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List of probes tested for in situ hybridization

Short name Name (Alm et al.) Target Specificity
Aqua828S-*-Aqua-0828-a-A-1816S rRNAAquabacterium spp.
Pomo828S-*-Pomo-0828-a-A-1816S rRNAPolaromonas vacuolata
Gor596S-G-Gor-0596-a-A-2216S rRNAGordonia (Gordona)
Fibr225S-G-Fibr-0225-a-A-2116S rRNAFibrobacter
ACA652 (ACA23A)S-G-Acin-0652-a-A-1816S rRNAAcinetobacter
Ade44116S rRNAAlcaligenes defragans
ALBO34a23S rRNABordetella spp., Alcaligenes spp. (sensu stricto)
ALF1BS-Sc-aProt-0019-a-A-1716S rRNAAlphaproteobacteria, some Deltaproteobacteria, Spirochaetes
ALF4-132216S rRNAalpha4-subgroup of Proteobacteria
ALF92116S rRNANevskia ramosa clone NO22
ALF96816S rRNAAlphaproteobacteria, except of Rickettsiales
AT145816S rRNAAzoarcus-Thauera cluster
Azo125116S rRNAAzoarcus tolulyticus strains Tol-4, Td-1, Td-15, Td-17, Td-19, Td-21, A. evansii KB740, Azoarcus sp. strain pF6
AZA483S-*-Aza-0645-a-A-1816S rRNAAzoarcus cluster
BAC303S-*-Bacto-0303-a-A-1716S rRNAmost Bacteroidaceae and Prevotellaceae, some Porphyromonadaceae
Bcv13b23S rRNABurkholderia vietnamensis, B. cepacia
BET42aL-C-bProt-1027-a-A-1723S rRNABetaproteobacteria
LSPotu11021-1127S-*-Lsp-1127-a-A-2016S rRNALachnospiraceae OTU_11021
BONE23A16S rRNAbeta1-group of Betaproteobacteria
BTWO23A16S rRNAcompetitor for BONE23A
CF319a16S rRNAmost Flavobacteria, some Bacteroidetes, some Sphingobacteria
CF319b16S rRNAsome Flavobacteria and Sphingobacteria
CFB28616S rRNAmost members of the genus Tannerella and the genus Prevotella of the class Bacteriodetes
CFB56316S rRNAmost Flavobacteria
CFB71916S rRNAmost members of the class Bacteriodetes, some Flavobacteria and Sphingobacteria
CFB97216S rRNAsome Flavobacteria
Chls-0523S-O-Chls-0523-a-A-1816S rRNAChlamydiales
cl81-64416S rRNAFew Desulfobacteraceae
CREN499S-K-Cren-0499-a-A-1816S rRNAmost Crenarchaeota
660(DBB660)S-G-Dsbb-0660-a-A-2016S rRNAsome Desulfobulbus
221(DBM221)S-G-Dsbm-0221-a-A-2016S rRNADesulfobacterium vacuolatum, D. niacini, D. autotrophicum
DCC209S-S-Dcc.mv-0209-a-A-1816S rRNADesulfococcus multivorans
DEM1164r16S rRNADesulfotomaculum cluster I and other Firmicutes
DNMA65716S rRNAsome Desulfonema
DRM43216S rRNADesulfuromonas spp., Pelobacter spp.
129(DSB129)S-G-Dsb-0129-a-A-1816S rRNAmost Desulfobacter
DSB98516S rRNADesulfobacter, Desulfobacula, Desulfospira, and Desulfotignum
DSBAC35516S rRNAmost Desulfobacterales and Syntrophobacterales
DSBO22416S rRNADesulfobotulus sapovorans, Desulfovibrio fairfieldensis, and other Deltaproteobacteria
DSC193S-*-Dsb-0193-a-A-1816S rRNADesulfosarcina variabilis
DSD131 (DSVAE131)S-S-Dsv.ae-0131-a-A-1816S rRNADesulfovibrio aestuarii
DSF67216S rRNADesulfofrigus, Desulfofaba gelida, Desulfomusa hansenii
DSMA48816S rRNADesulfarculus baarsii, Desulfomonile tiedjei, and Syntrophus
DSR651S-*-Dsb-0651-a-A-1816S rRNASome Desulfobulbaceae
DSS22516S rRNADesulfosarcina and many other Desulfobacteraceae
DSS658S-*-Dsb-0658-a-A-1816S rRNADesulfobacteraceae and other Bacteria
DSV1292S-*-Dsv-1292-a-A-1816S rRNASome Desulfovibrio and Bilophila wadsworthia
DSV21416S rRNAMost Desulfomicrobium
DSV40716S rRNAFew Desulfovibrionaceae, Desulfohalobiaceae, and Desulfonatronumaceae
687(DSV687)S-F-Dsv-0687-a-A-1616S rRNAMost Desulfovibrionales (excluding Lawsonia) and many Desulfuromonales
DSV69816S rRNASome Desulfovibrio, Bilophila wadsworthia, and Lawsonia intracellularis
Dtm(bcd)230S-*-Dtm(bcd)-0230-a-A-1816S rRNAMany Desulfotomaculum cluster I and other Firmicutes
Dtm229S-G-Dtm-0229-a-A-1816S rRNADesulfotomaculum cluster I and other Firmicutes
ECO1167 (ECO 45A)23S rRNAEscherichia coli
EUB338 (Bact338) (bacterial)S-D-Bact-0338-a-A-1816S rRNAmost Bacteria
EUB338 II (SBACT P 338)S-*-BactP-0338-a-A-1816S rRNAPlanctomycetales
EUB338 III (SBACT V 338)S-*-BactV-0338-a-A-1816S rRNAVerrucomicrobiales
EUK51618S rRNAEukarya
EURY498S-K-Eury-0498-a-A-1416S rRNAmost Euryarchaeota
FFE8b16S rRNAFlavobacterium ferrugineum
gam1-124616S rRNA“Candidatus Gilliamella apicola” or Gamma-1 (symbiotic Gammaproteobacteria phylotype in honey bee)
G123TS-G-Thioth-697-a-A-1816S rRNAThiothrix eikelboomii, T. nivea, T. unzii, T. fructosivorans, T. defluvii, Eikelboom type 021N group I, II, III
G1BS-*-021Ng1-1029-a-A-1816S rRNAEikelboom type 021N group I
G2MS-*-021Ng2-842-a-A-1816S rRNAEikelboom type 021N group II
G3MS-*-021Ng3-996-a-A-1816S rRNAEikelboom type 021N group III
GAM42aL-C-gProt-1027-a-A-1723S rRNAGammaproteobacteria
Goam192S-S-G.am-0192-a-A-1816S rRNAGordona amarae
H7-1014S-*-H7-1014-a-A-1816S rRNAactivated sludge clone H7
HGC69A (HGC)L-P-Grps-1901-a-A-1823S rRNAActinobacteria (high G+C Gram-positive bacteria)
HoAc1402S-*-HoAc-1402-a-A-1816S rRNAAcidobacteria, activated sludge clones A22, A34, H3, H44, S6
Hvu103416S rRNAHyphomicrobium vulgare
HYD20816S rRNAHydrogenophaga spp.
HYD56B23S rRNAHydrogenophaga spp.
Hydr540S-O-Hydr-0540-a-A-1916S rRNAAquificales
LEG22616S rRNALegionellaceae
LEG70516S rRNALegionella
LEGPNE116S rRNALegionella pneumophila
LGC354A16S rRNAFirmicutes (Gram-positive bacteria with low G+C content)
LGC354B16S rRNAFirmicutes (Gram-positive bacteria with low G+C content)
LGC354C16S rRNAFirmicutes (Gram-positive bacteria with low G+C content)
MB117416S rRNAMethanobacterium spp., Methanobrevibacter spp., Methanosphaera spp.
MC110916S rRNAMethanococcus spp.
MS141416S rRNAMethanosarcina spp., Methanococcoides spp., Methanolobus spp., Methanohalophilus spp.
MS821S-G-Msar-0821-a-A-2416S rRNAMethanosarcina frisius, Methanosarcina spp., Methanosarcina acidovorans, Methanosarcina thermophila, Methanosarcina barkeri, Methanoholophilus mahii, Methanophilus sp.
MSMX86016S rRNAMethanosarcina spp., Methanococcoides spp., Methanolobus spp., Methanohalophilus spp., Methanosaeta spp.
MX82516S rRNAMethanosaeta spp.
Myb736aS-*-Myb-0736-a-A-2216S rRNAMycobacterium complex
Myb736bS-*-Myb-0736-b-A-2216S rRNAMycobacterium complex
NAL120816S rRNANevskia clones NO2 and NO11, Mycoplana bullata, Brevundimonas diminuta
NAL65716S rRNANevskia clones NO2 and NO11
NIT3S-G-Nbac-1035-a-A-1816S rRNANitrobacter spp.
NmV (Ncmob)S-S-Nmob-0174-a-A-1816S rRNANitrosococcus mobilis (Nitrosomonas) lineage
NONEUB (NON338) (non-Bact338)16S rRNAcontrol probe complementary to EUB338
Nse1472S-*-Nse-1472-a-A-1816S rRNANitrosomonas europea, N. halophila, N. eutropha, Kraftisried-Isolat Nm103
Nsm156S-G-Nsm-0155-a-A-1916S rRNANitrosomonas spp., Nitrosococcus mobilis
Nso1225S-F-bAOB-1224-a-A-2016S rRNABetaproteobacterial ammonia-oxidizing bacteria
Nso190S-F-bAOB-0189-a-A-1916S rRNABetaproteobacterial ammonia-oxidizing bacteria
Nsv44316S rRNANitrosospira spp.
