La taxonomie répond à un besoin des microbiologistes de classer et identifier précisément les souches des microorganismes qu’ils isolent ou détectent sur la base de critères fiables. Parmi les bactéries, l’espèce est un taxon particulièrement difficile à définir car les critères utilisés sont difficiles à appliquer à tous les clades; ainsi savoir si deux souches appartiennent à deux espèces distinctes ou non repose souvent sur des critères arbitraires.
Si lors du développement de la microbiologie les critères taxonomiques étaient phénotypiques (coloration de Gram, caractères biochimiques…) et limités, l’apparition dans les années 1980 des techniques moléculaires a grandement modifié la taxonomie, en particulier le développement du séquençage dans les années 1970 puis des séquenceurs automatiques à partir des années 1990.
Les critères moléculaires actuellement utilisés sont l’hybridation ADN-ADN et la comparaison de séquences d’ADN comme l’ARNr 16S. Pour l’hybridation ADN-ADN, deux souches appartenant à la même espèce doivent présenter des valeurs d’hybridation supérieures à 70 % [Wayne et al., 1987 ; Stackebrandt et al., 2002]. Pour l’ARNr 16S, des niveaux d’identité nucléotidiques supérieurs ou égaux à 95 % et supérieurs ou égaux à 98,7 % sont requis aux niveaux du genre et de l’espèce, respectivement (ce dernier seuil était précédemment de 97%) [Stackebrandt et al., 1994 ; 2006].
L’ARNr 16S présente plusieurs limites : ce genre est conservé et ainsi ne permet pas systématiquement une détermination correcte au niveau de l’espèce ; il a été montré chez certaines souches la présence de plusieurs copies de l’ARNr 16S ainsi qu’une variabilité pouvant atteindre 1 %, voire dépasser 1,3 % chez certaines souches, ce qui correspond au seuil de l’espèce [Pei et al, 2010].
Si l’ARNr 16S présente les limites évoquées précédemment, actuellement sa séquence est disponible pour la plupart des souches-types des espèces possédant une nomenclature officielle, ce qui n’est pas le cas d’autres gènes. Près de 3 millions de séquences d’ARNr 16S sont actuellement disponibles dans les bases de données [http://www.http://rdp.cme.msu.edu/] ce qui rend encore plus solide cet outil. C’est pourquoi l’analyse de cette séquence demeure encore très largement pratiquée par les équipes de recherche.
Toutefois, il est clair que la variabilité des séquences d’ARNr 16S entre genres bactériens a été sous-évaluée lors de la mise au point des seuils de 95 % pour le genre et 98,7 % pour l’espèce et que ces valeurs sont loin de s’appliquer à tous les microorganismes. Les valeurs de 95 et 98,7 % restent arbitraires et ont été mises au point après analyse d’un nombre limité de taxa et il n’existe pas depuis de seuil applicable à l’ensemble des bactéries.
De plus, au sein de certains genres bactériens, il a été rapporté plusieurs espèces validées ayant présenté des séquences ARNr 16S identiques malgré des phénotypes différents, comme c’est le cas pour le genre Mycobacterium [Clarridge, 2004]. L’application stricte du critère en vigueur aboutirait à la suppression de nombreuses espèces validées.
Au niveau du genre, de nombreux auteurs ont critiqué la valeur seuil de 95 % car elle ne s’applique pas à tous les genres bactériens. Par exemple le pourcentage d’identité minimum observé entre les différentes espèces des genres Streptomyces et Chlorobium est de 78 et 86,1 %, respectivement, ce qui justifierait, en fonction des critères en vigueur, la création de nouveaux genres [Alexander et al., 2002].
Devant ces discordances, nous avons souhaité évaluer les variations de similarité des séquences ARNr 16S entre espèces bactériennes validées. Pour cela, nous avons focalisé notre analyse sur les bactéries appartenant à des genres associés à l’homme.
Les séquences ARNr 16S de ces espèces ont été obtenues dans la base de données LPSN (http://www.bacterio.net/). Les résultats sont présentés par genres, détaillant les valeurs minimum et maximum de similarité entre espèces validées.
Taxonomy responds to a requirement, for microbiologists, to classify and identify with precision the bacterial strains they isolate or detect, on the basis of reliable criteria.
Among bacteria, the species status is particularly difficult to describe as a taxon, because the criteria used are difficult to apply to every clade; thus, determining if two strains belong to distinct species or not often relies on arbitrary criteria.
Altough initially taxonomical criteria were phenotypic (Gram staining, biochemical features…), and were limited, the development in the 1980’s of molecular technologies has greatly changed the taxonomy, particularly the development of 16S rRNA sequencing in the 1970’s, then the development of automated sequencers from the 1990’s.
The official molecular criteria currently used include DNA-DNA hybridization (DDH) and comparison of 16S rRNA sequences. Using DDH, two strains belong to the same species if they exhibit hybridization values > to 70% [Wayne et al., 1987; Stackebrandt et al., 2002]. For16S rRNA, nucleotidic identity thresholds ≥ 95% and 98.7% are required at the genus and species levels, respectively [Stackebrandt et al., 1994; 2006].
However, 16S rRNA-based taxonomy suffers several limits: this gene is conserved and thus doesn’t provide an accurate determination at the species level; it has been shown, within some strains, the presence of several copies of 16S rRNA, and for some of these strains there is variability that can be > to 1,3%, that is actually the threshold of the species level for some strains [Pei et al, 2010].
