosaceusPeptococcus niger DSM 20475 (T)Peptostreptococcus anaerobhisPlanococcus citreus NCIMB 1493 (T)Planococcus kocurii NCIMB 629QuineUa ovalisSelenomonas lacticifcx DSM 20757Selenomonas ruminantium 1 subsp. lactilyuca DSM 2872Selenomonas niminantiiim 2Selenomonas ruminantium 3Selenomonas sputigena ATCC 35185Spiroplasma ATCC 43302Spiroplasma apis ATCC 33834Spiroplasma citri 1 ATCC 27556Spiroplasma citri 2Spiroplasma mirum ATCC 29335Spiroplasma sp. 1 ATCC 43153Spiroplasma sp. 2 ATCC 33827Spiroplasma sp. 3 ATCC 33835Spiroplasma sp. 4 ATCC 33825Spiroplasma sp. 5 ATCC 43210Spiroplasma sp. 6 ATCC 43525SporolactobaciUus inulinusSporomusa paucivoransSporomusa termhidaSporosarcina halophila NCIMB 2269Sporosarcina ureae NCIB 9251


Table 1. continued

Staphylccoccus aureus NCDO 949Staphylccoccus muscae CCM 4175 (T)Staphylococcus schleifcri DSM 4807 (T)Staphylococcus sciuriStreptococcus acidominimus NCDO 2025 (T)Streptococcus agaiarriflf. NCDO 1348 CDStreptococcus alactolytiens NCDO 1091 (T)Streptococcus anginosus NCTC 10713 (T)Streptococcus bovis 1 NCDO 597 (T)Streptococcus bovis 2Streptococcus canis DSM 20715 (T)Streptococcus cecoium NCDO 2674 (T)Streptococcus constdlatus NCTC 11325 (T)Streptococcus cremorisStreptococcus criae NCDO 2772 (T)Streptococcus cricetus NCDO 2720 (T)Streptococcus downei NCTC 11391 (T)Streptococcus dysgalactiae NCDO 2023 (T)Streptococcus equi NCDO 2493 (T)Streptococcus equinus NCDO 1037 (T)Streptococcus hanseniiStreptococcus hyointestinalis DSM 20770 (T)Streptococcus intermedius NCTC 11324 (T)Streptococcus lactisStreptococcus macacae NCTC 11558 (T)Streptococcus mutans NCTC 10449 (T)Streptococcus oralis NCTC 11427 (T)Streptococcus parasanguis NCTC 7863 (T)Streptococcus parauberis NCDO 651Streptococcus pleomorphus ATCC 29734Streptococcus pneumoniae NCTC 7465 (T)Streptococcus porcinus NCDO 600 (T)Streptococcus pyogenes NCDO 2381 (T)Streptococcus rattus NCDO 2723 (T)Streptococcus saccharotyticus NCDO 2594Streptococcus salivarius 1 NCDO 1779 (T)Streptococcus salivarius 2Streptococcus sanguis NCTC 7863Streptococcus sobrinus DSM 20742 (T)Streptococcus suis NCTC 10237 (T)Streptococcus thennophilus NCDO 573 (T)Streptococcus uberis NCDO 643Streptococcus vestibularis NCTC 12166 (T)Syntropbomonas wolfriSyntrophospora bryamiiUreaplasma urealytkum NCTC 10177Vagococcus fluvialis NCDO 2497Vagococcus salmoninarumWestern aster yellow MLO isolated from celeryZymophilus paucivorans DSM 20756

GRAM POSITIVES AND RELATIVES, fflGH G+CActinomyces bovis 1 DSM 43014Actinomyces bovis 2 DSM 43014Actinomyces israelii 1 DSM 43020Actinomyces israelii 2 DSM 43020Actinomyces naeslundii 1 DSM 43013Actinomyces naeslundii 2 DSM 43013Actinomyces odontolyticus 1 DSM 43331Actinomyces odontolyticus 2 DSM 43331Actinomyces pyogenes ATCC 19411Actinomyces viscosus 1 DSM 43027Actinomyces viscosus 2 DSM 43027ActinopoJyspora halophila ATCC 279Aeromkrobium erythreum NRRL B-3381 (T)Amycolata autotrophka DSM 43210 -Amycolata nitrifkans DSM newAmycolata petroleophila DSM newAmycolatopsis azurae NRRL 11412Amycolatopsis fastidiosa ATCC 31181Amycolatopsis metnanolica NCIB 11946 (T)Arthrobacter globiformisArthrobacter simplex ATCC 6946Arthrobacter sp.Atopobmm parvulum