Ntcoc84S-*-Ntcoc-84-a-A-1816S rRNANitrococcus mobilis
Ntspa1026S-*-Ntspa-1026-a-A-1816S rRNANitrospira moscoviensis, activated sludge clones A4 and A11
Ntspa662S-G-Ntspa-662-a-A-1816S rRNAgenus Nitrospira
Ntspa712S-*-Ntspa-712-a-A-2116S rRNAmost members of the phylum Nitrospirae
Ntspn693S-*-Ntspn-693-a-A-2016S rRNANitrospina gracilis
OTU1-1415S-*-OTU1-1415-a-A-2016S rRNAZoogloea ramigera, activated sludge clones A16, H7, H10, H11, H13, H22, H27. H40, S21
OTU14-129S-*-OTU14-0129-a-A-2016S rRNAHyphomicrobium spp., activated sludge clones A7b, A39
OTU16-1027S-*-OTU16-1027-a-A-1816S rRNAactivated sludge clones H4, H6, H29, S7
OTU16-1350S-*-OTU16-1350-a-A-1816S rRNAactivated sludge clones H4, H6, H29, S7
OTU17-66S-*-OTU17-0066-a-A-2016S rRNAactivated sludge clones H46, S43
OTU2-132 (ATDe132)S-*-ATDe-0132-a-A-1816S rRNAActivated sludge clones A33, H25, H30, H35, S3, S10, and S23 of the Azoarcus-Thauera-Denitromonas lineage
OTU2-467S-*-OTU2-0467-a-A-2016S rRNAactivated sludge clones A33, H25, H30, H35, S3, S10, S23
OTU25to31-1406S-*-OTU25to31-1406-a-A-1816S rRNAsome Anaerolineae
OTU26-650S-*-OTU26-0650-a-A-1816S rRNAactivated sludge clones A11b, A30, H1, H19
OTU28-1346S-*-OTU28-1346-a-A-1816S rRNAactivated sludge clones H39, S41
STEBA1426S-*-Steba-1426-a-A-1816S rRNASome members of the Sterolibacterium lineage
OTU31-656S-*-OTU31-0656-a-A-1816S rRNAactivated sludge clones H8, S9
OTU32-208S-*-OTU32-0208-a-A-1816S rRNAactivated sludge clones A31, S47
OTU32-630S-*-OTU32-0630-a-A-1816S rRNAactivated sludge clones A31, S47
OTU3-445S-*-OTU3-0445-a-A-2016S rRNAactivated sludge clones A13, H12, H20, H23, S28, S40
OTU43/44-360S-*-OTU43/44-0360-a-A-1816S rRNAAcidobacteria group a, activated sludge clones A22, A34, H3
OTU45-720S-*-OTU45-0720-a-A-2016S rRNAactivated sludge clones H44 and S6, soil clone C105, soil clone 11-25, Antarctic lake ice clone LB3-30
OTU4-645S-*-OTU4-0645-a-A-1816S rRNAAlcaligenes latus, activated sludge clones A2, A26b
OTU6-178S-*-OTU6-0178-a-A-1816S rRNABrachymonas denitrificans, activated sludge clone A6b
PAR1244S-G-Parc-1244-a-A-1916S rRNAgenus Paracoccus
PAR1457S-G-Parc-1457-a-A-1816S rRNAgenus Paracoccus
PAR651S-G-Parc-0651-a-A-1816S rRNAgenus Paracoccus
Pdv103116S rRNAParacoccus denitrificans, P. versutus
Pdv19816S rRNAParacoccus denitrificans, P. versutus
PLA46S-P-Planc-0046-a-A-1816S rRNAPlanctomycetales
PLA886S-P-Planc-0886-a-A-1916S rRNAPlanctomycetes
Ppu56a23S rRNAPseudomonas putida, P. mendocina
PS56a23S rRNAmost true Pseudomonas spp.
Ps-Ag123S rRNAPseudomonas fluorescens Ag1
SARCI551S-G-Sarci-0551-a-A-2016S rRNAgenus Methanosarcina
SARCI645S-G-Sarci-0645-a-A-1916S rRNAgenus Methanosarcina
SRB385 (SRB)S-*-Srb-0385-a-A-1816S rRNAMost Desulfovibrionales and other Bacteria
SRB385Db16S rRNADesulfobacterales, Desulfuromonales, Syntrophobacterales, Myxococcales, and other Bacteria
SUBU123716S rRNABurkholderia spp., Sutterella spp.
Sval42816S rRNASome Desulfobulbaceae (excluding most Desulfobulbus
Tbcil832S-*-Tbcil-0832-a-A-1816S rRNAthermophilic Bacillus spp.
Thus438S-G-Thus-0438-a-A-1816S rRNAThermus spp.
Ttoga660S-*-Ttoga-0660-a-A-1816S rRNAThermotogales
UNIV1390S-*-Univ-1390-a-A-1816S rRNAall Organisms
XAN81816S rRNAXanthomonas branch
ZAL16S rRNAZoogloea ramigera ATCC 19623
ZBE16S rRNAZoogloea ramigera ATCC 25935
ZRA23a (ZRA,ZOGLO647)S-*-Zoglo-0647-a-A-1816S rRNAMost members of the Zoogloea lineage, not Z. resiniphila
PcaeC9S-S-PcaeC9-217-a-A-1816S rRNACandidatus Paracaedibacter acanthamoebae (endosymbiont of Acanthamoeba sp. UWC9)
PcaeE39S-S-PcaeE339-217-a-A-1816S rRNACandidatus Paracaedibacter symbiosus (endosymbiont of Acanthamoeba sp. UWE39)
CaeAc998S-S-CaeAc-998-a-A-1816S rRNACandidatus Caedibacter acanthamoebae (endosymbiont of Acanthamoeba polyphaga HN-3)
Mg70516S rRNAtype I methanotrophs
Mg8416S rRNAtype I methanotrophs
Ma45016S rRNAtype II methanotrophs (Methylosinus/Methylocystis spp.)
Ma46416S rRNAtype II methanotrophs
Mg66916S rRNAMethylobacter spp., Methylomonas spp.
Mg100416S rRNAMethylomicrobium
Stemal16S rRNAStenotrophomonas maltophilia
Burcep16S rRNABurkholderia cepacia
Burkho16S rRNABurkholderia spp.
Haeinf16S rRNAHaemophilus influenzae
Sau16S rRNAStaphylococcus aureus
Spn16S rRNAStreptococcus pneumoniae
Ent16S rRNAEnterobacteriaceae except Proteus spp.
Kpn23S rRNAKlebsiella pneumoniae
Caal18S rRNACandida albicans
Cagl18S rRNACandida (Torulopsis) glabrata
Ckrus18S rRNACandida krusei
Cpara651 (Cpara)18S rRNACandida parapsilosis
PF218S rRNAall yeasts
Str16S rRNAStreptococcus spp.
Spy16S rRNAStreptococcus pyogenes
Saga16S rRNAStreptococcus agalactiae
Hpy-116S rRNAHelicobacter pylori
ClaR123S rRNAclarithromycin resistant Helicobacter pylori
ClaR223S rRNAclarithromycin resistant Helicobacter pylori
ClaR323S rRNAclarithromycin resistant Helicobacter pylori
ClaWT23S rRNAHelicobacter pylori (clarithromycin sensitve)
ATE23S rRNAAureobacterium testaceum
BKE23S rRNABrevibacterium sp. (B. ketoglutamicum)
CGL23S rRNACorynebacterium glutamicum
Pst6716S rRNAPseudomonas stutzeri, P. mendocina
Pst99716S rRNAPseudomonas stutzeri
Pae99716S rRNAPseudomonas spp.
ACI20816S rRNAAcidovorax spp.
COM142416S rRNAComamonas spp.
Ps23S rRNAPseudomonas spp.
Ppu23S rRNAPseudomonas spp.
Pce23S rRNABurkholderia spp.
Pdi16S rRNABrevundimonas (Pseudomonas) diminuta, Caulobacter spp., Mycoplana bullata
Cte16S rRNAComamonas spp., Acidovorax spp., Hydrogenophaga spp., Aquaspirillum spp.
NEUS-*-Nsm-0651-a-A-1816S rRNAMost halophilic and halotolerant Nitrosomonas spp.
PseaerA16S rRNAPseudomonas aeruginosa
PseaerA23S rRNAPseudomonas aeruginosa
Amx1900L-*-Amx-1900-a-A-2123S rRNAanaerobic ammonium-oxidizing bacteria, Candidatus `Brocadia anammoxidansapos and Candidatus `Kuenenia stuttgartiensisapos
Kst157S-S-Kst-0157-a-A-1816S rRNACandidatus Kuenenia stuttgartiensis
Ban162 (B. anam.)S-S-Ban-0162(B. anam.)-a-A-1816S rRNACandidatus Brocadia anammoxidans
Amx820S-*-Amx-0820-a-A-2216S rRNAanaerobic ammonium-oxidizing bacteria, Candidatus `Brocadia anammoxidansapos and Candidatus `Kuenenia stuttgartiensisapos
Syb701S-*-MUG28-0701-a-A-2016S rRNAclone MUG28
GNSB633S-*-GNSB-0633-a-A-2016S rRNAgreen nonsulfur clones MUG9, TUG8, TUG9, TUG10
DELTA495aS-C-dProt-0495-a-A-1816S rRNAMost Deltaproteobacteria and most Gemmatimonadetes
DELTA495bS-*-dProt-0495-b-A-1816S rRNAsome Deltaproteobacteria
DELTA495cS-*-dProt-0495-c-A-1816S rRNAsome Deltaproteobacteria
DSB706S-*-Dsb-0706-a-A-1816S rRNAMost Desulfobulbaceae and Thermodesulforhabdus
DSM213S-G-Dsm-0213-a-A-1816S rRNADesulfomicrobium
Tdsulfo848 (TDSV849)S-*-Tdsulfo-0848-a-A-18 (S-*-Tdsv-0849-a-A-18)16S rRNAMost Thermodesulfovibrio and some Magnetobacterium
Phasco74116S rRNAPhascolarctobacterium faecium, Acidaminococcus fermentans, Succiniclasticum ruminis
Veil22316S rRNAVeillonella dispar, Veillonella parvula, Veillonella atypica
Ehal146916S rRNAEubacterium hallii, Clostridium herbivorans, Clostridium polysaccharolyticum
Lach57116S rRNALachnospira multipara, Eubacterium eligens, Lachnospira pectinoschiza
Ecyl38716S rRNAEubacterium cylindroides, Clostridium innocuum, Eubacterium biforme, Eubacterium tortuosum, Eubacterium dolichum, Streptococcus pleomorphus
Rfla729S-*-Rfla-0729-a-A-1816S rRNARuminococcus albus, R. flavefaciens
Rbro730S-*-Rbro-0730-a-A-1816S rRNAClostridium sporosphaeroides, Ruminococcus bromii, Clostridium leptum
RHC439S-*-RHC-0439-a-A-1816S rRNARhodocyclus spp., most member of the Candidatus Accumulibacter cluster, Azospira lineage
RHW456S-G-Rhw-0456-a-A-1816S rRNABio-P enrichment culture clone R1
RHW991S-G-Rhw-0991-a-A-1816S rRNABio-P enrichment culture clone R1
RHX456S-G-Rhx-0456-a-A-1716S rRNACandidatus Accumulibacter phosphatis (clone R6)
RHX991S-G-Rhx-0991-a-A-1816S rRNACandidatus Accumulibacter phosphatis (clone R6)
MG-6416S rRNAtype I methanotrophs including Methylomonas spp., Methylomicrobium spp., Methylobacter spp., Methylococcus
MA-62116S rRNAtype II methanotrophs including Methylocystis spp., Methylosinus spp.
MA-22116S rRNAtype II methanotrophs including Methylocystis spp., Methylosinus spp.
Mc102916S rRNAMethylococcus spp.