Despite these limits, 16S rRNA sequences are currently available for almost all type strains of species with standing in nomenclature, which isn’t the case for other genes. Almost 3 millions of 16S rRNA sequences are currently available in databases [http://www.http://rdp.cme.msu.edu/]. This is why the analysis of this gene remains widely used by research teams.
However, it is clear that the variability of 16S rRNA sequences between bacterial genera has been underestimated. Values of 95% and 98.7% remain arbitrary and have been determined after analysis of a limited number of taxa.
Moreover, within some bacterial genera, it has been reported several validated species with identical 16S rRNA sequences while showing different phenotypes, as is the case for the genus Mycobacterium [Clarridge, 2004]. A strict application of the current criteria would result in to the suppression of many species with standing in nomenclature.
At the genus level, numerous authors also criticized the 95% threshold because it doesn’t apply to all bacterial genera. For instance the minimum percentage observed between the different species of Streptomyces and Chlorobium genera is 78 and 86.1% respectively, which would justify, according to the current criteria, creation of new genera [Alexander et al., 2002].
In front of these discrepancies, we wanted to estimate the variations of similarity of the 16S rRNA sequences among bacterial species and genera with standing in the nomenclature. To do this, we focused our analysis on bacteria associated with humans.
16S rRNA sequences were obtained from the LPSN database (http://www.bacterio.net/). Results are shown by genus and we detailed the minimum and maximum values between species for all genera.
Achromobacter
Range of percentages of similarity : 97,7 – 99,8 %
7 species studied
minimum : A. ruhlandii AF205370 – A. piedchaudii AB681803
maximum : A. spanius AY170848 – A. marplatensis EU150134
Acidovorax
Range of percentages of similarity : 95,5 – 99,9 %
13 species studied
minimum : A. konjaci AJ420325 – A. temperans AF078766
maximum : A. avenae NR_041757 – A. oryzae DQ360414
Acinetobacter
Range of percentages of similarity : 92,7 – 99,9 %
27 species studied
minimum : A. rudis EF204258 – A. tjernbergiae AF509825
maximum : A. calcoaceticus AJ888983 – A. pittii HQ180184
Actinobacillus
Range of percentages of similarity : 91,2 – 99,6 %
18 species studied
minimum : A. scotiae Y09653 – A. anseriformium AY172727 ; A. scotiae Y09653 – A. hominis AY362890
maximum: A. equuli EF166060 – A. suis AY362899
Actinobaculum
Range of percentages of similarity : 92,4 – 95,7 %
4 species studied
minimum : A. suis S83623 – A. urinale AJ439453
maximum : A. massiliense AF487679 – A. suis S83623
Actinomyces
Range of percentages of similarity : 85,0 – 98,0 %
39 species studied
minimum : A. neuii AM084228 – A. dentalis AJ697609
maximum : A. oris GQ421308 – A. naeslundii X81062
Aerococcus
Range of percentages of similarity : 93,2 – 99,7 %
7 species studied
minimum : A. christensenii Y17318 – A. suis AM230658
maximum : A. urinaequi D87677 – A. viridans AB680262
Aeromicrobium
Range of percentages of similarity : 95,7 – 99,0 %
10 species studied
minimum : A. ponti AM778683 – A. flavum EF133690
maximum : A. panaciterrae AB245387 – A. ginsengisoli AB245394
Aeromonas
Range of percentages of similarity : 90,2 – 100 %
31 species studied
minimum : A. simiae AJ536821 – A. sharmana DQ013306
maximum : A. bestiarum X60406 – A. salmonicida AB027542 – A. piscicola FM999971
Afipia
Range of percentages of similarity : 97,3 – 99,4 %
5 species studied
minimum : A. broomeae U87759 – A. birgiae AF288304
maximum : A. felis AGWZ01000001 – A. masiliensis AY029562
Aggregatibacter
Range of percentages of similarity : 94,0 – 97,0 %
3 species studied
minimum : A. actinomycetemcomitans CP001733 – A. segnis AF300472
maximum : A. segnis AF300472 – A. aphrophilus AY362906
Alcaligenes
Range of percentages of similarity : 98,5 %
2 species studied
minimum : A. faecalis D88008 – A. aquatilis JX986974
Aliivibrio
Range of percentages of similarity : 96,0 – 99,7 %
6 species studied
minimum : A. fischeri AY341436 – A. wodanis AJ132227
maximum : A. logei AJ437616 – A. salmonicida EU257756
Alistipes
Range of percentages of similarity : 90,1 – 97,1 %
5 species studied
minimum : A. shahii AY974072 – A. indistinctus AB490804
maximum : A. finegoldii AY643083 – A. shahii AY974072
Anaerococcus
Range of percentages of similarity : 92,3 – 97,2 %
6 species studied
minimum : A. tetradius AF542234 – A. vaginalis AF542229
maximum : A. tetradius AF542234 – A. prevotii NR_041939
Anaplasma