Atopobhim rimaeBifidobacterium adolescentisBifidobacterium asteroidesBifidobacterium bifidumBifidobacterium breveBifidobacterium ratrjiiilatumBifidobacterium coryneformeBifidobacterium cunnkuliBifidobacterium dentiumBifidobacterium globosumBifidobacterium indicumBifidobacterium infantisBifidobacterium longumBifidobacterium magnumBifidobacterium minimumBifidobacterium pseudolongumBifidobacterium suisClavibacter xyliCorynebacterium renale ATCC 19412Corynebacterium variabilis NCIB 9455, NCDO 2097 (T)Corynebacterium xerosisDermatophilus congolensisEubacterium suis DSM 20639, ATCC 33144 (T)Faenia rectivirgula ATCC 33515 (T)Frankia sp. 1Franlda sp. 2Frankia sp. 3Frankia sp. 4Frankia sp. 5Fusobacterium prausnitziiGardnerella vaginal isGordona terrae DSM 43249KflxJelosporangium aridum ATCC 39323Kitasatosporia griseola NRRL B-16229Kitasatosporia phosalacinea NRRL B-16230Kitasatosporia setae NRRL B-16185Lactobacillus minutusMkrococcus luteusMobiluncus curtisii ATCC 35421Mobiluncus mulieris ATCC 35423Mycobacterium akhiense ATCC 27280Mycobacterium asiatkum 1 ATCC 25276Mycobacterium asiatkum 2 ATCC 25276Mycobacterium aurum 1 ATCC 23366Mycobacterium aurum 2 ATCC 23366Mycobacterium avium 1Mycobacterium avium 2Mycobacterium avium 3 DSM 43216Mycobacterium avium 4Mycobacterium avium 5Mycobacterium avium 6Mycobacterium avhim 7Mycobacterium avium 8Mycobacterium avhun 9Mycobacterium avhim 10Mycobacterium bovis 1Mycobacterium bovis 2Mycobacterium chelonae ATCC 14472Mycobacterium chelonei ATCC 19977Mycobacterium chitae 1 ATCC 19627Mycobacterium chitae 2Mycobacterium chitae 3 ATCC 19627Mycobacterium chitae 4 ATCC 19627Mycobacterium chubuense ATCC 27278Mycobacterium confluentisMycobacterium cookii ATCC 49103, DSM 43922 (T)Mycobacterium diemhoferi ATCC 19340Mycobacterium fallax ATCC 35219Mycobacterium farcinogenes DSM 43294Mycobacterium flavescens 1 ATCC 14474Mycobacterium flavescens 2 ATCC 14474Mycobacterium fortuitum ATCC 6841 (T)Mycobacterium gadium 1Mycobacterium gadium 2 ATCC 27726Mycobacterium gastri ATCC 15754