Chlae-574S-F-Chlae-0574-a-A-1816S rRNAChlamydiaceae
Chla-0232S-G-Chla-0232-A-1816S rRNAChlamydia
Chlph-0583S-G-Chlph-0583-a-A-1816S rRNAChlamydophila
Ct-0623S-S-Ct-0623-a-A-1816S rRNAChlamydia trachomatis
Cpn-0214S-S-Cpn-0214-a-A-1816S rRNAChlamydophila pneumoniae
Cpn-0974S-S-Cpn-0974-a-A-1816S rRNAChlamydophila pneumoniae
Cps-1414S-S-Cps-1414-a-A-1816S rRNA“Chlamydophila psittaci” group including C. felis, C. abortus, and C. caviae
Cps-1353S-S-Cps-1353-a-A-1816S rRNA“Chlamydophila psittaci” group including C. felis, C. abortus, and C. caviae
Bn9-65816S rRNAsubgroup of the Parachlamydiaceae including Parachlamydia acanthamoebae (Hallaposs coccus), endosymbionts of Acanthamoebae sp. UWE25 and UWE1
ParaC-0658S-*-ParaC-0658-a-A-1816S rRNAsubgroup of the Parachlamydiaceae including Neochlamydia hartmannellae, endosymbiont of Acanthamoeba sp. UWC22
Ctaenio-998S-S-Ctaenio-998-a-A-1816S rRNACaedibacter taeniospiralis
TM730516S rRNAsubdivision 1 of candidate division TM7
TM790516S rRNAcandidate division TM7
TM752216S rRNAcandidate division TM7
TM756716S rRNAcandidate division TM7
CHL 1851S-F-t1851-0592-a-A-2016S rRNAfilamentous bacterium Eikelboom Type 1851
Enterbact D16S rRNAsome members of the Enterobacteriaceae
Enterbact B16S rRNAsome members of the Enterobacteriaceae and Vibrionaceae
ALT141316S rRNAAlteromonas, Colwellia
G Rb16S rRNARhodobacter, Roseobacter
G V16S rRNAVibrio
NOR1-5616S rRNANOR1 lineage (Gammaproteobacteria)
NOR2-145316S rRNANOR2 cluster group A (Gammaproteobacteria)
OCE23216S rRNAOceanospirillum
PSA18416S rRNAPseudoalteromonas, Colwellia
SAR86-124916S rRNASAR 86 cluster
SPH12016S rRNASphingomonas
Hypho-1241S-G-Hypho-1241-a-A-1916S rRNAHyphomicrobium
Gam1019S-S-g-Prot-1019-a-A-1816S rRNAphosphate accumulating bacteria (Gammaproteobacteria)
Gam1278S-S-g-Prot-1278-a-A-2016S rRNAphosphate accumulating bacteria (Gammaproteobacteria)
PAO846S-S-Rhodo-0846-a-A-1816S rRNACandidatus Accumulibacter phosphatis
actino-1011S-S-HGC-1011-a-A-1916S rRNATetrasphaera japonica, enhanced biological phosphorus removal clone Ebpr19, Ebpr20 (Actinobacteria)
NSR82616S rRNANitrospira moscoviensis, freshwater Nitrospira spp.
NSR115616S rRNANitrospira moscoviensis, freshwater Nitrospira spp.
NSR44716S rRNANitrospira spp.
MNP116S rRNAnocardioform actinomycetes
MLP16S rRNAMycobacterium sp. SMKN23, Mycobacterium sp. SMKN22, (nocardioform actinomycetes)
DLP16S rRNAnocardioform actinomycete sp.
GLP116S rRNAGordona sp. SMKN27, Gordona sp. SMKN12, Gordona sp. SMKN17, Gordona sp. SMKN14, (nocardioform actinomycetes)
GLP216S rRNAGordona sp. SMKN29, Gordona sp. SMKN15, (nocardioform actinomycetes)
GLP316S rRNAnocardioform actinomycete sp.
E.bar1237S-S-E.bar-1237-a-A-1816S rRNAEubacterium barkeri
E.bif462S-S-E.bif-0462-a-A-1816S rRNAEubacterium biforme
E.con1122S-S-E.con-1122-a-A-2016S rRNAEubacterium contortum
E.cyl461S-St-E.cyl-0461-a-A-1816S rRNAEubacterium cylindroides
E.cyl466S-St-E.cyl-0466-a-A-18-16S rRNAEubacterium cylindroides
E.dol183S-S-E.dol-0183-a-A-1816S rRNAEubacterium dolichum
E.had579S-S-E.had-0579-a-A-2016S rRNAEubacterium hadrum (Anaerostipes hadrus)
E.len194S-S-E.len-0194-a-A-1816S rRNAEubacterium lentum
E.lim1433S-S-E.lim-1433-a-A-1816S rRNAEubacterium limosum E. callanderi
E.mon84S-S-E.mon-0084-a-A-1816S rRNAEubacterium moniliforme
E.ven66S-S-E.ven-0066-a-A-1816S rRNAEubacterium ventriosum
GSB-532S-F-GSB-532-a-A-1516S rRNAgreen sulfur bacteria, Chlorobiaceae
GSB-822S-F-GSB-822-a-A-1916S rRNAgreen sulfur bacteria, Chlorobiaceae
GNSB-94116S rRNAphylum Chloroflexi (green nonsulfur bacteria)
CFX122316S rRNAphylum Chloroflexi (green nonsulfur bacteria)
CFX10916S rRNAsome members of the class Chloroflexi
CFX78416S rRNAsome members of the class Anaerolineae
EUK119518S rRNAEukarya
Glsc40718S rRNAGlaucoma scintillans
Glsc41318S rRNAGlaucoma scintillans
Glsc65118S rRNAGlaucoma scintillans
Glsc112918S rRNAGlaucoma scintillans
R-BT06516S rRNAsubgroup of Betaproteobacteria
R-FL61516S rRNAsubgroup of Bacteriodetes
TGP69016S rRNAPelotomaculum thermopropionicum
Pchl45416S rRNAPseudomonas chlororaphis
muD118S rRNAPseudo-Nitzschia multiseries (Bacilliarophyceae)
auD118S rRNAPseudo-Nitzschia australis (Bacilliarophyceae)
puD118S rRNAPseudo-Nitzschia pungens (Bacilliarophyceae)
CHLO0218S rRNAChlorophyta
CHLO0118S rRNAMost Chlorophyta, some Non-Chlorophyta
NCHLO0118S rRNAMost Non-Chlorophyta, some Chlorophyta (Chromista)
PI118S rRNAParaphysomonas imperforata (Chrysophyceae)
PI218S rRNAParaphysomonas imperforata (Chrysophyceae)
PIMP168318S rRNAParaphysomonas imperforata (Chrysophyceae)
PIMP63518S rRNAParaphysomonas imperforata (Chrysophyceae)
PIMP63518S rRNAParaphysomonas imperforata (Chrysophyceae)
PV118S rRNAParaphysomonas vestita (Chrysophyceae)
PV218S rRNAParaphysomonas vestita (Chrysophyceae)
PV318S rRNAParaphysomonas vestita (Chrysophyceae)
PV418S rRNAParaphysomonas vestita (Chrysophyceae)
PV518S rRNAParaphysomonas vestita (Chrysophyceae)
405_Pro16S rRNAProchlorococcus (Cyanophyceae)
181_ProHLI16S rRNAProchlorococcus HLI (Cyanophyceae)
645_ProHLI16S rRNAProchlorococcus HLI (Cyanophyceae)
645_ProHLII16S rRNAProchlorococcus HLII (Cyanophyceae)
1445_ProNATL16S rRNAProchlorococcus LL (Cyanophyceae)
181_ProLL16S rRNAProchlorococcus LL (Cyanophyceae)
645_ProLL16S rRNAProchlorococcus LL (Cyanophyceae)
405_Syn16S rRNASynechococcus (Cyanophyceae)
NA118S rRNAAlexandrium tamarense (North America)
P.pisc18S rRNAPfiesteria piscicida
EUK120918S rRNAEukarya
PAO651 (ACCBA651)S-G-Accba-0651-a-A-1816S rRNAMost members of the Candidatus Accumulibacter cluster
GAOQ43116S rRNACandidatus Competibacter phosphatis
GAOQ98916S rRNACandidatus Competibacter phosphatis
ACAC16S rRNAActinobacillus actinomycetemcomitans
B(T)AFO16S rRNATannerella forsythensis (Bacteroides forsythus)
POGI16S rRNAPorphyromonas gingivalis
PRIN16S rRNAPrevotella intermedia
FUSO16S rRNAFusobacterium spp.
VEPA16S rRNAVeillonella parvula
CREN51216S rRNAmost Crenarchaeota
CREN56916S rRNAmost environmental Crenarchaeota
EURY49616S rRNAMethanomicrobiales group and VAL 47, VAL 1, VAL9, VAL78 clones
EURY49916S rRNAMethanosarcina, Methanosaeta, Methanomicrobiales groups and VAL 47,VAL 1, VAL9, VAL78 clones
EURY51416S rRNAmost Euryarchaeota
Cap142816S rRNACandidatus capitivii acidiprotistae
EUKb119318S rRNAnearly all Eukarya
EUKb50318S rRNAnearly all Eukarya
EUKb31018S rRNAnearly all Eukarya
LKC59S-*-eProt-0059-a-A-1816S rRNAEpsilonproteobacterial group I from Lower Kane Cave
LKC1006S-*-eProt-1006-a-A-1816S rRNAEpsilonproteobacterial group II from Lower Kane Cave
HHY16S rRNAHaliscomenobacter hydrossis
TNI16S rRNAThiothrix nivea
LMU16S rRNALeucothrix mucor
21N16S rRNAEikelboom type 021N strain II-26
LDI16S rRNALeptothrix discophora
SNA16S rRNASphaerotilus natans
Hp16S-116S rRNAHelicobacter pylori
beta-57216S rRNACandidatus Snodgrassella alvi or Beta (symbiotic Neisseriaceae phylotype in honey bee)
OalgGAM44516S rRNAGammaproteobacterial, sulfur-oxidizing symbiont of Olavius algarvensis
OalgDEL13616S rRNADeltaproteobacterial symbiont of Olavius algarvensis
I. leu. (IleuSYM581)16S rRNAGammaproteobacterial symbiont of Inanidrilus leukodermatus
O. tan. (OtanSYM581)16S rRNAGammaproteobacterial symbiont of Olavius tantalus
PRYM0218S rRNAPrymnesiophyceae
PTB-6-7/103016S rRNAPTB 6/7 cluster
PTB-6-7/99716S rRNAPTB 6/7 cluster
PTB-1/48216S rRNAPTB 1 cluster, Stappia stellulata, bacterium (AB010864)
PTB-1/101416S rRNAPTB 1 cluster, Stappia stellulata
PTB-all/64616S rRNAAlphaproteobacterial clade (all PTB)
PELA0218S rRNAPelagophyceae clade containing Aureococcus, Pelagomonas, Pulvinaria, CCMP 1395
PELA0118S rRNAPelagophyceae
PAO46216S rRNACandidatus Accumulibacter phosphatis
ALBO57716S rRNAAlcaligenes, Bordetella and close relatives
DEV67716S rRNADevosia riboflavina and relatives
ENT18316S rRNAEnterobacteriaceae
FLX10116S rRNAFlavobacterium ferrugineum, Flexibacter elegans, F. sancti
MET121716S rRNAMethylophilus
NEV81716S rRNANevskia ramosa and relatives
PED67216S rRNAPedobacter heparinus and relatives
SPH49216S rRNASphingomonas, Erythrobacter
Ecras65118S rRNAEuplotes crassus
Ecras124618S rRNAEuplotes crassus
Evan65118S rRNAEuplotes vannus
Emin61918S rRNAEuplotes minuta
Emin65118S rRNAEuplotes minuta
PNA18S rRNAMacrorhabdus ornithogaster
Mcaps-103216S rRNAMethylocapsa acidiphila
Msint-126816S rRNAMethylosinus trichosporium
Msins-64716S rRNAMethylosinus sporium
Mcyst-143216S rRNAMethylocystis
Mcyst-126116S rRNApeat-inhabiting subgroup of Methylocystis spp.