Range of percentages of similarity : 95,6 – 99,7 %
6 species studied
minimum : A. bovis U03775 – A. marginale AF309866
A. bovis U03775 – A. ovis AF309865
maximum : A. bovis U03775 – A. ovis AF309865
Arthrobacter
Range of percentages of similarity : 79,6 – 100 %
70 species studied
minimum : A viscosus AJ639832 – A. psychrolactophilus AF134179
maximum : A. oxydans X83408 – A. polychromogenes X80741
Atopobium
Range of percentages of similarity : 92,3 – 96,5 %
4 species studied
minimum : A. rimae AF292371 – A. minutum X67148
maximum : A. rimae AF292371 – A. parvulum AF292372
Bacillus
Range of percentages of similarity : 82,7 – 100 %
178 species studied
minimum : B. decisifrondis DQ465405 – B. schlegelii AB042060
maximum : B. mycoides AB021192 – B. weihenstephanensis AB021199 ;
B. aerophilus AJ831844 – B. stratosphericus AJ831841
Bacteroides
Range of percentages of similarity : 74,8 – 98,7 %
41 species studied
minimum : B. coprocola AB200224 – B. galacturonicus DQ497994
maximum : B. faecis AB547640 – B. thetaiotaomicron AB510710
Bartonella
Range of percentages of similarity : 97,3 – 99,8 %
25 species studied
minimum : B. chomelii AY254309 – B. vinsonii subsp. berkhoffii DQ228135
maximum : B. bovis AF293391 – B. schoenbuchii AJ278187
Bifidobacterium
Range of percentages of similarity : 90,7 – 100 %
45 species studied
minimum : B. animalis D86185 – B. psychroaerophilum AY174108
maximum : B. merycicum D86193 – B. magnum GU361824
Bordetella
Range of percentages of similarity : 98,0 – 100 %
8 species studied
minimum : B. avium AF177666 – B. petrii AJ249861
maximum : B. bronchiseptica AB680479 – B. parapertussis AF366577
Borrelia
Range of percentages of similarity : 94,5 – 99,9 %
21 species studied
minimum : B. japonica L40597 – B. miyamotoi D45192
maximum : B. crocidurae GQ358191 – B. duttonii AF107363
Bosea
Range of percentages of similarity : 97,4 – 99,9 %
8 species studied
minimum : B. lathyri FR774993 – B. minatitlanensis AF273081
maximum : B. eneae AF288300 – B. vestrisii AF288306
Brachyspira
Range of percentages of similarity : 95,6 – 99,7 %
7 species studied
minimum : B. pilosicoli AY155458- B. aalborgi Z22781
maximum : B. intermedia CP002874 – B. hyodysenteriae U14930
Bradyrhizobium
Range of percentages of similarity : 96,4 – 99,5 %
13 species studied
minimum : B. elkanii U35000 – B. iriomotense AB300992
maximum : B. canariense AJ558025 – B. japonicum U69638
Brevibacillus
Range of percentages of similarity : 92,4 -99,8 %
17 species studied
minimum : B. laterosporus D16271 – B. aydinogluensis HQ419073
maximum : B. formosus AB112712 – B. brevis GU125635
Brevibacterium
Range of percentages of similarity : 79,0 – 99,5 %
30 species studied
minimum : B. mcbrellneri X93594- B. frigoritolerans AM747813
maximum : B. massiliense EU868814 – B. ravenspurgense EU086793
Brevundimonas
Range of percentages of similarity : 95,1 – 99,9 %
23 species studied
minimum : B. bacteroides AJ227782 – B. diminuta AB021415
maximum : B. vesicularis AJ227780 – B. nasdae AB071954
Brucella
Range of percentages of similarity : 99,4 – 100 %
10 species studied
minimum : B. inopinata EU053207 – B. ovis L26168
maximum : B. abortus AM158979 – B. ceti AM158982 ;
B. melotensis AY594215 – B. neotomae AY594216 – B. microti AM392286 – B. pinnipedialis AM158981 – B. suis AM158980
Burkholderia
Range of percentages of similarity : 92,2 – 99,8 %
63 species studied
minimum : B. silvatlantica AY965240 – B. andropogonis DQ786951
maximum : B. arboris AM747630 – B. lata AM905038
Campylobacter
Range of percentages of similarity : 89,1 – 99,3 %
23 species studied
minimum : C. helveticus U03022 – C. hominis AJ251584
maximum : C. lari subsp. lari AY621114 – C. volucris FM883694
Capnocytophaga
Range of percentages of similarity : 89,3 – 98,6 %
8 species studied
minimum : C. granulosa U41347 – C. haemolytica AB671760
maximum : C. canimorsus AY643075 – C. cynodegmi AY643076
Caulobacter
Range of percentages of similarity : 96,3 – 99,7 %
7 species studied
minimum : C. fusiformis AJ227759 – C. henricii AJ227758
maximum : C. segnis AB023427 – C. vibrioides AJ009957
Cedecea
Range of percentages of similarity : 96,8 – 99,2 %
3 species studied
minimum : C. neteri AB086230 – C. lapagei AB273742
maximum : C. neteri AB086230 – C. davisae AF493976
Cellulomonas
Range of percentages of similarity : 93,3 – 99,6 %
18 species studied
minimum : C. bogoriensis X92152 – C. phragmiteti AM902253
maximum : C. biazotea X83802 – C. fimi X83803
Chlamydia
Range of percentages of similarity : 97,2 – 98,4 %
3 species studied
minimum : C. trachomatis D89067 – C. suis NR_029196
maximum : C. muridarum D85718 – C. trachomatis D89067