Mycobacterium gtfvum ATCC 43909Mycobacterium gordonae 1 ATCC 14470Mycobacterium gordonae 2 ATCC 14470Mycobacterium intraceUulare 1 ATCC 15985Mycobacterium intraceUulare 2Mycobacterium intraceUulare 3Mycobacterium intraceUulare 4Mycobacterium intraceUulare 5Mycobacterium intraceUulare 6Mycobacterium kansasii 1 DSM 43224Mycobacterium kansasii 2 ATCC 12478Mycobacterium komossense ATCC 33013Mycobacterium leprae 1Mycobacterium leprae 2Mycobacterium leprae 3Mycobacterium madagascarienseMycobacterium malmoense 1 ATCC 29571Mycobacterium mahnoense 2Mycobacterium marinumMycobacterium neoaurum ATCC 25795Mycobacterium nonchromogenicum 1 ATCC 19530Mycobacterium nonchromogenicum 2 ATCC 19530Mycobacterium obuense ATCC 27023Mycobacterium paratuberculosis 1Mycobacterium paratuberculosis 2Mycobacterium paratuberculosis 3Mycobacterium paratuberculosis 4Mycobacterium paratuberculosis 5Mycobacterium paratuberculosis 6Mycobacterium paratuberculosis 7Mycobacterium paratuberculosis 8Mycobacterium paratuberculosis 9 ATCC 19698Mycobacterium phlei ATCC 11758Mycobacterium scrofulaceum ATCC 19981Mycobacterium senegalense ATCC 35796Mycobacterium simiae ATCC 25275Mycobacterium smegmatis ATCC 14468Mycobacterium sphagni ATCC 33026Mycobacterium szulgai 1 ATCC 25799Mycobacterium szulgai 2Mycobacterium terrae 1 ATCC 15755Mycobacterium terrae 2 ATCC 15755Mycobacterium tbermoresistible 1 ATCC 19527Mycobacterium thermoresistible 2 ATCC 19527Mycobacterium triviale ATCC 23292Mycobacterium tuberculosis 1Mycobacterium tuberculosis 2Mycobacterium tuberculosis 3 NCTC 7416Mycobacterium ulceransMycobacterium vaccae ATCC 15483Mycobacterium xenopi 1 ATCC 19250Mycobacterium xenopi 2 ATCC 19250Mycobacterium sp. 1Mycobacterium sp. 2Mycobacterium sp. 3Nocardia asteroides 1 DSM 43005Nccardia asteroides 2 ATCC 3306Nocardia otitidis-caviarumNocardioides albus DSM 43109Nocardioides festidiosa NCIB 12713 (T)Nocardioides jensenii DSM 29641Nocardioides luteus NCIB 11455Nocardioides simplex 1 NCIB 8929Nocardioides simplex 2 NCIB 8929 (T)Propiombacterium acidi-propionici DSM 20272Propkmibacterium acnes 1 DSM 1897Propionibacterium acnes 2Propionibacterium freudenreichii DSM 20271Propionibacterium jensenii DSM 20535Propionibacterium propkmicus DSM 43307Propionibacterium thoenii DSM 20276Pseudonocardia thermophila 1 ATCC 19285 (T)Pseudonocardia thermophila 2 ATCC 19285 (T)Renibacterium salmoninarum ATCC 33209 (T)Rhodococcus equi Equine lungRhodococcus erythropolis DSM 43188Rhodococcus fescians DSM 20131

RoChia dentocariosaSaccharomonospora viridis ATCC 15386Saccharopolyspora erythraea NRRL 2338Saccharopolyspora hirsuta 1 ATCC 27875 (T)Saccharopolyspora hirsuta 2Saccharopolyspora hordeiSaccharothrix australiensis ATCC 31947Streptomyces albus DSM 40313, ISP 5313 (T)Streptomyces ambofaciens ATCC 23877Streptomyces brasfliensis DSM 43159 (T)Streptomyces coelicolor 1Streptomyces coelicolor 2Streptomyces diastaticus DSM 40496, ISP 5496 (T)Streptomyces griseus subsp. griseus ATCC 10137Streptomyces lavendulae DSM 2014, ISP 5069 (T)Streptomyces lividansStreptomyces purpureus DSM 43460 (T)StreptoverticiUium abikoense DSM 40831 (T)StreptovertidUium baldaciiStreptoverticillium cinnamoneum spp. azacolutumStreptoverticiUium cinnamoneum spp. cinnamoneumStreptoverticiUium ladakanum DSM 40587 (T)StreptoverticiUium luteorcticuliStreptoverticfllium olivoreticuli ssp. ceUulophilumStreptoverticiUium salmonisTerrabacter tumescens NCIB 8914Tropheryma whippeliiTsukamureUa aurantiacus NCTC 10741TsukamureUa paurometabolum 1 DSM 20162, NCTC 10741Tsukamurella paurometabolum 2 NCTC 10741

GREEN NON SULFURChloroflexus aurantiacusHerpetosiphon aurantiacus ATCC 23779Sphaerobacter thermophilus DSM 20745 (T)Thermomicrobium roseum ATCC 27502