Cluster6a192 (6a192)S-*-Nsm6a-0192-a-A-2016S rRNANitrosomonas oligotropha lineage (Cluster 6a)
PBR2S-S-Pbr2-0182-a-A-1916S rRNABifidobacterium breve
EBAC1790S-*-EBAC-1790-a-A-1823S rRNAEnterobacteriaceae
Ntspa685S-G-Ntspa-0685-a-A-2216S rRNANitrospira moscoviensis, Nitrospira marina and 710-9 clone
Myc657S-*-Myc-0657-a-A-1616S rRNAMycobacterium subdivision (mycolic acid-containing actinomycetes)
Hpy16S16S rRNAHelicobacter pylori
COR653S-*-Cor-0653-a-A-1816S rRNACoriobacterium group (Coriobacterium and Collinsella)
ATO291S-*-Ato-0291-a-A-1716S rRNAAtopobium cluster
Nscry1004S-*-Nscry-1004-a-A-1916S rRNANitrosomonas cryotolerans
Nscoc65S-*-Nscoc-65-a-A-1816S rRNANitrosococcus oceani, Nitrosococcus halophilus
Nscoc1248S-*-Nscoc-1248-a-A-1816S rRNANitrosococcus oceani, Nitrosococcus halophilus
Dhe1259t16S rRNAsome Dehalococcoides spp.
Dhe1259c16S rRNAsome Dehalococcoides spp.
Sca1309S-G-Sca-1309-a-A-2116S rRNAgenus Candidatus Scalindua
Scabr1114S-*-Scabr-1114-a-A-2216S rRNACandidatus Scalidua brodae
Amx368S-*-Amx-0368-a-A-1816S rRNAall ANAMMOX bacteria
BS820S-*-BS-820-a-A-2216S rRNACandidatus Scalidua wagneri, Candidatus Scalidua sorokinii
NSMR7616S rRNANitrosomonas marina-like ammonia-oxidizing bacteria
NSMR3416S rRNANitrosospira tenius-like ammonia-oxidizing bacteria
Nmo21816S rRNANitrosomonas oligotropha-lineage
Bfra602S-*-Bfra-0602-a-A-1916S rRNABacteroides fragilis group
Bdis656S-*-Bdis-0656-a-A-1816S rRNABacteroides distasonis
Clit135S-*-Clit-0135-a-A-1916S rRNAsome of the Clostridium lituseburense group (Clostridium cluster XI)
Chis150S-*-Chis-0150-a-A-2316S rRNAmost of the Clostridium histolyticum group (Clostridium cluster I and II)
Erec482S-*-Erec-0482-a-A-1916S rRNAmost of the Clostridium coccoides-Eubacterium rectale group (Clostridium cluster XIVa and XIVb)
Strc493S-*-Strc-0493-a-A-1916S rRNAmost Streptococcus spp. and some Lactococcus spp.
GB16S rRNAnovel gammaproteobacterial group
GB_G1 (GAOQ989)16S rRNAnovel gammaproteobacterial group
GB_G216S rRNAnovel gammaproteobacterial group
GB_416S rRNAnovel gammaproteobacterial group
GB_6 (Gam1019)16S rRNAnovel gammaproteobacterial group
GB_716S rRNAnovel gammaproteobacterial group
CFB56016S rRNAsubgroup of Bacteroidetes
CFB56216S rRNAsubgroup of Bacteroidetes
CFB37616S rRNAsubgroup of Bacteroidetes
Lis-63716S rRNAListeria spp., except L. grayi
Mka22016S rRNAsubgroup of Bacteroidetes
Mkb22116S rRNAsubgroup of Bacteroidetes
Mkc21916S rRNAsubgroup of Bacteroidetes
Mkd111116S rRNAsubgroup of Bacteroidetes
SGR22016S rRNASaprospira grandis
SGR120016S rRNASaprospira grandis and relatives
SGR142516S rRNASaprospira grandis and relatives
Bak65516S rRNACandidatus Magnospira bakii
Bak140816S rRNACandidatus Magnospira bakii
ARC9416S rRNAArcobacter
ARC143016S rRNAArcobacter
ACA652b16S rRNAsome unknown Acinetobacter-like species
T25-102816S rRNAclone T25 and T19 of a subgroup within the Betaproteobacteria
T25-22016S rRNAclone T25 and other clones of a subgroup within the Betaproteobacteria, not clone T19
T28-64916S rRNAclone T28 and T29 of a subgroup within the Alphaproteobacteria, Sphingomonas capsulata
T28-143516S rRNAclone T28 and T29 of a subgroup within the Alphaproteobacteria
GAM42_C103323S rRNAcurrently unknown
Lbrev16S rRNALactobacillus brevis
Lcoll16S rRNALactobacillus collinoides
Lcory16S rRNALactobacillus coryniformis
Lfarc16S rRNALactobacillus farciminis
Lhilg16S rRNALactobacillus hilgardii
Lmali16S rRNALactobacillus mali
Lpara16S rRNALactobacillus casei, Lactobacillus paracasei
Lzeae16S rRNALactobacillus zeae, Lactobacillus casei
Ooeni16S rRNAOenococcus oeni
Pdamn16S rRNAPediococcus damnosus
Pparv16S rRNAPediococcus parvulus
Urobe63aS-*-Urobe-0063-a-A-2016S rRNAuncultured Ruminococcus obeum-like bacteria
Urobe63bS-*-Urobe-0063-b-A-2016S rRNAuncultured Ruminococcus obeum-like bacteria
CFX123816S rRNAChloroflexus
RFX123816S rRNARoseiflexus assemblage
Pchl45416S rRNAPseudomonas chlororaphis
b9116S rRNAmealybug betaproteobacterial endosymbionts
b16216S rRNAmealybug betaproteobacterial endosymbionts
b88616S rRNAmealybug betaproteobacterial endosymbionts
b127316S rRNAmealybug betaproteobacterial endosymbionts
g8016S rRNAsecondary endosymbiont of Planococcus citri
g45816S rRNAsecondary endosymbiont of Planococcus citri
g63016S rRNAsecondary endosymbiont of Planococcus citri
g127316S rRNAsecondary endosymbiont of Planococcus citri
NLIMI 91S-G-N.limI-0091-a-A-1816S rRNANostocoida limicola I
NLIMII 175S-S-N.limII-0175-a-A-1816S rRNANostocoida limicola II strains except strain Ben 70
NLIMII 192S-S-N.limII-0192-a-A-1816S rRNANostocoida limicola II strain Ben 70
NLIMIII 301S-S-N.limIII-0301-a-A-1816S rRNANostocoida limicola III strains
NLIMIII 729S-S-N.limIII-0729-a-A-1816S rRNANostocoida limicola III strain Ben 220
NLIMIII 830S-S-N.limIII-0830-a-A-1816S rRNANostocoida limicola III strains except Ben 220
Bmy843S-*-Bmy-0843-a-A-1816S rRNABacillus
Ver620S-*-Ver-0620-a-A-1816S rRNAVerrucomicrobium
MIB661S-S-Bacm-0661-a-A-1816S rRNAmouse intestinal bacteria
MIB724S-S-Bacm-0724-a-A-1816S rRNAmouse intestinal bacteria
LGC16S rRNAFirmicutes (low G+C Gram-positives)
Clost I16S rRNAsubgroup of Clostridia cluster I and II
AW16S rRNAsome Acetobacterium species, E. limosum
DSV (DSV321)16S rRNASome Desulfovibrionaceae, Desulfomicrobiaceae, Desulfohalobiaceae, and other Bacteria
AMAR 839S-G-AMAR-0839-a-A-2216S rRNAAmaricoccus spp.
RSOLA23S rRNARalstonia solanacearum, Ralstonia syzygii, blood disease bacterium (BLDB)
RSOLB23S rRNARalstonia solanacearum, Ralstonia syzygii, blood disease bacterium (BLDB)
TTI-73216S rRNATreponema cluster I
Dev1-48616S rRNAectosymbiotic spirochetes on Devescovina sp. and Stephanonympha sp.
Dev14-48616S rRNAectosymbiotic spirochetes on Devescovina sp. and Stephanonympha sp.
Dev14-Tp65216S rRNAectosymbiotic spirochetes on Devescovina sp. and Stephanonympha sp.
Oxy8-Tp44416S rRNAectosymbiotic spirochetes on Oxymonas sp. and Stephanonympha sp.
Oxy26-Tp128116S rRNAectosymbiotic spirochetes on Oxymonas sp. and Stephanonympha sp.
Doh29918S rRNAAMD Dothideomycete fungi
Eur110818S rRNAEurotiomycetes, including AMD fungi
Oil84518S rRNAAMD Dothideomycete fungi
AcRic90S-*-AcEnd-0090-a-A-1816S rRNARickettsia-related endosymbionts of Acanthamoeba strains UWC8 and UWC36
AcRic1196S-*-AcEnd-1196-a-A-1816S rRNARickettsia-related endosymbionts of Acanthamoeba strains UWC8 and UWC36
MPH-73016S rRNAMethylophaga
MPHm-99416S rRNAMethylophaga marina
REX7216S rRNABacillus
LGC353b16S rRNABacillus
Aph1180S-G-Aph-1180-a-A-1816S rRNACandidatus Amoebophilus asiaticus
RhabdoS-S-RhaC-0992-a-A16S rRNACandidatus Rhabdochlamydia porcellionis
SBR9-1aS-D-s91a-0578-b-A-2016S rRNAAlphaproteobacterial SBR9 clone 1 (AY254694)
SBR9-1bS-D-s91a-0778-b-A-1816S rRNAAlphaproteobacterial SBR9 clone 1 (AY254694)
PAG59S-G-Pan-0059-a-A-1816S rRNAPantoea spp.