Chlamydophila
Range of percentages of similarity : 94,8 – 99,8 %
6 species studied
minimum : C. felis D85701 – C. pneumoniae NR_026527
maximum : C. abortus D85709 – C. psittaci NR_036864
Chlorobium
Range of percentages of similarity : 95,7 – 96,9 %
4 species studied
minimum : C. phaeovibrioides AJ290834 – C. clathratiforme AM086645
maximum : C. phaeovibroides AJ290834 – C. limicola CP001097
Chryseobacterium
Range of percentages of similarity : 91,5 – 99,6 %
61 species studied
minimum : C. antarcticum AY553293 – C. taeanense AY883416
maximum : C. solincola EU516352 – C. treverense FN297836
Citrobacter
Range of percentages of similarity : 96,5 – 99,7 %
10 species studied
minimum : C. gillenii AF025367 – C. rodentium AF025363
maximum : C. braakii AF025368 – C. gillenii AF025367
Clostridium
Range of percentages of similarity : 78,4 – 99,9 %
162 species studied
minimum : C. caminithermale AF458779 – C. rectum X77850
maximum : C. scatologenes AB610553 – C. carboxidivorans FR733710
Collinsella
Range of percentages of similarity : 92,2 – 97,7 %
4 species studied
minimum : C. intestinalis AB031063 – C. aerofaciens AB011816
maximum : C. intestinalis AB031063 – C. stercoris AB031061
Comamonas
Range of percentages of similarity : 92,8 – 99,9 %
14 species studied
minimum : C. koreensis AF275377 – C. badia AB164432
maximum : C. testosteroni M11224 – C. thiooxydans DQ322069
Cytophaga
Range of percentages of similarity : 81,3 -98,6 %
4 species studied
minimum : C. aurantiaca AB681044 – C. fermentans AB517712
maximum : C. aurantiaca AB681044 – C. hutchinsonii AB517710
Delftia
Range of percentages of similarity : 97,5 – 99,8 %
4 species studied
minimum : D. acidovorans AB021417 – D. litopenaei GU721027
maximum : D. lacustris EU888308 – D. tsuruhatensis AB075017
Dermacoccus
Range of percentages of similarity : 98,3 – 99,9 %
4 species studied
minimum : D. abyssi AY894323 – D. nishinomyaensis X87757
maximum : D. barathri AY894328- D. profundi AY894329
Desulfovibrio
Range of percentages of similarity : 84,2 – 99,5 %
54 species studied
minimum : D. acrylicus U32578 – D. africanus subsp. africanus X99236
maximum : D. carbinolicus AY626035 – D. magneticus D43944
Dialister
Range of percentages of similarity : 92,7 – 95,4 %
5 species studied
minimum : D. pneumosintes X82500 – D. succinatiphilus AB370249
maximum : D. invisus AY162469 – D. propionicifaciens AY850119
Dietzia
Range of percentages of similarity : 94,2 – 99,8 %
13 species studied
minimum : D. psychroalcalophilus AB049630 – D. papillomatosis AY643401
maximum : D. schimae EU375845 – D. maris X79290
Edwardsiella
Range of percentages of similarity : 94,2 – 99,8 %
3 species studied
minimum : E. tarda AB050827 – E. hoshinae AB050825
maximum : E. tarda AB050827 – E. ictaluri AB050826
Eggerthella
Range of percentages of similarity : 96,7 %
2 species studied
E. lenta AB558167 – E. sinensis AY321958
Ehrlichia
Range of percentages of similarity : 96,7 – 98,1 %
5 species studied
minimum : E. muris U15527 – E. ruminantium CR925678
maximum : E. canis AF162860 – E. chaffeensis M73222
Enterobacter
Range of percentages of similarity : 94,9 – 99,8 %
19 species studied
minimum : E. nimipressuralis Z96077 – E. pulveris DQ273684
maximum : E. oryzae EF488759 – E. radicincitans HF569043
Enterococcus
Range of percentages of similarity : 93,4 – 100 %
41 species studied
minimum : E. cecorum AF061009 – E. faecalis AB012212
maximum : E. caccae AY943820 – E. silesiacus AM039966 ;
E. pseudoavium AF061002 – E. vikkiensis HQ378515
Enterorhabdus
Range of percentages of similarity : 97,3 %
2 species studied
E. caecimuris DQ789120 – E. mucosicola AM747811
Erwinia
Range of percentages of similarity : 94,8 – 99,7 %
16 species studied
minimum : E. oleae GU810925 – E. piriflorinigrans GQ405202
maximum : E. aphidicolaFN547376 – E. persicina U80205
Erysipelothrix
Range of percentages of similarity : 96,6 – 99,8 %
3 species studied
minimum : E. tonsillarum AB055906 – E. inopinata AJ550617
maximum : E. tonsillarum AB055906 – E. rhusiopathiae AB034200
Escherichia
Range of percentages of similarity : 95,3 – 99,1 %
5 species studied
minimum : E. coli X80725 – E. vulneris AF530476
maximum : E. albertii AJ508775 – E. fergusonii AF530475
Eubacterium
Range of percentages of similarity : 79,1 – 99,5 %
37 species studied
minimum : E. cylindroides AB558487 – E. yurii GU269551
maximum : E. callanderi X96961- E. limosum AB595134
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Flavobacterium
Range of percentages of similarity : 75,6 – 99,3 %
86 species studied
minimum : F. acidificum JX986959 – F. ummariense HQ329187
maximum : F. beibuense GQ245972 – F. rakeshii JF830803