RADIORESISTANT MICROCOCa AND RELATIVESDeinococcus radiodurans UWO 298Thenmis aquaticus 1Thermus aquaticus 2Thermus aquaticus 3 ATCC 27978Thermus filifonnis 1 ATCC 43280Thermus filiformis 2Thermus flavus 1 ATCC 33923Thermus flavus 2Thermus ruber 1 ATCC 35948Thermus ruber 2Thermus thermophilus 1Thermus thennophilus 2 ATCC 27634Thermus thennophilus 3 ATCC 27634Thermus thermophilus 4Thermus sp. 1Thermus sp. 2Thermus sp. 3Thermus sp. 4Thermus sp. 5Thermus sp. 6Thermus sp. 7Thermus sp. 8Thermus sp. 9Thermus sp. 10

THERMOTOGALESFervidobacteriuni nodosum ATCC 35602Fervidobacterium islandicum DSM 5733 (T)Thermosipho arricanusThermotoga maririma DSM 3109

PLANCTOMYCES AND RELATIVESGemmata obscuriglobus 1 UQM 2246Gemmata obscuriglobus 2 UQM 2246Isosphaera paUidaPireUula marina DSM 3645Planctomyces limnophilus ATCC 43296Planctomyces maris ATCC 29209 (T)Planctomyces staleyi


Table 1. continued

UNCERTAIN AFFILIATIONAquifex pyrophilusFlexistipes sinusarabici DSM 4947Haloanaerobium praevalensLeptospirillum sp. DSM 2391Sporohalobacter lortetiiSynergistis jonesii

PLASTIDS

PLANTAEBRYOPHYTAMARCHANTIOPSIDA

Marchantia polymorpha

MAGNOUOPHYTALILJOPSIDA

Oryza sativaZea mays

MAGNOUOPSIDAConopbolis americanaEpifagus virginianaGlycine maxNicotiana plumbaginifoliaNicotians tabacum 1Nicotiana tabacum 2Pisum salivum 1Pisum sativum 2


CHLOROPHYTAChlamydomonas eugametosChlamydomonas moewusiiChlamydomonas reinhardtiiChlorella ellipsoideaChlorella kessleriChlorella mirabilisChlorella protothecokksChlorella sorokinianaChlorella vulgaris

ASSEMBLAGE CHROMOBIONTSCHRYSOPHYTA

Ochromonas danicaOlisthodiscus lutcus

HAPTOPHYTAOchrosphaera spec.

PHAEOPHYTAPylaiella littoralis 1

ASSEMBLAGE CRYPTOMONADSCRYPTOPHYTA

Cryptomonas phiPyrenomonas salina

ASSEMBLAGE EUGLENOZOAEUGLENOPHYTA

Astasia longaEuglena gracilis

ASSEMBLAGE RHODOPHYTESRHODOPHYTA

Antithamnion sp.Cyanidium cald&rium

MITOCHONDRIA

ANIMALIACHORDATA

VERTEBRATAMAMMALIAAepyceros melampusAmblysomus bottentotus

Antilocapra americanaAtelerix albiventrisBalaenoptera physalusBathyergus janettaBatbyergus suillusBlarina brevicaudaBos taumsBoselaphus tragocamelusCapra hircusCephalopbus maxwelliCervus unicokjrCryptomys hottentotus 1Cryptomys hottentotus 2Cryptomys hottentotus damarensisDamaliscus dorcasGazdla tbomsoniGeorychus capensisGorilla gorillaHeliophobius argenteocinereusHeterocephalus glaberHomo sapiens 1Homo sapiens 2Hydropotes incrmisKobus ellipsiprymnusMadoqua lortiMuntiacus reevesiMus musculusOdocoileus virginianusOryx gazellaPan paniscusPan troglodytesPetromus typicusPhoca vhulinaPongo pigmaeusRattus norvegicus 1Rattus norvegicus 2Thryonomys swinderianusTragelaphus imberbisTragulus napu

AVESCotumix japonicaGallus gallus

AMPHIBURana catesbeianaXenopus laevis

OSTEICHTYESCrossostona lacustreCyprinus carpio

ECHINODERMATAECHINOIDEA

Paracentrotus lividusStrongylocentrotus purpuratus

ARTHROPODAINSECTA

Apis mellifera ligusticaDrosophila virilisDrosophila yakuba

NEMATODASECERNENTEA

Ascaris suumCaenorhabditis elegans

PLANTAEBRYOPHYTA

MARCHANTIOPSIDA

Marchantia polymorpha

MAGNOUOPHYTALHJOPSIDA

Secale cerealeTritjcum aestivum


Zea diplopercnnisZea mays 1Zea mays 2

MAGNOLJOPSIDAGlycine maxLupinus tuteusOenothera sp.

