FISH examples


Atopobium
Fecal sample with Atopobium probe
Bacteroides
Fecal sample with Bacteroides probe
Borrelia afzelii
Borrelia afzelii with Borellia spp. probe
Borelli burgdorfii
Borrelia burgdorfii with Borellia spp. probe
Bifido fecal
Fecal sample with Bifido spp. probe
B. animalis
Bifidobacterium animalis with Bifido spp. probe
B. adolecentis
Bifidobacterium adolecentis with Bifido spp. probe
B. breve
Bifidobacterium breve with Bifido spp. probe
B. bifidum
Bifidobacterium bifidum with Bifido spp. probe
B. catenulatum
Bifidobacterium catenulatum with Bifido spp. probe
B. infantis
Bifidobacterium infantis with Bifido spp. probe

B. longum
Bifidobacterium longum with Bifido spp. probe

B. suis
Bifidobacterium suis with Bifido spp. probe
B. animalis animalis probe
Bifidobacterium animalis with B. animalis probe
B. animalis
Fecal sample with B.animalis probe
C. coccoides
Fecal sample with Eubacterium rectale-Clostridium coccoides probe
C. leptum
Clostrium leptum with C. leptum probe

C. difficile
Fecal sample with Clostridium difficle probe

C. lituseburense
Fecal sample with C. lituseburense probe
C. perfringens
Clostridium perfringens with C. perfringens probe
C. albicans
Candida albicans with C. albicans probe
E. coli
Escherichia coli with E. coli probe
E. faecium
Fecal sample with E. faecium probe
K, pneumoniae
Klebsiella pneumoniae with K. pneumoniae probe
L. brevis milk
Milk with Lactobacillus brevis probe
L. reuteri
Milk with Lactobacillus reuterii probe
L. salivarius
Milk with Lactobacillus salivarius probe
Legionella spp
Water with Legionella spp. probe

P. aeruginosa
Pseudomonas aeruginosa with P. aeruginosa probe

P. assacharolyticus
Pedicoccus asaccharoliticus with P. asaccharolyticus probe
P. acidilactici
Pediococcus acidilactici with P. acidilactici probe
Peptostreptococcus an
Peptostreptococcus anaerobius with P. ana probe
P. gingivalis
Porphyromonas gingivalis with P. gingivalis probe
P. gulae
Porphyromonas gulae with P. gulae probe

Prausnitzi
Fecal sample with Feacalibacterium prausnitzi probe
S. aureus
Blood with Staphylococcus aureus probe