Francisella
Range of percentages of similarity : 96,6 – 99,4 %
5 species studied
minimum : F. halioticida JF290376 – F. tularensis subsp. tularensis Z21931
maximum : F. noatunensis subsp. noatunensis DQ295795 – F. philomiragia AY928394
Fusobacterium
Range of percentages of similarity : 92,1 – 99,4 %
14 species studied
minimum : F. naviforme AJ006965 – F. necrophorum AJ867039
maximum : F. canifelinum AY162221 – F. nucleatum AB573068
Gemella
Range of percentages of similarity : 93,5 – 98,5 %
6 species studied
minimum : G. cuniculi AJ251987 – G. asaccharolytica EU427463
maximum : G. haemolysans L14326 – G. sanguinis Y13364
Globicatella
Range of percentages of similarity : 99,7 %
2 species studied
G. sanguinis S50214 – G. sulfidifaciensAJ297627
Gordonia
Range of percentages of similarity : 94,5 – 99,9 %
34 species studied
minimum : G. caeni JF806526 – G. sinesedis AF380834
maximum : G. cholesterolivorans EU244645 – G. sihwaniensis J416151
Granulicatella
Range of percentages of similarity : 95,4 – 97,1 %
3 species studied
minimum : G. balaenopterae Y16547 – G. elegans AF016390
maximum : G. elegans AF016390 – G. adiacens AY879299
Haemophilus
Range of percentages of similarity : 86,2 – 99,3 %
13 species studied
minimum : H. felis AF224292 – H. piscium JN175340
maximum : H. aegyptius AY362905 – H. influenzae AY613528
Hafnia
Range of percentages of similarity : 98,6 %
2 species studied
H. alvei AB519795 – H. paraalvei FM179943
Helcococcus
Range of percentages of similarity : 92,7 – 94,6 %
3 species studied
minimum : H. kunzii X69837 – H. sueciensis AJ579914
maximum : H. kunizii X69837 – H. ovis Y16279
Helicobacter
Range of percentages of similarity : 91,2 – 99,2 %
31 species studied
minimum : H. cynogastricus DQ004689 – H. mesocricetorum AF072471
maximum : H. felis M57398 – H. salomonis U89351
Herbaspirillum
Range of percentages of similarity : 96,2 – 99,8 %
13 species studied
minimum : H. rhizosphaerae DQ188986 – H. canariense HQ830496
maximum : H. hiltneri DQ150563 – H. lusinatum AF543312
Holospora
Range of percentages of similarity : 98,1 %
2 species studied
H. obtusa JF713682 – H. undulata HE797906
Ignatzschineria
Range of percentages of similarity : 98,5 – 99,3 %
3 species studied
minimum : I. larvae AJ252143 – I. indica EU008088
maximum : I. larvae AJ252143 – I. ureiclastica EU008089
Janibacter
Range of percentages of similarity : 96,3 – 98,9 %
6 species studied
minimum : J. melonis AY522568- J. corallicola AB286023
maximum : J. hoylei FR749912 – J. anophelis AY837752
Janthinobacterium
Range of percentages of similarity : 99,1 %
2 species studied
J. agaricidamnosum Y08845 – J. lividum Y08846
Kingella
Range of percentages of similarity : 94,3 – 96,0 %
4 species studied
minimum : K. denitrificans M22516 – K. potus AJ629192
maximum : K. kingae AY551999 – K. oralis ACJW02000005
Klebsiella
Range of percentages of similarity : 96,4 – 99,7 %
6 species studied
minimum : K. granulomatis AF010251 – K. oxytoca AF129440
maximum : K. pneumoniae subsp. pneumoniae X87276 – K. variicola AJ783916
Kluyvera
Range of percentages of similarity : 98,4 – 98,8 %
4 species studied
minimum : K. crypcrascens AF310218 – K. intermedia JQ917919
maximum : K. intermedia JQ917919 – K. ascorbata AF008579
Kocuria
Range of percentages of similarity : 94,4 – 99,5 %
17 species studied
minimum : K. aegyptia DQ059617 – K. kristinae X80749
maximum : K. polaris AJ278868 – K. rosea
Kurthia
Range of percentages of similarity : 96,3 – 97,6 %
3 species studied
minimum : K. zopfii AB271740 – K. sibirica AJ605774
maximum :K. gibsonii AB271738 – K. zopfii AB271740
Kytococcus
Range of percentages of similarity : 98,3 – 99,9 %
4 species studied
minimum : K. schroeteri AJ297722 – K. sedentarius CP001686
maximum : K. schroeteri AJ297722 – K. aerolatus FM992368
Lactobacillus
Range of percentages of similarity : 79,4 – 99,9 %
150 species studied
minimum : L. oris X94229 – L. rogosae GU269544
maximum : L. plantarum AJ965482 – L. pentosus D79211
Lactococcus
Range of percentages of similarity : 90,7 – 98,4 %
7 species studied
minimum : L. chungangensis EF694028 – L. fujiensis AB485959
maximum : L. chungangensis EF694028 – L. raffinolactis EF694030
Legionella
Range of percentages of similarity : 91,3 – 99,5 %
53 species studied
minimum : L. geestiana Z49723 – L. oakridgenesis Z32642
maximum : L. sainthelensi Z49734 – L. santicrucis HF558374
Leminorella
Range of percentages of similarity : 90,7 – 98,4 %
2 species studied
L. grimontii AJ233421 – L. richardii HF558368
Leptospira
Range of percentages of similarity : 87,6 – 99,7 %
16 species studied