Apur453S-S-Lpcpur-0453-a-A-2616S rRNALamprocystis purpurea (DSM4197), strain A12 3 and clone 345, Lake Cadagno.
Cmok453S-S-Chrok-0453-a-A-2616S rRNAChromatium okenii (DSM169) and clone 359, Lake Cadagno.
Laro453S-S-Lpcro-0453-a-A-2616S rRNALamprocystis roseopersicina (DSM229) and clone 136, Lake Cadagno
S453DS-*-Lpc-0453-a-A-2616S rRNALamprocystis-related bacteria (strain D21 and clone 261, Lake Cadagno)
S453FS-*-Lpc-0453-b-A-2616S rRNALamprocystis - related bacteria (clones 335, 371 and strain cad16, Lake Cadagno)
DSC213S-S-Dscthz-0213-a-A-1816S rRNADesulfocapsa thiozymogenes
DSC441S-*-Dsc-0441-a-A-1916S rRNAFew Desulfocapsa
S453HS-*-Tcs-0453-a-A-2616S rRNAThiocystis minor-related bacteria (clones 222, 13 and strain H1.1, Lake Cadagno)
S448S-*-Tcs-0448-a-A-2116S rRNAThiocystis gelatinosa-related bacteria (clone 130 and strain 448.10, Lake Cadagno)
SRB44116S rRNAFew Desulfobulbaceae
DsmA455S-*-Dmn-0455-a-A-2616S rRNADesulfomonile-related Lake Cadagno clones 618, 624, 626, and 651
DsmB455S-*-Dmn-0455-b-A-2616S rRNADesulfomonile-related Lake Cadagno clone 650
Chlp441S-S-Chlphb-0441-a-A-2316S rRNAChlorobium phaeobacteroides (DSM 266), strain 1VIID7 and clone 366 Lake Cadagno.
Chlc190S-S-Chlctf-0190-a-A-2216S rRNAChlorobium clathratiforme (DSM 5477), strain 4DE and clones 810, 827, 849 Lake Cadagno.
UV7-763S-St-UV7-763-a-A-1816S rRNAParachlamydia sp. UV-7
TG1-Ta-RsaS-S-E.tri-1023-a-A-2016S rRNACandidatus Endomicrobium trichonymphae
TG1-Pv-RsaS-S-E.pyr-1023-a-A-2016S rRNACandidatus Endomicrobium pyrsonymphae
Arglo32S-O-Arglo-0032-a-A-2016S rRNAArchaeoglobales
Aqui1197S-O-Aqui-1197-a-A-2016S rRNAAquificales
Tcoc164S-O-Tcoc-0164-a-A-2016S rRNAThermococcales
APL63716S rRNAAplasma, acid mine drainage Thermoplasmatales
GPL64216S rRNAGplasma, acid mine drainage Thermoplasmatales
TPL75916S rRNATplasma, Thermoplasma spp.
BPL83016S rRNABplasma, acid mine drainage Thermoplasmatales
Meiot83616S rRNAMeiothermus sp.
Proca438S-G-Proca-0438-a-A-1816S rRNACandidatus Procabacter sp.
MB31116S rRNAMethanobacteriales
MB117416S rRNAMethanobacteriales (minus Methanothermus)
MC50416S rRNAMethanocaldococcaceae(+some Methanococcaceae)
MC110916S rRNAMethanococcaceae
MG1200b16S rRNAmost Methanomicrobiales
MS82116S rRNAMethanosarcina
MS141416S rRNAMethanosarcina, Methanococcoides, Methanolobus
MSMX86016S rRNAMethanosarcinales (all Methanosarcina and Methanosaeta)
MX82516S rRNAsome Methanosaetaceae
MX825b16S rRNAMethanosaetaceae subgroup
MX825c16S rRNAMethanosaetaceae subgroup
MX136116S rRNAMethanosaetaceae
HEL27416S rRNAHelicobacter sp., Wolinella sp.
HEL71716S rRNAHelicobacter sp., Wolinella sp.
HEP64216S rRNAHelicobacter hepaticus
GAN123716S rRNAHelicobacter ganmani
CTE998-101516S rRNACollimonas sp.
ZNS1439S-*-Znsym-1439-a-A-2016S rRNAZoothamnium niveum ectosymbiont
ZNS196S-*-Znsym-0196-a-A-1916S rRNAZoothamnium niveum ectosymbiont
MPA16S rRNACandidatus Microthrix
PPx3-142816S rRNACandidatus Alysiomicrobium bavaricum
Noli-64416S rRNACandidatus Alysiosphaera europaea
Sita-64916S rRNACandidatus Sphaeronema italicum
Combo-103116S rRNACandidatus Combothrix italica
Cate-101316S rRNACandidatus Catenimonas italica
MZ116S rRNAThauera spp. mzt1t
GAM42a_T1038_G103123S rRNARepresentatives of the Xanthomonas group
GAM42a_T103823S rRNARepresentatives of the Xanthomonas group
GAM42a_A1041_A104023S rRNARepresentatives of the Xanthomonas group and the Alphaproteobacteria, Brevundimonas diminuta
Cren53716S rRNACrenarchaea
Eury80616S rRNAEuryarchaea
PnecABCD-44516S rRNAPolynucleobacter cluster
Actino-221S-S-Actino-221-a-A-1816S rRNAActinobacterial PAO
Actino-658S-S-Actino-658-a-A-1816S rRNAActinobacterial PAO
Ih820S-*-Ih820-0820-a-A-1816S rRNADesulfotomaculum subcluster Ih (Pelotomaculum and Cryptanaerobacter)
ProCo1264S-*-ProCo-1264-a-A-2316S rRNARuminococcus productus and relatives
Csac67S-S-Csac-67-a-A-2016S rRNAClostridium saccharogumia
Betthio1001L-G-bThiob-1001-a-A-2123S rRNABetaproteobacterial Thiobacilli
Creno445S-S-Cpoly-445-a-A-1816S rRNACrenothrix polyspora
Cp653-A16S rRNACrenothrix polyspora sequence cluster I
Cp653-B16S rRNACrenothrix polyspora sequence cluster II-IV
Cp1130-A16S rRNACrenothrix polyspora sequence cluster I-II
Cp1130-B16S rRNACrenothrix polyspora sequence cluster III-IV
VIB572a16S rRNAGenus Vibrio
PSU73016S rRNAGenus Pseudoalteromonas
SHEW22716S rRNAGenus Shewanella
MX825b16S rRNAMethanosaetaceae subgroup
MX825c16S rRNAMethanosaetaceae subgroup
MX136116S rRNAMethanosaetaceae
MG1200b16S rRNAmost Methanomicrobiales
MB31116S rRNAMethanobacteriales
MC50416S rRNAMethanocaldococcaceae
CST44016S rRNAGroup 1 clones (AC044 and AC051), closely related to Clostridium stercorarium
CTH125816S rRNAGroup 2 clones (AC020 and AC033), closely related to Clostridium thermocellum
CUE124016S rRNAGroup 3 clones (AC014 and AC036), closely related to Clostridium sp. strain XB90
CUE64716S rRNAGroup 4 clones (AC007 and AC039)
BCE18216S rRNAGroup 5 clones (AC065 and MC049), closely related to Bacteroides cellulosolvens
DEF988S-S-Bact-1020-a-A-2216S rRNADefluvicoccus vanus-related organisms, cluster 2
FMR073216S rRNAsome iron-oxidising acidophilic Actinobacteria and some acid mine drainage clones
ABl019916S rRNAsome acidophilic Acidobacteriaceae and an acid mine drainage clone
ABl100216S rRNAsome acidophilic Acidobacteriaceae
TM1G013816S rRNAGroup 1 Thiomonas species
TM2G013816S rRNAGroup 2 Thiomonas species
WJ2064616S rRNAacidophilic gamma-Proteobacteria WJ2 and PK51 and some acid mine drainage clones
GALTS008416S rRNAacid mine drainage clones related to Gallionella ferruginea
BSC045916S rRNAacid mine drainage beta-proteobacterial clones
LGC035516S rRNAFirmicutes (Low G+C gram-positive bacteria)
ATT022316S rRNAAcidithiobacillus thiooxidans
Ntspa1431S-*-Ntspa-1431-a-A-1816S rRNASublineage I of the genus Nitrospira
Ntspa1151S-*-Ntspa-1151-a-A-2016S rRNASublineage II of the genus Nitrospira
Apr820S-*-Apr-0820-a-A-2116S rRNACand. “Anammoxoglobus propionicus”
E2d21002S-*-Rhob-1002-a-A-1816S rRNAsome Rhodobacteraceae
E1e3 1150S-*-Ualp-1150-a-A-1816S rRNAsome unclassified Alphaproteobacteria
Ualp-1109S-*-Ualp-1109-a-A-1816S rRNAsome unclassified Alphaproteobacteria
Sphm-0742S-*-Sphm-0742-a-A-1816S rRNAsome Sphingomonadales
Bete-1250S-*-Bete-1250-a-A-1816S rRNAsome unclassified Bacteroidetes
Bete-1419S-*-Bete-1419-a-A-1816S rRNAsome unclassified Bacteroidetes
Chro-1137S-*-Chro-1137-a-A-1816S rRNAsome Chromatiales
Caul-1262S-*-Caul-1262-a-A-1816S rRNAsome Caulobacterales
Ubac-1430S-*-Ubac-1430-a-A-1816S rRNAsome unclassified Bacteria
Ubac-1241S-*-Ubac-1241-a-A-1816S rRNAsome unclassified Bacteria
uBet-0984S-*-uBet-0984-a-A-1816S rRNAsome unclassified Betaproteobacteria
Ubet-0834S-*-Ubet-0834-a-A-1816S rRNAsome unclassified Betaproteobacteria
Ubet-0990S-*-Ubet-0990-a-A-2116S rRNAsome unclassified Betaproteobacteria
Rhoc-0998S-*-Rhoc-0998-a-A-1816S rRNAsome Rhodocyclaceae
Rhoc-1425S-*-Rhoc-1425-a-A-1816S rRNAsome unclassified Rhodocyclaceae
Thio-1032S-*-Thio-1032-a-A-1816S rRNAsome Thiobacillus and some unclassified Betaproteobacteria
Ach-22116S rRNAAchromobacter xylosoxidans
Alc-47616S rRNAAlcaligenes faecalis
Flavo1004S-St-Iso8-1004-a-A-1816S rRNAFlavobacterium isolate 8
CLOBU1022S-S-Cl.bu.-1022-a-A-1816S rRNAClostridium butyricum, Elbe `river snowapos isolates 9.1, 9.2, 9.4
AERO1244S-G-Aero-1244-a-A-2116S rRNAAeromonadaceae
Ppu646S-G-Ppu-0646-a-A-1816S rRNAPseudomonas spp.