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List of possible FISH probes for Bacteria & Archaea
Name 
Acetate-denitrifying cluster  
Acetate-denitrifying cluster and some members of the Comamonadaceae family  
Achromatium 16S rRNA 
Achromatium oxaliferum 16S rRNA
Achromobacter xylosoxidans  
Acidobacteria subdivision 1  
Acidovorax spp.  
Acinetobacteria spp. 16S rRNA
Actinobacillus actinomycetemcomitans  
Actinobacteria (high G+C Gram-positive bacteria)  
Actinomyces naeslundii  
Aeromonadaceae  
Aeromonas hydrophilia
Aeromonas spp. 16S rRNA
Aeromonas spp. 23S rRNA 
Alcaligenes defragans  
Alcaligenes faecalis  
Alcaligenes latus
Alcaligenes, Bordetella
Alexandrium tamarense
all ANAMMOX bacteria  
All bacteria
all Organisms  
all yeasts  
alpha4-subgroup of Proteobacteria  
Alphaproteobacteria, except of Rickettsiales  
Alphaproteobacteria, some Deltaproteobacteria, Spirochaetes  
Alphaproteobacterial
Alteromonas, Colwellia  
Amaricoccus
Amaricoccus spp.  
Amoebobacter purpureus
Anammoxoglobus propionicus
Aquabacterium spp.  
Archaeoglobales  
Arcobacter  
Atopobium
Aureobacterium testaceum  
Azoarcus cluster  
Azoarcus-Thauera cluster  
Bacillus amyloliquefaciens
Bacterioides distasonis 16S rRNA 
Bacteroides - Prevotella
Bacteroides distasonis  
Bacteroides fragilis 16S rRNA 
Bacteroides fragilis group  
Bacteroides spp. & Prevotella spp. 16S rRNA
Beggiatoa spp. 16S rRNA 
beta1-group of Betaproteobacteria  
Betaproteobacteria  
Betaproteobacterial ammonia-oxidizing bacteria  
Betaproteobacterial Thiobacilli  
Bifidobacterium animalis
Bifidobacterium breve  
Bifidobacterium spp.
Blastochloris viridis  
Bordetella spp., Alcaligenes spp. (sensu stricto)  
Borrelia spp.
Brachymonas denitrificans
Brachyspria/Serpulina pilosicoli rRNA 
Brevibacterium sp. (B. ketoglutamicum)  
Brevundimonas (Pseudomonas) diminuta, Caulobacter spp., Mycoplana bullata  
Brevundimonas diminuta rRNA
Burkholderia cepacia  
Burkholderia cepacia 16S rRNA 
Burkholderia spp.  
Burkholderia spp. 16S rRNA 
Burkholderia spp., Sutterella spp.  
Burkholderia vietnamensis, B. cepacia  
C. orbicularis symbiont  
Caedibacter taeniospiralis  
Campylobacter jejuni subsp
Campylobacter spp.
Candida (Torulopsis) glabrata  
Candida albicans
Candida albicans  
Candida boidinii  
Candida catenulata  
Candida intermedia  
Candida krusei  
Candida parapsilosis  
Candidate phylum “Poribacteria”  
Candidatus "Accumulibacter phosphatis"  
Candidatus "Competibacter phosphatis"  
Candidatus "Scalidua brodae"  
Candidatus "Scalidua wagneri", Candidatus "Scalidua sorokinii"  
Candidatus “Brocadia fulgida”  
Candidatus Accumulibacter phosphatis (clone R6)  
Candidatus Alysiomicrobium bavaricum  
Candidatus Alysiosphaera europaea  
Candidatus Amoebophilus asiaticus  
Candidatus Brocadia anammoxidans  
Candidatus Caedibacter acanthamoebae (endosymbiont of Acanthamoeba polyphaga HN-3)  
Candidatus capitivii acidiprotistae  
Candidatus Catenimonas italica  
Candidatus Combothrix italica  
Candidatus Endomicrobium pyrsonymphae  
Candidatus Endomicrobium trichonymphae  
Candidatus Kuenenia stuttgartiensis  
Candidatus Magnospira bakii  
Candidatus Microthrix  
Candidatus Paracaedibacter acanthamoebae (endosymbiont of Acanthamoeba sp. UWC9)  
Candidatus Paracaedibacter symbiosus (endosymbiont of Acanthamoeba sp. UWE39)  
Candidatus Paraholospora nucleivisitans  
Candidatus Procabacter sp.  
Candidatus Rhabdochlamydia porcellionis  
Candidatus Sphaeronema italicum  
Chlamydia  
Chlamydia trachomatis  
Chlamydiaceae  
Chlamydiales  
Chlamydophila  
Chlamydophila pneumoniae  
Chlamydophila psittaci group including C. felis, C. abortus, and C. caviae  
Chlorobium clathratiforme (DSM 5477)