minimum : L. meyeri AY631878 – L. wolffii AKWX01000041
maximum : L. broomii AY796065 – L. fainei AY631885
Leptotrichia
Range of percentages of similarity : 88,6 – 97,2 %
7 species studied
minimum : L. goodfellowii AY029807 – L. wadei AY029802
maximum : L. hongkongensis EU919515 – L. trevisanii AF206305
Leuconostoc
Range of percentages of similarity : 93,3 – 99,7 %
14 species studied
minimum : L. fallax AF360738 – L. inhae AF439560
maximum : L. citreum AF111948 – L. holzapfelii AM600682
Listeria
Range of percentages of similarity : 95,6 – 99,6 %
8 species studied
minimum : L. rocourtiae FJ557241 – L. grayi X98526
maximum : L. innocua X98527 – L. monocytogenes JF967620
Massilia
Range of percentages of similarity : 94,2 – 99,4 %
19 species studied
minimum : M. aurea AM231588 – M. alkalitolerans AY679161
maximum : M. albidiflava AY965999- M. lutea AY966001
Methylobacterium
Range of percentages of similarity : 92,8 – 100 %
44 species studied
minimum : M. gnaphalii AB627071 – M. nodulans AF220763
maximum : M. dichloromethanicum AB175631 – M. extorquens AB175632
Microbacterium
Range of percentages of similarity : 92,0 – 100 %
75 species studied
minimum : M. lindanitolerans EU873539 – M. ginsengisoli AB271048
maximum : M. agarici FJ807673 – M. lindanitolerans EU873539
Micrococcus
Range of percentages of similarity : 95,3 – 99,8 %
8 species studied
minimum : M. flavus DQ491453 – M. lactis FN673681
maximum : M. yunnanensis FJ214355 M. luteus AJ536198
Micromonospora
Range of percentages of similarity : 96,3 – 99,7 %
43 species studied
minimum : M. rifamycinica AY561829 – M. fulviviridis X92620
maximum : M. aurantiaca JQ659911 – M. marina AB196712
Microvirga
Range of percentages of similarity : 95,9 – 98,7 %
8 species studied
minimum : M. aerophila GQ421848 – M. flocculans AB098515
maximum : M. aerilata GQ421849 – M. zambiensis HM362433
Mobiluncus
Range of percentages of similarity : 97,9 %
2 species studied
Mobiluncus curtisii AJ318408 – Mobiluncus mulieris AJ318410
Moraxella
Range of percentages of similarity : 89,4 – 99,1 %
18 species studied
minimum : M. atlantae AB680638 – M. cuniculi AF005188
maximum : M. equi AF005184 – M. lacunata D64049
Morganella
Range of percentages of similarity : 98,2 %
2 species studied
M. morganii subsp. morganii AJ301681 – M. psychrotolerans DQ358135
Mycobacterium
Range of percentages of similarity : 92,2 – 100 %
149 species studied
minimum : M. salmoniphilum DQ866768 – M. xenopi AJ536033
maximum : several species :
M. africanum AF480605 – M. tuberculosis AM283534
M. senegalense AY457081 – M. farcinogenes AY457084 – M. houstonense AY457067
M. gastri AF480602 – M. kansasii AJ536035
M. murale AB537171 – M. tokaiense AF480590
M. paraseoulense DQ536404 – M. seoulense DQ536403
Mycoplasma
Range of percentages of similarity : 68,7- 99,8 %
114 species studied
minimum : M. felis U09787 – M. suis AY492086
maximum : M. capricolum U26046 – M. leachii U26053
Neisseria
Range of percentages of similarity : 83,1 – 99,9 %
21 species studied
minimum : N. iguanae GU233442 – N. ovis AF005186
maximum : N. flava AJ239301 – N. macacae HF558383
Neorickettsia
Range of percentages of similarity : 99,1 %
2 species studied
N. risticii M21290 – N. sennetsu M73219
Nitrosomonas
Range of percentages of similarity : 92,0 – 98,0 %
9 species studied
minimum : N. europaea HE862405 – N. ureae FR828472
maximum : N. marina FR828473 – N. aestuarii FR828476
Nocardia
Range of percentages of similarity : 93,1 – 99,9 %
85 species studied
minimum : N. pigrifrangens AF219974 – N. coublieae DQ235688
maximum : N. sienata AB121770 – N. testacea AB192415
Nocardioides
Range of percentages of similarity : 91,0- 99,2 %
55 species studied
minimum : N. iriomotensis AB544079 – N. agariphilus EF466113
maximum : N. marinisabuli AM422448 – N. basaltis EU143365 ; N. basaltis EU143365 – N. salarius DQ401092
Nocardiopsis
Range of percentages of similarity : 99,2 – 99,9 %
35 species studied
minimum : N. kunsanensis AF195412 – N. rhodophaea AY619714
maximum : N. arvandica EU410477 – N. sinus persici EU410476
Ochrobactrum
Range of percentages of similarity : 94,8 – 100 %
17 species studied
minimum : O. gallinifaecis AJ519939 – O. intermedium AM114411
maximum : O. anthropi U70978 – O. intermedium AM114411
Paenibacillus
Range of percentages of similarity : 89,8 – 99,4 %
130 species studied
minimum : P. siamensis AB295645 – P. pueri EU391155
maximum : P. antarcticus AJ605292 – P. macquariensis AB073193 ;
P. cellulositrophicus FJ178001 – P. cineris JQ762408
Pandoraea
Range of percentages of similarity : 95,8- 99,7 %
9 species studied
minimum : P. norimbergensis Y09879 – P. thiooxydans EF397578