AcI-840-1 (AC840a)16S rRNASubgroup of acI lineage (Actinobacteria)
AcI-840-2 (AC840b)16S rRNASubgroup of acI lineage (Actinobacteria)
AcI-121416S rRNAacI lineage of limnic Actinobacteria
DEN6716S rRNAMethanol-utilizing denitrifying cluster
DEN12416S rRNAAcetate-denitrifying cluster
DEN58116S rRNAAcetate-denitrifying cluster
CteAS-S-Cte-0462-a-A-2016S rRNAComamonas testosteroni
Nm143-446-116S rRNANitrosomonas sp. Nm143-related clones
Nm143-446-216S rRNANitrosomonas sp. Nm143-related clones
Nspmar6216S rRNANitrospira marina-related clones
Nmar83116S rRNANitrosomonas marina-related clones
DSS44916S rRNASome Desulfosarcina
DSS13816S rRNAFew Desulfobacteraceae
DSR125616S rRNAFew Desulfobulbaceae
Dblb124316S rRNADesulfobacterium catecholicum-related strains LacK1, LacK4 and LacK9
Dcap103116S rRNAFew Desulfocapsa including strain LacK10
Dblb103216S rRNADesulfobacterium catecholicum and related strains LacK1 and LacK9
Dsr18616S rRNADesulfobacterium catecholicum and related strains LacK1 and LacK9
DSV18516S rRNADesulfovibrio acrylicus
DSV44516S rRNADesulfovibrio strain EtOHK3
DSV6416S rRNADesulfovibrio strain EtOHK2
OcraDEL116S rRNADeltaproteobacterial symbiont 1 of Olavius crassitunicatus
OcraDEL216S rRNADeltaproteobacterial symbiont 2 of Olavius crassitunicatus
OcraDEL316S rRNADeltaproteobacterial symbiont 3 of Olavius crassitunicatus
DSBAC35716S rRNAMost Desulfobacteraceae and Syntrophobacteraceae
EPSY549S-C-eProt-0549-a-A-1816S rRNAEpsilonproteobacteria
MB16S rRNAMethylobacterium
PS516S rRNAPseudomonas synxantha and related species of the Pseudomonas fluorescens subgroup
E1116S rRNAEubacteria
Nost993S-*-Nost-993-a-A-1816S rRNAFilamentous Alphaproteobacteria
PPx1002S-*-PPx-1002-a-A-1816S rRNAFilamentous Alphaproteobacteria
EU25-1238S-*-EU25-1238-a-A-2016S rRNAFilamentous Chloroflexi
CribseqS-S-Crib-0064-a-A-2016S rRNACriblamydia sequanensis
DSV82716S rRNAmembers of the genus Desulfovibrio
DSBA101716S rRNADesulfobacca acetoxidans
Pint649S-S-P.int-0649-a-A-1916S rRNAPrevotella intermedia
Pnig657S-S-P.nig-0657-a-A-1916S rRNAPrevotella nigrescens
Pden654S-S-P.den-0654-a-A-1916S rRNAPrevotella denticola
FUS664S-G-Fuso-0664-a-A-1916S rRNAmost Fusobacterium sp.
SAR92_62716S rRNASAR92 clade
TBD1419S-S-Tb.den-1419-a-A-1816S rRNAThiobacillus denitrificans
TBD121S-*-Tbdt-0121-a-A-1816S rRNAThiobacillus denitrificans and Thiobacillus thioparus
TMD131S-S-Tm.den-0131-a-A-1816S rRNAThiomicrospira denitrificans
RHGA702S-S-Nsgar-702-a-A-1816S rRNA“Candidatus Nitrososphaera gargensis”
Tbm1282S-G-Tbm-1282-a-A-1816S rRNA most of Thermoanaerobacterium sp.
Tbmthsacc184S-S-Tbmthsacc-0184-a-A-1816S rRNAThermoanaerobacterium thermosaccharolyticum
Ccs432S-G-Ccs-0432-a-A-1816S rRNAmost of Caldicellulosiruptor sp.
TG1End1023T116S rRNAEndomicrobia phylotypes ZnTc-1, HsTc-1, RsTG1
TG1-TriG1-Hsj16S rRNAEndomicrobia HsTc-1
TG1-Joe-Kf16S rRNAEndomicrobia phylotype KfJe-1
TG1-Dev-Nca16S rRNAEndomicrobia phylotype NcDv-1
Flg-Dine-Hsj18S rRNADinenympha sp. HsDnA
Flg-Tricho1-Hsj18S rRNATrichonympha sp. HsTcA
Flg-Joe-Kfl18S rRNAJoenia sp. KfJeA of K. flavicollis
ACIDO22816S rRNAAcidobacteria subdivision 1
Bfu61316S rRNACandidatus “Brocadia fulgida”
Oilv/OcraGAM116S rRNAOlavius ilvae / O. crassitunicatus Gamma 1 symbiont
Oalg/OilvGAM316S rRNAOlavius algarvensis / O. ilvae Gamma 3 symbionts
OilvDEL116S rRNAOlavius ilvae Delta 1 symbiont
Oalg/OilvDEL316S rRNAOlavius algarvensis/ O. ilvae Delta 3 symbiont
OalgDEL416S rRNAOlavius algarvensis Delta 4 symbiont
SPIRO16S rRNAOlavius algarvensis / O. crassitunicatus /O. loisae spirochete symbionts
tios_434S-G-Tios-0434-a-A-2016S rRNAcluster TIOS44
HHY-T5S-*-Hhy-T5-654-a-A-1816S rRNAClone T5, micromanipulated from sludge
HHY-654S-*-Hhy-654-a-A-1816S rRNAseveral Haliscomenobacter species among others the type strain and an isolate named Plant1 Iso10B
hspec92516S rRNACandidatus Paraholospora nucleivisitans
GNS93416S rRNAChloroflexi sponge cluster I
POR113016S rRNACandidate phylum “Poribacteria”
POR38916S rRNACandidate phylum “Poribacteria”
POR60016S rRNACandidate phylum “Poribacteria”
DSV11916S rRNADesulfovibrio strain L3
DSV13916S rRNADesulfovibrio strain L7
APC98718S rRNAnovel eukaryotic phyla, APC
HLB107418S rRNAHeterolobosea
VAH104418S rRNAVahlkampfiidae
NAE104118S rRNANaegleria spp.
Ccat26S rRNACandida catenulata
Cint26S rRNACandida intermedia
Geo26S rRNAGeotrichum sp.
Ylip26S rRNAYarrowia lipolytica
DF198S-*Bact-0198-a-A-2016S rRNADefluviicoccus related organisms, cluster III
DF1004S-*-Bact-1004-a-A-1816S rRNADefluviicoccus related organisms, some cluster III
DF1013S-*Bact-0198-a-A-2016S rRNADefluviicoccus related organisms. some cluster III
DF181AS-*-Bact-0181-a-A-2016S rRNADefluviicoccus vanus related organisms, some cluster IV
DF181BS-*-Bact-0181-b-A-1816S rRNADefluviicoccus related organisms, some cluster IV
LS_HOL189L-P-Acido-0189-a-A-1823S rRNAAcidobacteria
SS_HOL1400S-P-Acido-1400-a-A-1716S rRNAAcidobacteria
LS_ALP544L-*-kan1–0544-a-A-1823S rRNALS_LKC21_kan1
LS_ALP761L-*-Sub7–0761-a-A-1823S rRNAParts of Acidobacterial subgroup 7 (including LS_LKC21_kan1, DON29, DON30, DON31)
SS_subd7_UB55–585S-*-Sub7–0585-a-A-1816S rRNAClone SS_LKC22_UB55, subgroup 7 SS_LKC22_UA71, SS_LKC21_kan1
SS_subd7_UB55–632S-*-Sub7–0632-a-A-1816S rRNAClone SS_LKC22_UB55, subgroup 7 SS_LKC22_UA71, SS_LKC21_kan1
LS_subd8_SGB1223L-*-Sub8–1223-a-A-1823S rRNAAcidobacterial subgroup 8 LS_LKC11_kan2, LS_LKC22_kan3, LS_LKC11_kan4, LS_LKC21_kan5 (LS_LKC11_kan6), clone ZC6, G. fermentans, H. foetida
LS_subd8_SGB1420L-*-Sub8-1420-a-A-1823S rRNAAcidobacterial subgroup 8 LS_LKC11_kan2, LS_LKC22_kan3, LS_LKC11_kan4, LS_LKC21_kan5, LS_LKC11_kan6, clone ZC6, G. fermentans, H. foetida,
LS_GFER2787L-*-Gfer-2787-a-A-1823S rRNAG. fermentans and relatives (no LKC clones)
S-S-T.int-0442-a-A-1816S rRNAThiomonas intermedia
S-S-T.plum-450-a-A-1816S rRNAThiobacillus plumbophilus
S-S-H.neap-635-a-A-1916S rRNAHalothiobacillus neapolitanus
RB45416S rRNAPirellula sp. strain SH1
PIR122316S rRNAGenus Pirellula
YDC6916S rRNAuncultivated magnetotactic cocci (Candidatus Magnetococcus yuandaducum)
L2CG35323S rRNALeptospirillum ferriphilum 5-way CG
L2UBA35323S rRNALeptospirillum rubarum UBA
BDE52516S rRNAGenus Bdellovibrio
OilvGAM1S-S-OicG1-064316S rRNAOlavius ilvae and Olavius crassitunicatus Gamma 1 symbionts
Oalg/OilvGAM3S-G-OaiG3-0665-a-A-1816S rRNAOlavius algarvensis / Olavius ilvae Gamma 3 symbionts, some env. Clones
OalgDEL1S-S-OaD1-0136-a-A-1816S rRNAOlavius algarvensis Delta 1 symbiont
OilvDEL1S-S-OiD1-0136-a-A-1816S rRNAOlavius ilvae Delta 1 symbiont, unc. bacterium AY907763
Oalg/OilvDEL3S-G-OaiD3-1449-a-A-1816S rRNAOlavius algarvensis/ Olavius ilvae Delta 3 symbiont
OalgDEL4S-S-OaD4-1427-a-A-1816S rRNAOlavius algarvensis Delta 4 symbiont
SPIROS-G-OISpi-0136-a-A-1816S rRNAspirochete symbiont group of gutless oligochaetes
XenoGam44116S rRNAXenoturbella bocki gammaproteobacterial endosymbiont and relatives
XenoGam66616S rRNAXenoturbella bocki gammaproteobacterial endosymbiont and relatives
XenoGam72716S rRNAXenoturbella bocki gammaproteobacterial endosymbiont and relatives
SymLl125116S rRNAL. lacteus symbiont
SymAf57616S rRNAA. fragilis symbiont
SymAf127216S rRNAA. fragilis symbiont
Symco216S rRNAC. orbicularis symbiont
Rhodano 227S-*-Rno-0227-a-A-2116S rRNAUncultured Rhodanobacter species closely related to Rhodanobacter thiooxydans
LEE8216S rRNASome members of the genus Leeuwenhoenkiella
DOK82716S rRNASome members of the genus Dokdonia
FL19716S rRNAmarine uncultured Flavobacteria clade VIS4
VIS6-81416S rRNAmarine uncultured Flavobacteria clade VIS6
VIS5-58616S rRNAmarine uncultured Flavobacteria clade VIS5
FL84516S rRNAmarine uncultured Flavobacteria clade VIS2
VIS3-18316S rRNAmarine uncultured Flavobacteria clade VIS3
VIS1-57516S rRNAmarine uncultured Flavobacteria clade VIS1
PSE22716S rRNAPseudomonas spp.