FUNGIASCOMYCOTINA

HEMIASCOMYCETESSaccharomyces cerevisiae 1Saccharomyces cerevisiae 2Saccharomyces cerevisiae 3Saccharomyces cerevisiae 4Saccharomyces cerevisiae 5

EUASCOMYCETESAspergillus nidulansPodospora anserina

UNCERTAIN AFFILIATIONSchizosaccharomyces pombe


CHLOROPHYTAChlamydomonas reinhardtiiPrototheca wickerhamii

ASSEMBLAGE CTLIATESCILIOPHORA

Paramecium aureliaParamecium primaureliaParamecium tetraureliaTetrahymena pyriformis 1Tetrahymena pyriformis 2

ASSEMBLAGE EUGLENOZOAHNETOPLASTIDS

Crithidia fascinilfltRI ^.ishmnnifl tarentolaeLeptomonas sp.Trypanosoma brucei

ASSEMBLAGE SPOROZOAAPICOMPLEXA

Plasmodium faJciparum 1Plasmodium fakiparum 2

(a) Some species names are listed several times followed by a sequential number.This means that the SSU rRNA sequence has been determined several times,usually by different authors. The sequences are not necessarily the same sincethey may have been determined for different varieties or strains of a species,or for different genes of the same organism. The systematics followed for thethree domains are mentioned in the text. Plastidial and mitochondria! structuresare listed according to the systematics followed for the host organism. In the caseof Archaca and Bacteria, the species name is followed by the culture collectionname and number if specified by the author. This number is followed by (T)if it is a type species. Abbreviations of culture collection names can be foundin the catalogs of the American Type Culture Collection (ATCC), DeutscheSammlung von Mikroorganismen (DSM), and Laboratorium voor MicrobiologieUniversiteit Gent (LMG). The assignment of the archaeal and bacterial speciesto taxa is based on the tree shown in outline in Fig. 1. These taxa correspondto the divisions and subdivisions distinguished by Woese and coworkers (10—12),except for the bacterial genera Fibrobaaer and Fusobaaerium, which form separateclusters and therefore are listed as separate taxa. The taxon of Gram positivebacteria of low GC contents and relatives comprises a number of genera withgram negative cell walls: Megasphaera, Pectinatus, Selenomonas, Sporomusa,and Zymophitus. For the Archaca, the classification is slightly different from thatfollowed by Olsen and Woese (12), as explained in the text.

(b) Most of the species listed under the heading 'Proteobacteria gamma*' areattributed to the Proteobacteria 7 group by Woese (11), although they clusterwith the Proteobacteria 0 in the tree of Rg . 1. Exceptions are Xanthomonasmahophilia and Xylella Jastidiosa which belong to the Proteobacteria (3 groupaccording to the same author (11).

Table 2. Helix occupancy in eukaryotic SSU rRNAs.

Taxon & Species*E81

E101 2

E231 2 3 4

Helicesb

5 6 7 8 9 10 11 12E451

Insecta -Plaryhelminthes -Schizosaccharomyces pombe(Ascomycotina) -Euplota aediculams (Ciliopbora) *Euglena gradlis (Euglenophyta) •Bodo caudatus (Kinetoplastidea) *Tritridxomonas foetus (Kinetoplastidea) -Trypanosoma cruzi (Kinetoplastidea) *Other Kinetoplastidea *BlastocladieUa emersonii(Chytridiomycota) -Encephalitozoon cuniculi(Microsporidia) -Vairimorpha necatrix (Microsporidia) —Giardia (Polymastjgotes) -Acaruhamoeba castellanii (Amoebozoa) —Naegleria gruberi (Amoebozoa) -Other Amoebozoa -Physarum potycephatum (Eumycetozoa) •Babesia (Apicomplexa) -Plasmodium (Apicomplexa) —Other Eukarya -