maximum : P. sputorum JQ839144 – P. oxalativorans AB469785 ; P. vervacti AB510956 – P.pnomenusa AY268170
Pantoea
Range of percentages of similarity : 95,9 – 99,5 %
19 species studied
minimum : P. calida GQ367478 – P. rodasii JF295053
maximum : P. allii AY530795 – P. ananatis U80196
Pasteurella
Range of percentages of similarity : 86,1 – 98,8 %
14 species studied
minimum : P. lymphangitidis HF558372 – P. pneumotropica GU809183
maximum : P. P. dagmatis AY362920 – P. stomatis AY362925
Peptoniphilus
Range of percentages of similarity : 86,8 – 97,9 %
10 species studied
minimum : P. olsenii DQ911242 – P. ivoricii Y07840
maximum : P. asaccharolyticus AF542228 – P. indolicus AY153431
Peptostreptococcus
Range of percentages of similarity : 95,3 – 98,8 %
3 species studied
minimum : P. stomatis DQ160208 – P. russellii AY167952
maximum : P. stomatis DQ160208 – P. anaerobius AY326462
Photobacterium
Range of percentages of similarity : 97,6 – 99,4 %
21 species studied
minimum : P. angustum D25307 – P. ganghwense AY960847
maximum : P. indicum AB016982 – P. frigidiphilum AY538749
Photorhabdus
Range of percentages of similarity : 97,6 – 98,0 %
3 species studied
minimum : P. asymbiotica subsp. asymbiotica Z76755 – P. temperata subsp. temperata AJ007405
maximum : P. asymbiotica subsp. asymbiotica Z76755 – P. luminescens subsp. luminescens X82248
Planctomyces
Range of percentages of similarity : 84,2 – 87,2 %
3 species studied
minimum : P. brasiliensis AJ231190 – P. limnophilus X62911
maximum : P. brasiliensis AJ231190 – P. maris AJ231184
Porphyromonas
Range of percentages of similarity : 84,4 – 99,9 %
16 species studied
minimum : P. uenonis AB547668 – P. bennonis EU414673
maximum : P. cansulci AB547655 – P. crevioricanis GU233446
Prevotella
Range of percentages of similarity : 82,6 – 98,1 %
46 species studied
minimum : P. pallens Y13105 – P. tannerae AF183404
maximum : P. malaninogenica AY323525 – P. scopos FJ545434
Propionibacterium
Range of percentages of similarity : 89,3 – 99,2 %
11 species studied
minimum : P. acidifaciens EU979537 – P. jensenii AJ704571
maximum : P. avidum AJ003055 – P. propionicum AJ003058
Proteus
Range of percentages of similarity : 94,5 – 99,3 %
7 species studied
minimum : P. penneri DQ885258 – P. rettgeri AM040492
maximum : P. penneri DQ885258 – P. vulgaris DQ885262
Providencia
Range of percentages of similarity : 97,5 – 99,5 %
8 species studied
minimum : P. alcalifaciens AJ301684 – P. vermicola AM040495
maximum : P. vermicola AM040495 – P. rettgeri AM040492
Pseudoclavibacter
Range of percentages of similarity : 92,8 – 96,6 %
4 species studied
minimum : P. caeni HQ266601- P. helvolus X77440
maximum : P. chungagensis FJ514934 – P. helvolus X77440
Pseudomonas
Range of percentages of similarity : 82,3 – 100 %
142 species studied
minimum : P. aeruginosa X06684 – P. carboxydohydrogena AB021393
maximum : P. parafulva AB046999 – P. cremoricoloranta AB060137
Psychrobacter
Range of percentages of similarity : 93,0 – 99,9 %
34 species studied
minimum : P. immobilis U39399 – P. lutiphocae FM165580
maximum : P. marincola AJ309941 – P. submarinus AJ309940
Ralstonia
Range of percentages of similarity : 97,6 – 99,0 %
5 species studied
minimum : R. insidiosa AF488779 – R. mannitolilytica AJ270258
maximum : R. solanacearum EF016361 – R. sygygii NR_025975
Raoultella
Range of percentages of similarity : 98,7 – 99,3 %
3 species studied
minimum : R. ornithinolytica U78182 – R. terrigena Y17658
maximum : R. ornithinolytica U78182 – R. planticola AF129443
Rhizobium
Range of percentages of similarity : 86,9 – 99,9 %
54 species studied
minimum : R. aggregatus X73041 – R. lupini X87273
maximum : R. fabae DQ835303 – R. pisi AY509899
Rhodobacter
Range of percentages of similarity : 92,2 – 99,9 %
12 species studied
minimum : R. aestuarii AM748926 – R. ovatus AM690348
maximum : R. johrii AM398152 – R. sphaeroides NR_029215
Rhodococcus
Range of percentages of similarity : 93,8 -100 %
32 species studied
minimum : R. fascians X79186 – R. gordoniae EU741104
maximum : R. jialingiae DQ185597 – R. qingshengii DQ090961
Rickettsia
Range of percentages of similarity : 97,5 – 99,8 %
26 species studied
minimum : R. akari L36099 – R. canadensis
maximum : R. conorii AF541999 – R. slovaca L36224
R. rickettsii L36217 – R. peacockii DQ062433
Rothia
Range of percentages of similarity : 95,2 – 97,9 %
6 species studied
minimum : R. aeria AB071952 – R. terrae DQ822568
maximum : R. aeria AB071952 – R. dentocariosa CP002280
Ruminococcus
Range of percentages of similarity : 82,0 – 96,8 %
9 species studied
minimum : R. bromii EU266549 – R. obeum X85101
maximum : R. feacis FJ611794 – R. torques L76604