Chlorobium phaeobacteroides (DSM 266)
Chloroflexi sponge cluster I  
Chloroflexus  
Chlorophyta  
Chromatium okenii
Chromatium vinosum 16S rRNA 
clarithromycin resistant Helicobacter pylori  
Clostridium (Cluster IV)
Clostridium butyricum
Clostridium coccoides
Clostridium difficile
Clostridium histolyticum 16S rRNA 
Clostridium lituseburense 16S rRNA 
Clostridium perfringens
Clostridium saccharogumia  
Clostridium sporosphaeroides, Ruminococcus bromii, Clostridium leptum  
Coliforms
Collimonas sp.  
Comamonas spp.  
Comamonas spp., Acidovorax spp., Hydrogenophaga spp., Aquaspirillum spp.  
Comamonas testosteroni  
Corynebacterium glutamicum  
Crenarchaea  
Crenothrix polyspora  
Crenothrix polyspora sequence cluster I  
Crenothrix polyspora sequence cluster I-II  
Crenothrix polyspora sequence cluster III-IV  
Crenothrix polyspora sequence cluster II-IV  
Criblamydia sequanensis  
Cytophaga spp.  
Cytophaga/Flavobacterium 16S rRNA 
Desulfarculus baarsii, Desulfomonile tiedjei, and Syntrophus  
Desulfobacca acetoxidans  
Desulfobacter Proteobacteria-delta rRNA
Desulfobacter, Desulfobacula, Desulfospira, and Desulfotignum  
Desulfobacteraceae
Desulfobacterium vacuolatum, D. niacini, D. autotrophicum  
Desulfobotulus sapovorans, Desulfovibrio fairfieldensis, and other Deltaproteobacteria  
Desulfocapsa thiozymogenes  
Desulfococcus multivorans  
Desulfofrigus, Desulfofaba gelida, Desulfomusa hansenii  
Desulfomicrobium  
Desulfosarcina and many other Desulfobacteraceae  
Desulfosarcina variabilis  
Desulfotomaculum cluster I and other Firmicutes  
Desulfotomaculum subcluster Ih (Pelotomaculum and Cryptanaerobacter)  
Desulfovibrio acrylicus  
Desulfovibrio aestuarii  
Desulfovibrionaceae rRNA
Desulfuromonas spp., Pelobacter spp.  
Devosia riboflavina and relatives  
Dinenympha sp. HsDnA  
Enterobacteriaceae  
Enterobacteriaceae 16S rRNA 
Enterobacteriaceae except Proteus spp.  
Enterococci
Enterococcus faecalis
Enterococcus faecalis & Enterococcus sulfuricus 16S rRNA 
Enterococcus faecalis 23S rRNA 
Enterococcus faecium
Enterococcus spp. 23S rRNA 
Epsilonproteobacteria  
Epsilonproteobacterial group I
Epsilonproteobacterial group II
Erythrobacter  
Escherichia coli  
Escherichia coli 16S rRNA 
Eubacteria  
Eubacterium barkeri  
Eubacterium barkeri 16S rRNA 
Eubacterium biforme  
Eubacterium biforme 16S rRNA 
Eubacterium contortum  
Eubacterium contortum 16S rRNA 
Eubacterium cylindroides  
Eubacterium cylindroides 16S rRNA 
Eubacterium cylindroides, Clostridium innocuum, Eubacterium biforme, Eubacterium tortuosum, Eubacterium dolichum, Streptococcus pleomorphus  
Eubacterium dolichum  
Eubacterium dolichum 16S rRNA 
Eubacterium hadrum  
Eubacterium hadrum 16S rRNA 
Eubacterium hallii, Clostridium herbivorans, Clostridium polysaccharolyticum  
Eubacterium lentum  
Eubacterium lentum 16S rRNA 
Eubacterium limosum 16S rRNA 
Eubacterium limosum; E. callanderi  
Eubacterium moniliforme  
Eubacterium moniliforme 16S rRNA 
Eubacterium rectale, Clostridium coccoides  
Eubacterium ventriosum  
Eubacterium ventriosum 16S rRNA 
Euplotes crassus  
Euplotes minuta  
Euplotes vannus  
Eurotiomycetes, including AMD fungi  
Euryarchaea  
Faecalibacterium prausnitzii
Fibrobacter succinogenes rRNA
Filamentous Alphaproteobacteria  
filamentous bacterium Eikelboom Type 1851  
Filamentous Chloroflexi  
Firmicutes (Gram-positive bacteria with low G+C content)  
Firmicutes LGC 16S rRNA (Firmicutes with low DNA G+C content) 
Flavobacterium ferrugineum  
Flavobacterium ferrugineum, Flexibacter elegans, F. sancti  
Frasassi Beggiatoa clade  
Fusobacterium nucleatum,  
Fusobacterium spp.  
G. fermentans and relatives
Gallibacterium  
Gammaproteobacteria  
Genus Bdellovibrio  