PSE128416S rRNAPseudomonas spp.
TOL1028S-S-TOL-1028-a-A-1816S rRNAStrain TOL (from oleate enrichment)
TSP436S-*-0436-a-A-1816S rRNAClones TPA, TST, and JA2 (from Palmitate, Stearate, and Oleate enrichments, respectively)
MPA1446S-*-1446-a-A-1816S rRNAStrain MPA (from Palmitate enrichment)
MST445S-*-0445-a-A-1816S rRNAClone MST (from Stearate enrichment)
MSP1445S-*-1445-a-A-1816S rRNAClones MOL and MLI (from Oleate and Linoleate enrichment, respectively)
DEN22016S rRNAAcetate-denitrifying cluster and some members of the Comamonadaceae family
DEN220a16S rRNAAcetate-denitrifying cluster and some members of the Rhodocyclaceae family
DEN44116S rRNAAcetate-denitrifying cluster and some members of the Rhodocyclaceae family
DEN44416S rRNAAcetate-denitrifying cluster
DEN145416S rRNAAcetate-denitrifying cluster
FB64816S rRNAThioturbo danicus and strain DK4
FB74116S rRNAThioturbo danicus and strain DK4
FB84216S rRNAStrain DK4
Rotcl116S rRNACluster related to Methanosaeta concilii
Rotcl216S rRNACluster related to endosymbiont of P. nasuta
WPF46416S rRNAfilaments from hydrothermal vents near White Point
VSO67316S rRNAUnattached, vacuolate, sulfur-oxidizing bacteria
DEN6716S rRNAMethanol-utilizing denitrifying cluster group A closely related to the obligate methylotrophs Methylobacillus and Methylophilus in the order Methylophilales
SAP55316S rRNAMostly Saprospiraceae family
Geo/Blasto16S rRNAGeodermatophilus/Blastococcus group
Modesto16S rRNAModestobacter genus
UP23b16S rRNAUrothoe poseidonis clone UP23b
Curvi99716S rRNAGenus Curvibacter
CYT144816S rRNACytophaga spp.
CYT143816S rRNACytophaga spp.
NOR5-73016S rRNANOR5 cluster (Gammaproteobacteria)
NOR5-13016S rRNANOR5 isolate KT71 (Gammaproteobacteria)
ROS53716S rRNAMarine alpha cluster
KT13-23116S rRNAKT1117 (Roseobacter lineage isolate)
KT09b16S rRNAKT0917 (Roseobacter lineage isolate)
KT09c16S rRNAKT0917 (Roseobacter lineage isolate)
RC103116S rRNAKT0202a (Roseobacter lineage isolate)
RC123916S rRNAKT0202a (Roseobacter lineage isolate)
Ros7-102916S rRNAJP7.1 group (marine alpha cluster)
Erythro6916S rRNAJP13.1 group (Erythrobacter)
Rhizo21816S rRNAJP66.1 group (Phyllobacterium)
Lis-125516S rRNAGenus Listeria, Bacillus thermosphacta, Bacillus campestris
Salm-6323S rRNASalmonella spp., Plesiomonas shigelloides
BEG81116S rRNAFrasassi Beggiatoa clade
18Alf-0218S-*-18ALF-0218-a-A-1816S rRNAMethanotrophic symbiont of Sphagnum mosses
18Alf-1437S-*-18ALF-1437-a-A-1816S rRNAMethanotrophic symbiont of Sphagnum mosses
SEEP1a-473S-*-SP1a-0473-a-A-2316S rRNADesulfosarcina/Desulfococcus subgroup SEEP-SRB1a (ANME-2 partner)
SEEP1a-1441S-*-SP1a-1441-a-A-1816S rRNADesulfosarcina/Desulfococcus subgroup SEEP-SRB1a (ANME-2 partner)
SEEP1f-153S-*-SP1f-0153-a-A-1816S rRNADesulfosarcina/Desulfococcus subgroup SEEP-SRB1f
Pedo_125016S rRNAPedomicrobium strains
Cboid198S-S-C.boid-0198-a-A-1818S rRNACandida boidinii
S-*-CFB-0655-a-A-18S-*-CFB-0655-a-A-1816S rRNAOTU 8 of CFB (Cytophaga-Flavobacterium-Bacteroides)
S-*-CFB-0730-a-A-18S-*-CFB-0730-a-A-1816S rRNAOTU 9 of CFB (Cytophaga-Flavobacterium-Bacteroides)
S-*-GNS-0667-a-A-18S-*-GNS-0667-a-A-1816S rRNAOTU 11 and 12 of GNSB (green nonsulfur bacteria)
S-*-Opitu-0744-a-A-18S-*-Opitu-0744-a-A-1816S rRNAOTU 13 of Verrucomicrobia
ANA10316S rRNAActinomyces naeslundii
FUS66416S rRNAFusobacterium nucleatum,
MIT58816S rRNAStreptococcus oralis
ODB102116S rRNAOctadecabacter spp.
RSHP99516S rRNARoseobacter sp. strain Shippagan group
GPU62216S rRNAGlaciecola punicea
GVstr21416S rRNAGlaciecola sp. strain GVstr214.6
SF82516S rRNAShewanella frigidimarina
PSYB47616S rRNAPsychrobacter spp.
MB-IC02216S rRNAMarinobacter sp. strain IC022 group
PB22316S rRNAPolaribacter spp.
GAN85016S rRNAGallibacterium
VP40316S rRNAVerrucomicrobium, most Prosthecobacter, and uncultured relatives
SPA71416S rRNAMost Spartobacteria and uncultured relatives
SPA64916S rRNAUncultured humic and acidic lake Spartobacteria
OPT116916S rRNAOpitutus spp. and uncultured relatives
Blsv103016S rRNABlastochloris viridis
Rbla137216S rRNARhodobacter blasticus
Rbmr15116S rRNARhodobium marinum, Rhodopseudomonas julia
Rvsl13916S rRNARhodovulum sulfidophilum
Cboid198S-S-C.boid-0198-a-A-1818S rRNACandida boidinii
KIN51618S rRNAKinetoplastida
CFX197S-*-Bact-0197-a-A-1816S rRNAEikelboom type 0092 Chloroflexi
CFX223S-*-Bact-0223-a-A-1816S rRNAEikelboom type 0092 Chloroflexi
CFX67aS-*-Bact-0067-a-A-1816S rRNAEikelboom type 0914 Chloroflexi
CFX67bS-*-Bact-0067-b-A-1816S rRNAEikelboom type 0914 Chloroflexi
ERY17416S rRNASome Novosphingomonas, Erythrobacter and Porphyrobacter
PARA73916S rRNAOrder Rhodobacterales
RHIZ124416S rRNAOrder Rhizobiales
Lepto17516S rRNALeptothrix ochracea
Dbact653S-F-Dsb-0653-a-A-1816S rRNADesulfococcus/Desulfosarcina/Desulfonema
DSU65516S rRNAGenus Desulfurella
ATAM01S-S-A.tam-0775(A. Tamarense)-a-A-1818S rRNAAlexandrium tamarense species complex
ATNA02L-St-At.NA-373(A. tamarense)-a-A-1828S rRNAAlexandrium tamarense /North American clade/Orkney strains
ATWE0328S rRNAAlexandrium tamarense /Western European clade
ATME0428S rRNAAlexandrium tamarense / Mediterranean clade
DINO01S-C-DINO-1404(A. tamarense)-a-A-2018S rRNADinoflagellates / Dinophyceae
AOST01L-S-A.ost-484(A. ostenfeldii)-a-A-1828S rRNAAlexandrium ostenfeldii
AOST02S-S-A.ost-0232(A. ostenfeldii)-a-A-1818S rRNAAlexandrium ostenfeldii
Bfi826S-S-But-0826-a-1816S rRNAButyrivibrio fibrisolvens-related clones, phylum Firmicutes
Rum831S-S-Rum-0831-a-1616S rRNARumen clones in family Ruminococcaceae, phylum Firmicutes
Lac435S-S-Lac-0435-a-1616S rRNAClones in family Lachnospiraceae, phylum Firmicutes
Ral1436S-S-Rum-1436-1516S rRNARuminococcus albus-related clones, phylum Firmicutes
Rfl155S-S-Rum-0155-a-1516S rRNARuminococcus flavefaciens-related clones, phylum Firmicutes
Bac1080S-S-Bac-1080-a-1816S rRNAClones in order Bacteroidales, phylum Bacteroidetes
fir5-57516S rRNAFirm-5 (symbiotic Firmicutes phylotype in honey bee)
But1243S-S-But-1243-a-1816S rRNArumen Butyrivibrio clones
Clo549S-S-Clo-0549-a-1816S rRNAunclassified Rumen Clostridia clones
Inc852S-S-Inc-0852-a-1816S rRNARumen Inceatae Sedis XIII clones
Pse1257S-S-Pse-1257-1816S rRNARumen Pseudobutyrivibrio clones
Ace731S-S-0731-a-1816S rRNARumen Acetivibrio clones
Vei732S-S-0732-a-1816S rRNARumen Veillonellaceae clones
Pseudo12016S rRNArRNA group I pseudomonads
SUB 19616S rRNAStreptococcus uberis
APYO 18316S rRNAArcanobacterium pyogenes
Syner19516S rRNASynergistes group 4 (Synergistetes PD-UASB-13)
Lmon16S rRNAListeria monocytogenes
CLOSs146S-S-CLOS-0146-a-1816S rRNAIncertae Sedis XI
CLOSs654S-S-CLOS-0654-a-1816S rRNAGrocilibacteraceae
RUMs278S-S-Rum-0278-a-1816S rRNARuminococcaceae
FIMs1029S-S-FIM-1029-1-1816S rRNAClostridiaceae 2
Cboid19818S rRNACandida boidinii
CJ216S rRNAPolaromonas naphthalenivorans strain CJ2
NebProb203S-S-Neby-0203-a-A-1816S rRNACandidatus Nebulobacter yamunensis
FNFProb759S-*-Bact-0759-a-A-1716S rRNABacteroidetes, Francisellaceae, other prokaryotes
Ng0216S rRNANosema / Vairimorpha genus (microsporidia)
Dd0416S rRNADictyocoela (microsporidia)
AQI33816S rRNAPhylum Aquificae (except Desulfurobacteriaceae)
SFH64616S rRNASulfurihydrogenibium spp. (except S. Yellowstonense) including Nakabusa microbial mat sequences
Deflu_197S-S-Deflu-0197-a-A-2016S rRNACandidatus Defluviella procrastinata
CyrIn_142S-S-Cyrz-0142-a-A-2316S rRNACandidatus Cyrtobacter zanobii
Faecali69816S rRNAFaecalibacterium and relatives
Clep866S-*-Clep-0866-a-A-1816S rRNAmembers of the Clostridium leptum subgroup
Rcal733S-*-Rcal-0733-a-A-2016S rRNAmembers of the Ruminococcus callidus species
Cvir1414S-*-Cvir-1414-a-A-1816S rRNAClostridium viride cluster
Edes635S-*-Edes-0635-a-A-1816S rRNAEubacterium desmolans species
Bfrag 998S-S-Bfrag-0998-a-A-2016S rRNABacteroides fragilis
Bvulg 1017S-S-Bvulg-1017-a-A-2116S rRNABacteroides vulgatus
Fprau0645S-*-Fprau-0645-a-A-2316S rRNAFeacalibacterium (Fusobacterium) prausnitzii and relatives
Mcs487S-S-Mcs-0487-a-A-2116S rRNAMucispirillum spp.