Salmonella
Range of percentages of similarity : 98,3 %
2 species studied
S. bongori AF029227 – S. enterica subsp. Enterica AE006468
Sanguibacter
Range of percentages of similarity : 95,3 – 99,1 %
6 species studied
minimum : S. soli EF547937 – S. keddieii CP001819
maximum : S. inulinus X79451 – S. keddieii CP001819
Serratia
Range of percentages of similarity : 95,5 – 99,6 %
15 species studied
minimum : S. rubidaea AB004751 – S. proteamaculans AJ233434
maximum : S. grimesii AJ233430 – S. proteamaculans AJ233430
Shewanella
Range of percentages of similarity : 90,2 – 100 %
57 species studied
minimum : S. olleyana AF295592 – S. fodinae FM203122
maximum : S. marinintestina AB081757 – S. sairae AB081762
Shigella
Range of percentages of similarity : 98,5 – 99,9 %
4 species studied
minimum : S. dysenteriae X96966 – S. boydii AB273731
maximum : S. flexneri X96963 – S. sonnei FR870445
Sphingomonas
Range of percentages of similarity : 89,6 – 94,9 %
70 species studied
minimum : S. adhaesiva D13722 – S. roseiflava D84520
maximum : S. aquatilis AF131295 – S. melonis AB055863
Spirochaeta
Range of percentages of similarity : 81,6 – 99,3 %
17 species studied
minimum : S. perfilievii AY337318 – S. zuelzerae FR749929
maximum : S. asiatica X93926 – S. dissipatitropha AY995150
Spiroplasma
Range of percentages of similarity : 86,0 – 99,9 %
36 species studied
minimum : S. ixodetis GU585671 – S. penaei AY771927
maximum : S. atrichopogonis AB681165- S. insolitum AY189133
Staphylococcus
Range of percentages of similarity : 95,4 – 99,9 %
45 species studied
minimum : S. simulans D83373 – S. fleurettii AB233330
maximum : S. intermedius D83369 – S. pseudintermedius AJ780976
Stenotrophomonas
Range of percentages of similarity : 96,1 – 99,7 %
11 species studied
minimum : S. daejeonensis GQ241320 – S. rhizophila AJ293463
maximum : S. maltophilia AB294553 – S. pavanii FJ748683
Streptococcus
Range of percentages of similarity : 90,6 – 99,7 %
73 species studied
minimum : S. macacae AY188351 – S. orisratti AF124350
maximum : S. infantarius AF177729 – S. lutesiensis AJ297215
Streptomyces
Range of percentages of similarity : 88,4 – 100 %
532 species studied
minimum : S. gardneri AB184754 – S. cinereus AB184072
maximum : S. asiaticus AB249947 – S. rhizosphaericus AB249941 ;
S. hygroscopicus AB184428 – S. endus AY999911
S. catenulae AJ621613 – S. misakiensis AB217605
Thermotoga
Range of percentages of similarity : 89,4 – 99,7 %
9 species studied
minimum : T. elfii X80790 – T. neapolitana AB039768
maximum : T. neapolitana AB039768 – T. maritima M21774
Tissierella
Range of percentages of similarity : 93,8 – 94,8 %
3 species studied
minimum : T. praeacuta X80832 – T. creatinophila GQ461823
maximum : T. creatinini FR749955 – T. praeacuta X80832
Treponema
Range of percentages of similarity : 81,4 – 98,2 %
15 species studied
minimum : T. isoptericolens AM182455 – T. succinifaciens NR_074755
maximum : T. denticola AF139203 – T. putidum AJ543428
Tsukamurella
Range of percentages of similarity : 95,2 – 100 %
11 species studied
minimum : T. spongiae AY714239 – T. soli FJ917743
maximum : T. pseudospumae AY238513 – T. sunchonensis AF150494
Ureaplasma
Range of percentages of similarity : 93,6 – 99,1 %
7 species studied
minimum : U. cati D78649 – U. gallorale U62937
maximum : U. parvum AF073456 – U. urealyticum AF073450
Vagococcus
Range of percentages of similarity : 94,2 – 99,3 %
8 species studied
minimum : V. elongatus AF445297 – V. fessus AJ243326
maximum : V. carniphilus AY179329 – V. fluvialis Y18098
Veillonella
Range of percentages of similarity : 92,7 – 99,1 %
11 species studied
minimum : V. magna EU096495 – V. montpelliereni AF473836
maximum : V. dispar AY995770 – V. parvula AB538437
Vibrio
Range of percentages of similarity : 92,2 – 99,8 %
88 species studied
minimum : V. ruber AF462458 – V. gallaecicus EU541605
maximum : V. atlanticus EF599163 – V. kanaloae AM162657
Wolbachia
Range of percentages of similarity : 77,7 – 83,7 %
3 species studied
minimum : W. pipientis AY026913 – W. Persica KC294230
maximum : W. Persica KC294230 – W. Melophagi X89110
Xanthomonas
Range of percentages of similarity : 97,1 – 100 %
30 species studied
minimum : X. melonis Y10756 – X. phaseoli GU993265
maximum : X. arboricola Y10757 – X. hortorum Y10759 ; X. campestris AB680404 – X. cynarae AF208315 – X. gardneri FR749911 ; X. cucurbitae AB680438 – X. dyei JQ955625
Yersinia
Range of percentages of similarity : 97,5 – 99,9 %
18 species studied
minimum : Y. Enterocolitica subsp. enterocolitica AF366378 – Y. ruckeri AF366385
maximum : Y. pestis AF366383 – Y. pseudotuberculosis AF366375