genus Candidatus "Scalindua"  
Genus Listeria, Bacillus thermosphacta, Bacillus campestris  
genus Methanosarcina  
genus Nitrospira  
genus Paracoccus  
Genus Pirellula  
Genus Pseudoalteromonas  
Genus Shewanella  
Genus Vibrio  
Geodermatophilus/Blastococcus group  
Geotrichum sp.  
Glaciecola punicea  
Glaciecola sp. strain GVstr214.6  
Glaucoma scintillans  
Gordona amarae  
Gordonia (Gordona)  
GPB-HGC 16S rRNA (Gram-positive bacteria with high DNA G+C content) 
GPB-LGC 16S rRNA (Gram-positive bacteria with low DNA G+C content) 
green sulfur bacteria, Chlorobiaceae  
Group 1 Thiomonas species  
Group 2 Thiomonas species  
Haemophilus influenzae  
Haemophilus influenzae 16S rRNA 
Haliscomenobacter hydrossis  
Halothiobacillus neapolitanus  
Helicobacter ganmani  
Helicobacter hepaticus  
Helicobacter pylori  
Helicobacter pylori clarithromycin resistant 23S rRNA 
Helicobacter sp., Wolinella sp.  
Helicobacter spp.
Heterolobosea  
Hydrogenophaga spp.  
Hyphomicrobium  
Hyphomicrobium vulgare  
Joenia sp. 
Kinetoplastida  
Klebsiella pneumoniae  
Lachnospira multipara, Eubacterium eligens, Lachnospira pectinoschiza  
Lactobacilli + Enterococci
Lactobacillus brevis  
Lactobacillus casei - para
Lactobacillus casei, Lactobacillus paracasei  
Lactobacillus collinoides  
Lactobacillus coryniformis  
Lactobacillus farciminis  
Lactobacillus hilgardii  
Lactobacillus mali  
Lactobacillus reuteri
Lactobacillus salivarius
Lactobacillus zeae, Lactobacillus casei  
Lamprocystis - related bacteria
Lamprocystis purpurea (DSM4197)
Lamprocystis roseopersicina (DSM229)
Lamprocystis roseopersicina 16S rRNA 
Legionella  
Legionella pneumophila  
Legionellaceae  
Leptospirillum ferriphilum
Leptospirillum rubarum
Leptothrix discophora  
Leptothrix spp 16S rRNA 
Leucothrix mucor  
limnic Actinobacteria  
Listeria spp., except L. grayi  
Macrorhabdus ornithogaster  
Many Desulfotomaculum cluster I and other Firmicutes  
Marine alpha cluster  
Marinobacter sp.
mealybug betaproteobacterial endosymbionts  
Meiothermus sp.  
members of the genus Desulfovibrio  
Methanobacteriales  
Methanobacteriales (minus Methanothermus)  
Methanobacterium spp., Methanobrevibacter spp., Methanosphaera spp.  
Methanocaldococcaceae  
Methanococcaceae  
Methanococcus spp.  
Methanol-utilizing denitrifying cluster  
Methanosaeta concilii 16S rRNA 
Methanosaeta spp.  
Methanosarcina  
Methanosarcina barkeri 16S rRNA 
Methanosarcina frisius, Methanosarcina spp., Methanosarcina acidovorans, Methanosarcina thermophila, Methanosarcina barkeri, Methanoholophilus mahii, Methanophilus sp.  
Methanosarcina spp., Methanococcoides spp., Methanolobus spp., Methanohalophilus spp.  
Methanosarcina spp., Methanococcoides spp., Methanolobus spp., Methanohalophilus spp., Methanosaeta spp.  
Methanosarcina, Methanococcoides, Methanolobus  
Methanosarcinales (all Methanosarcina and Methanosaeta)  
Methylobacter spp., Methylomonas spp.  
Methylobacterium  
Methylocapsa acidiphila  
Methylococcus spp.  
Methylocystis  
Methylomicrobium  
Methylophaga  
Methylophaga marina  
Methylophilus  
Methylosinus sporium  
Methylosinus trichosporium  
Modestobacter genus  
most Bacteroidaceae and Prevotellaceae, some Porphyromonadaceae   
Most Chlorophyta, some Non-Chlorophyta  
most Crenarchaeota  
Most Deltaproteobacteria and most Gemmatimonadetes  
most Desulfobacter  
Most Desulfobacteraceae and Syntrophobacteraceae  
Most Desulfobulbaceae and Thermodesulforhabdus  
Most Desulfomicrobium  
Most Desulfovibrionales (excluding Lawsonia) and many Desulfuromonales  
Most Desulfovibrionales and other Bacteria  
most environmental Crenarchaeota  
most Euryarchaeota  
most Flavobacteria  
most Flavobacteria, some Bacteroidetes, some Sphingobacteria  