Mcs547S-S-Mcs-0547-a-A-2016S rRNAMucispirillum spp.
MUC-1437S-G-Akk-1437-a-A-2016S rRNAAkkermansia muciniphila
Bacid116S rRNAB. acidifaciens Group 1
Bacid316S rRNAB. acidifaciens Group 3
Bot16S rRNAB. ovatus and B. thetaiotaomicron
Bova16S rRNABacteroides ovatus
Bthe16S rRNABacteroides thethaiotaomicron
Buni16S rRNABacteroides uniformis
Bcac16S rRNABacteroides caccae
P(T)AFO16S rRNATannerella forsythensis (Bacteroides forsythus)
POGI16S rRNAPorphyromonas gingivalis and uncultured Porphyromonas
PRIN16S rRNAPrevotella intermedia, Prevotella falsenii and uncultured Prevotella
Bovat 1028S-S-Bovat-1028-a-A-1916S rRNABacteroides ovatus
Bdist 1025S-S-Bdist-1025-a-A-1916S rRNABacteroides distasonis (Parabacteroides distasonis)
Bputre 698S-S-Bputre-698-a-A-2016S rRNABacteroides putredinis (Alistipes putredinis)
Efs23S rRNAEnterococcus faecalis FAIR E 92
LPLANG16S rRNALactobacillus plantarum 423
LSAL16S rRNALactobacillus salvirius 241
Lba23S rRNALactobacillus acidophilus (cluster A1)
Lbg23S rRNALactobacillus gasseri (cluster B1)
Lbj23S rRNALactobacillus johnsonii (cluster B2)
LSPotu9468-999S-*-Lsp-999-a-A-2016S rRNALachnospiraceae OTU_9468
LSPotu9468-1259S-*-Lsp-1259-a-A-2016S rRNALachnospiraceae OTU_9468
Chis150S-*-Chis-0150-a-A-2316S rRNAmost of the Clostridium histolyticum group (Clostridium cluster I and II)
LSPotu11021-1448S-*-Lsp-1448-a-A-1816S rRNALachnospiraceae OTU_11021
Law116S rRNALawsonia intracellularis
Lab158S-G-Lab-0158-a-A200S rRNALactobacilli Enterococci
Rrec58416S rRNARoseburia
Prop85316S rRNAClostridial cluster IX
Bx183S-S-B.x-0183-a-A-1816S rRNABrachyspira aalborgi clusters 2 and 3
Aalborgi183S-S-B.aalborgi-0183-a-A16S rRNABrachyspira aalborgi cluster 1
Erec834S-S-Erec-0834-a-A-1816S rRNAEubacterium rectale
Erec838S-S-Erec-0838-b-A-2016S rRNAEubacterium rectale
Etor727S-S-Etor-0727-a-A-1816S rRNAEubacterium tortuosum
Etor129S-S-Etor-0129-b-A-1816S rRNAEubacterium tortuosum
Lbd23S rRNALactobacillus delbrueckii subsp.
EC 1531L-S-Eco-1531-a-A-2123S rRNAEscherichia coli BJ4
Sym_Stau_30316S rRNABacteroidales clone Candidatus Vestibaculum illigatum
Ntlc439S-G-Ntlc-439-a-A-1816S rRNANitrolancetus hollandicus
Bif228S-G-Bif-228-a-A-1816S rRNABifidobacteria
Ntlc804S-G-Ntlc-804-a-A-1816S rRNANitrolancetus hollandicus
Alsym16SS-G-Burk-0642-a-A-1916S rRNABurkholderia (Alydidae gut symbionts)
MCP5216S rRNAMollicutes
CPla-116S rRNA„Termite planctomycete cluster 1“
CPla-216S rRNA„Termite planctomycete cluster 2“
CPla-316S rRNA„Termite planctomycete cluster 2“
LytiProb_433S-G-Lyti-0433-a-A-2116S rRNAgenus Lyticum
Lflag_268S-S-Lfla-0268-a-A-2316S rRNALyticum flagellatum
Lsinu_268S-S-Lsin-0268-a-A-2316S rRNALyticum sinuosum
Pse136S-S-Pse-136-a-A-2016S rRNASome Pseudomonas populations
Pse136bS-S-Pse-136b-a-A-2016S rRNASome Pseudomonas populations
Pse910S-S-Pse-910-a-A-1816S rRNASome Pseudomonas populations
Hal180S-S-Hal-180-a-A-2216S rRNASome Halomonas populations
Elo1-1250S-S-Elo1-1250-a-A-1816S rRNATetrasphaera elongata and related clones
Tet1-823S-S-Tet1-823-a-A-1816S rRNATetrasphaera elongata-related clones
Tet1-266S-S-Tet1-266-a-A-1816S rRNATetrasphaera Clone ASM31
Tet2-842S-S-Tet2-842-a-A-1816S rRNAClones related to Tetrasphaera jenkinsii, Tetrasphaera australiensis, and Tetrasphaera veronensis
Tet2-831S-S-Tet2-831-a-A-1816S rRNATetrasphaera australiensis, Tetrasphaera veronensis, and uncultured Tetrasphaera
Tet2-892S-S-Tet2-892-a-A-1816S rRNATetrasphaera Clone ASM47
Tet2-87S-S-Tet2-87-a-A-1816S rRNAUncultured Tetrasphaera
Tet2-174S-S-Tet2-174-a-A-1816S rRNATetrasphaera jenkinsii, Tetrasphaera australiensis, Tetrasphaera veronensis, and Candidatus Nostocoida limicola
Tet3-654S-S-Tet3-654-a-A-1816S rRNA3 Uncultured Tetrasphaera
Tet3-19S-S-Tet3-19-a-A-1816S rRNATetrasphaera Clone ASM57
Str56S-S-Str-56-a-A-1816S rRNAStreptococcus spp.
Lac93S-S-Lac-93-a-A-1816S rRNALactococcus spp.
Pro60S-S-Pro-60-a-A-1816S rRNAPropionicimonas spp.
LasA3720_1281S-*-LspA-1281-a-A-2316S rRNAsubgroup A of unclassified Lachnospiraceae OTU
LasB3720_1281S-*-LspB-1281-a-A-2316S rRNAsubgroup B of unclassified Lachnospiraceae OTU
Bac16065_472S-*-Bada-0472-a-A-2416S rRNAunclassified Bacteroidales cluster S24-7 OTU
Bac3732_846S-*-Bada-0846-a-A-2416S rRNAunclassified Bacteroidales cluster S24-7 OTU
Bac11839_649S-*-Bada-0649-a-A-2316S rRNAunclassified Bacteroidales cluster S24-7 OTU
Bac15326_476S-*-Bada-0476-a-A-2316S rRNAunclassified Bacteroidales cluster S24-7 OTU
Bac13481_437S-*-Bada-0437-a-A-2216S rRNAunclassified Bacteroidales cluster S24-7 OTU
All3256_484S-*-Allb-0484-a-A-2216S rRNAsubgroup of genus Allobaculum
Baci731A_87S-*-Baci-0087-a-A-2416S rRNABacteroides acidifaciens Group-2
Baci731B_87S-*-Baci-0087-a-A-2216S rRNABacteroides acidifaciens Group-1
Rum14644A_184S-*-Ruco-0184-a-A-2316S rRNAunclassified Oscillibacter OTU
Rum14644B_64S-*-Ruco-0064-a-A-2416S rRNAunclassified Oscillibacter OTU
Rum17903_443S-*-Ruco-0443-a-A-2016S rRNAunclassified Ruminococcaceae OTU
LasA5944_580S-*-LspA-0580-a-A-2416S rRNAsubgroup A of unclassified Lachnospiraceae OTU
LasB5944_580S-*-LspB-0580-a-A-2416S rRNAsubgroup B of unclassified Lachnospiraceae OTU
Lab9057_570S-S-Lbad-0570-a-A-2316S rRNALactobacillus taiwanensis - L. johnsonii - L. gasseri group
Lab2185_87S-*-Lbre-0087-a-A-2416S rRNALactobacillus reuteri
UCB-82316S rRNAPlasticicumulans acidivorans
ULB-45016S rRNAPlasticicumulans lactivorans
UCB-12716S rRNAPlasticicumulans acidivorans
L.mars_symb116S rRNAEndosymbiont type A of Lamellibrachia anaximandri (Marsili seamount)
L.mars_symb216S rRNAEndosymbiont type B of Lamellibrachia anaximandri (Marsili seamount)
volv-83516S rRNARickettsial endosymbionts hosted by Carteria, Pleodorina, Volvox (green algae) and Diophrys appendiculata (ciliate)
PDD8_64416S rRNACandidatus Cochliophilus cryoturris, symbiont of Cochliopodium minus
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  • Color codes

    • Primer
    • Probes used for FISH