—**_*

—I

1

[

i

i

I i

N *

» *

H *

N *

N *

k *

t *

*

*

*

*

*

*

*

(a)In the case of the genera Giardia, Babesia, and Plasmodium, the helix occupancy applies to all species of the genus.(b)The presence of a helix is indicated by an asterisk. Only eukaryote-specific helices are listed since universal helices are present in all known eukaryotic SSUrRNAs except those of Vairimorpha necatrix, which lacks helices 10, 11, 43, and 46 and of Encephalitozoon cuniculi, which lacks helices 11, 18, 43, and 46.The structure of the SSU rRNA of the insect Acyrtosyphon pisum in area V4 (helices E23-n), which is exceptionally large in this species, is not yet known.


Distance 0.1

Proteobacteria y (143)

Proteobacteria y' (51)

Proteobacteria 0 (54)

Proteobacteria a (103]

Proteobacteria 6 (43)

Proteobacteria c (50)

Green sulfur bacteria (4)

Ravobacteria & relatives (69)

Chlamydiae (3)fibrobacter (15)

Spirochetes (54)

Fusobacterium (24)

Cyanobacteria & plastids (38)

Gram positives low G+C (374)Bacteria with gram negative cell walls (13)Heliobacterium ch/orum

Archaea

Gram positives high G+C (205)

Green non sulfur bacteria (4)Radioresistant micrococci & relatives (24)

Triermotogales (4)Planctomyces (7)

Methanobacteriales (17)Thermococcus caler

MeChanopyrus kandleriArchaeoglabus Madus

Metrianococcales (5)Thermop/asma aadophium

— — • • Halobacteria (10)H i ^ ^ B ^ H Methanormcrobum group (23)Crenarchaeota (6)

Tjhaeoca

Figure 1. Evolutionary tree reconstructed from archaeal, bacterial and plastidial SSU rRNA sequences. The tree was constructed as described in the text from atotaLof 1348 SSU rRNA sequences. Clusters distinguishable in the tree are simplified to isosceles triangles with a height approximately equal to the average distanceseparating the terminal nodes from the deepest branching point within the cluster, and a base proportional to the number of sequences composing it, mentionedin brackets after the taxon name. If a taxon is represented by a single sequence, the species name is mentioned in italics. Each cluster corresponds to a taxon listedin Table 1. The cluster labeled Proteobacteria 7* is in faa more closely related to the Proteobacteria 0 than to the Proteobacteria 7 in the present tree. However,its position between the latter two clusters is not stable and it consists mainly of species classified as Proteobacteria 7 by Woese (11) (see also footnote b to Table1). The scale on top measures evolutionary distance expressed in substitutions per nucleotide.


39

P23-1

17 • ; / • . . .16 15 ? b 5

* • • a

14 °

1 < 3 ' . • • • • • • • •

12*. , '

V210

Figure 2. Secondary structure model for prokaryotic SSU rRNAs. Sites are divided into five equally numerous categories of increasing variability, indicated byfull circles of increasing diameter. Sites that are invariant among presently known sequences are indicated as hollow squares. Areas containing the most variablesites are labded VI to V9. The helix numbering system is explained in the text. Helices P37-1 and P37-2 are absent in archaeal SSU rRNAs.


39 o D 42

25

V 5 „.„•>. . ^ //U s o° V- . . -o o.o- r. n o*' °-. 26 / !-V.

:...D....:' ? . . . / VE23-7 . - • •

«MMM •E23 -2 | |M"!*' J |

E23-1V3^/ 6., „

•y 16 15 ...v'-. 6 \

17 14° :„::::

13 :.::::::

>••

50 . • D *

"*. 7 V1

12

. • * . • . o • 9

. • • '

^•' V2 ;E10-1

FTgnre 3. Secondary structure model for eukaryotic SSU rRNAs. Conventions are as in Fig. 2. The shape of the model is based on Saccbaromyces cerevisiae SSUrRNA, and hollow circles represent nucleotides deleted in most other eukaryotic SSU rRNAs. The area corresponding to V6 in prokaryotic SSU rRNAs is moreconserved among eukaryotic SSU rRNAs.


Escherlctila coll

25 V/

P23-1

U "" A uU A

24 .'

27

39 42.CA*

43

41 *^SA- UA O

°U40

P37-2 «".c° 38

»,,Acipi!lUO, A V ^ % A

P37-1 r,7AV?'

O . UA ae»- c

A o* ci « * A

A A - Uif A a

29.

36 gu

c oc • oo- c

a

u -au . aa-ca. u

46

.=*••, 45

« o • 28 S:8Q.3O "c»"*35 3 4 ^ ° '

23 ^ " " • - ^ '

21

iCOACUU ? f AC « C A

u u O

CUCA uuftoA* c uA c u o * * a c^*.°b

" 2 * \ u . 32 e* Oli AUC V U f

C - O Ac- a uu- A © " O C A "

uoacAccn A

/ 48

e \

« 3 '-. \ <*£ C Q A A * A A _ A O A A , ,o CACCAUOO OLIOOOUUOCAAA ÛAOOU cyu c c u uu auaaaauc UACUUAOUOUUU CAUUCO _ ooa a a a

c

« AO c^c C A U

u cuuuaouc CCCOCACMAA OAAAUOAO OQOCOACUU ,

18 " « . . / .A.0"A>U c < ; \ c5 0

auuaacoucc A

C C _ i - ^ " U A

""17 . " f - j . 0 " "O...-C*caci6 S:J. 5

c = u . .

. - 7. , ° 0 QC A OA 0 AA 0 -

O O U C C A O

o CAAOOOC _cf

14 '" j , S:S 7A ?[jf C 'O '

^ Q U C U O O U C O

13 s*

11 V

c 5:o'

Scca

" .<

aooacocc

A

10

. u . , 9CUACUOCUUOOC

A."C

Figure 4. Secondary structure model for SSU rRNA of the bacterium Escherichia coli.


Habbacterium halobium

25 V

24 o

26£ 27

39 42

u

4i

u Qcuca aoac

... ..c V40 •

••*=.36

3 7 ^

36

A • Uc oQ . Cc oQ . C

\ 2 8 s:L 30

43

Auuacij:ca<Mj*uAAuoaoucAu

46oc c*cucc° .co a* 00.0u c o *

IU ^7*9

23

auccacuC A O O C O A

33

#•••'#••

47

21a • cc -ac • a

2 AU o 32

A caccouccij ACCOUUCCUCOU

:• 3

uoococac,, i

/ 4849

UOCCACAUOUUU

18 u U c^

UUAOOOOO coccocoaouCuA CUOOJCOCOA A A * * S

\

<\lAOCCOUAOO°Q

OUCOOCOUCU . *

17 °COC-Oo-co* c .

c o

15uv°=»

<Aê*j;r"713

c- ou* oc • oO- Ca- CA

s:ru 812

1 1 '

c* a

?:S 10

Figure 5. Secondary structure model for SSU rRNA of the archaebacteriurri Halobacterium halobiwn.


Palmaria palmata

41u"c39 *2 43

U • O %. A ' to-y U -A A

N C-0 A C

. U nf

V-V°a 25

V \V - • , co ca '*• V

26

_ .o D.X o-c

«u-*o o'.L l-l 44•" ?:2* | : |

o L „ 38 S ou. 5 : |*o • c *;

. « ' • .

C A°u.-.->u

O C -

24E23-8

E23-9

*?:SC 27A°-S

A uO A

•«</•«„ -ô

U- 0A A

29 36

C*U.. O

\ 28 "|:|*u «;?$...„„«£?.lAOUAAUOA" ' " U C A * " * C O * OAO * AC?* c A " % ' '

COO 7 A A OUU VUUU AUCUUUOOVUC OOCU UOCU ugr yn C y C C^"S S ui;u;o;«u; . OA c J V»A*» ,• °o •

oc&o JOOA- ° ° „ 23 \ u O > o ' c<.«3oU

U C C W*COA.A C OSO . U * A * U 2 2 ° ' • ,

E23-6 . , / / " % , .

34

31

46

ACOOTV CC O U U U # C » A *

45 / V0"*o°5... , . c

/ 47?^

''*'Acuouc«o<icououc0 a ° E 2 3 - 2., caou au u acoc ao

E23-5c . o "

E23-1

121

C , C • O O C • 0 * A U *C

:0 *9?9-f-oc» «:j » %

IICMOOAUCC A<> A . U 4

18

17

*AOCOUOOOUC* cu £

u ocococcci cu u u u A

A * " ^

49W Q A C C O A UU flÂ 0 i

UCCUACC yyoAouOAu oau oocu o fuocco^yyyuApaco'AOOAAio ^ OAUUCACU^ O C C A A ^ C O U ^ gC OCUOACOCCOOUCCOC ,

o 5 . - 15 5 : ° . A O U

A*°0 / " ""uc<;vs V1"-""111-

C yCA CA "

u . • " cK W «e / *A° °CA°

0^ CCOAOOO^ A °

13 ouocûUcc?o:=0 7

C « ^ C A'

o ua* . Au * o - c *

U V u <J • A„" . c ..c-o.

ouuucca*j*oou0

OAAOOCOUCC A *

rE10-1 » Q . C

c aCO

:? 10

Figure 6. Secondary structure model for SSU rRNA of the red alga Pabnaria palmata.


Oiardia duodenalis

41 e .39

43

c CQ4i CO QO*OC OOCOCC O

cc°cc rE23-7 s g *

cCBuyo uoao

• a u

"V'f \tt-c S.

OCCCCOAO

27

40 | :• c 5:

»? i:38°:

c >o

-• * \

' . / E23-6

• A . O - 2 2

21

cc°ua.c"".A O . C A

O u • A Uc- c' ° 0°

," . Cn

a> cC'Oc • oo* co* c

00 c • a28 a . %

OAOUUUCA

36 !iuc»

<+ 35 34"^-% *

_31 33 A

46

45 cc>af»aoaccf<>c

o l -^ 47

, « Z C A M » **• 'I ApO UOACOAOOOOUA

ACMCCauCC ACUOUUCCCCCKI ccocacoc. c

»° 48

i f l A cccocc

'ccc^j,

1 7°c .C

49

AOOAAOO A oouccocaccccca coccooo d"A * A « « t ;

X 5°UAUCCOUAOOW0auAoocaucc . *ot: 5

? : S A

'16c*ct

"'We,;• ^ ». ccoooca ' 1

1 « ooaui*cuCccao*c .

ccacuoocoo oc«

u co u

O- CA Qa. cc O

COOC OCOGGCc*U 'o. .cC

a* cc* ao-c*

c'-oc 0

c°Co 10a 0

Figure 7. Secondary structure model for SSU rRNA of the polymastigote Giardia duodenalis.


Homo sapiens mitochondrion

41 <a .^ CV o c A«

Q .c c•oc. r it 11

25 \ - \

24?

Z7 a- ca-c

C U ' * c

38

36

! • * *

45•V

UAOAUUUUOU

% , / 23 •<

\ 2s A - ;«AACAOUiJ U

c C r° *UCOUCAA A C « V Ua* '""*<» U " * l * c

c • cA J ' c * A U 3 5 coA- VV...«««.c«K>. . •<

33 ^« « " 2 2 Cl='

-••"c Ac»uuu .-Aorr ^2 c c

21

/ 8 : i c ; rO U-A U * . uC I U O U • A

>n'=.ccJ-4<.c« j :u 3

OOA UOOCOUOCULrCA

CCU ACUOCOCOAAOU•IACUAAO" *Q "

UUOAUUC A CA

1 9 y *•"

49

„ 4

. 0 .

« ? »Ju»0u»* u

" ?16 ^

A

1 5 ^C

c

13<«" , f

AM1 2 J

cA0

c

cAc .

0c

0

4

cccuc

0

cA

5

6A U

c

7

O

8

\°auAAauou

OUUCACC0

50ACU°O

tUOA A A

Figure 8. Secondary structure model for SSU rRNA of Homo sapiens mitochondrion.

Compilation of small ribosomal subunit RNA structures€¦ · TAXONOMIC CLASSIFICATION OF SPECIES For the Eukarya, the taxonomic classification of the species listed in Table 1 is

Documents