most Fusobacterium sp.  
Most halophilic and halotolerant Nitrosomonas spp.  
Most members of the Candidatus "Accumulibacter" cluster  
most members of the class Bacteriodetes, some Flavobacteria and Sphingobacteria  
most members of the genus Tannerella and the genus Prevotella of the class Bacteriodetes  
most members of the phylum Nitrospirae  
Most members of the Zoogloea lineage, not Z. resiniphila   
most Methanomicrobiales  
Most Non-Chlorophyta, some Chlorophyta (Chromista)  
most of Caldicellulosiruptor sp.  
most of the Clostridium coccoides-Eubacterium rectale group (Clostridium cluster XIVa and XIVb)  
most of the Clostridium histolyticum group (Clostridium cluster I and II)  
most of Thermoanaerobacterium sp.  
Most Spartobacteria and uncultured relatives  
most Streptococcus spp. and some Lactococcus spp.  
Most Thermodesulfovibrio and some Magnetobacterium  
most true Pseudomonas spp.  
Mostly Saprospiraceae family  
Naegleria spp.  
Nevskia ramosa and relatives  
Nitrobacter spp.  
Nitrococcus mobilis  
Nitrosococcus oceani, Nitrosococcus halophilus  
Nitrosolobus multiformis, Nitrosospira briensis, & Nitrosovibrio tenuis 16S rRNA 
Nitrosomonas 16S rRNA 
Nitrosomonas C-56, europaea, eutropha, & mobilis 16S Rrna 
Nitrosomonas cryotolerans  
Nitrosomonas marina-like ammonia-oxidizing bacteria  
Nitrosomonas oligotropha-lineage  
Nitrosomonas spp., Nitrosococcus mobilis  
Nitrosospira spp.  
Nitrosospira tenius-like ammonia-oxidizing bacteria  
Nitrospina gracilis  
Nitrospira moscoviensis
Nitrospira moscoviensis & Nitrospira marina 16S rRNA 
Nitrospira moscoviensis16S rRNA 
Nitrospira spp.  
nocardioform actinomycete sp.  
Nostocoida limicola I  
Nostocoida limicola II
Nostocoida limicola III
Oceanospirillum  
Octadecabacter spp.  
Oenococcus oeni  
Opitutus spp. and uncultured relatives  
Order Rhizobiales  
Order Rhodobacterales  
Pantoea spp.  
Parachlamydia sp. UV-7  
Paracoccus denitrificans, P. versutus  
Paraphysomonas imperforata (Chrysophyceae)  
Paraphysomonas vestita (Chrysophyceae)  
Pasteurella pneumotropica
Pediococcus acidilactici
Pediococcus damnosus  
Pediococcus parvulus  
Pedobacter heparinus and relatives  
Pedomicrobium strains  
Pelagophyceae  
Pelagophyceae clade containing Aureococcus, Pelagomonas, Pulvinaria, CCMP 1395  
Pelotomaculum thermopropionicum  
Peptoniphilus asaccharo
Peptostreptococ anae - stom
Pfiesteria piscicida  
Phascolarctobacterium faecium, Acidaminococcus fermentans, Succiniclasticum ruminis  
phosphate accumulating bacteria (Gammaproteobacteria)  
Phyllobacterium  
phylum Chloroflexi (green nonsulfur bacteria)  
Pirellula sp. strain SH1  
Planctomycetales  
Planctomycetes  
Polaribacter spp.  
Polaromonas vacuolata  
Polynucleobacter cluster  
Porphyromonas gingivalis
Porphyromonas gulae
Prevotella denticola  
Prevotella intermedia  
Prevotella nigrescens  
Prochlorococcus (Cyanophyceae)  
Proteobacteria-alpha 16S rRNA
Proteobacteria-beta 16S rRNA 
Proteobacteria-beta 23S rRNA
Proteobacteria-beta ammonia-oxidizing 16S rRNA 
Proteobacteria-delta 16S rRNA 
Proteobacteria-gamma 
Proteus mirabilis
Prymnesiophyceae  
Pseudoalteromonas, Colwellia  
Pseudomonas aeruginosa
Pseudomonas chlororaphis  
Pseudomonas fluorescens Ag1  
Pseudomonas putida, P. mendocina  
Pseudomonas spp.  
Pseudomonas stutzeri  
Pseudomonas stutzeri, P. mendocina  
Pseudomonas synxantha and related species of the Pseudomonas fluorescens subgroup  
Pseudo-Nitzschia australis (Bacilliarophyceae)  
Pseudo-Nitzschia multiseries (Bacilliarophyceae)  
Pseudo-Nitzschia pungens (Bacilliarophyceae)  
Psychrobacter spp.  
Ralstonia solanacearum, Ralstonia syzygii, blood disease bacterium (BLDB)  
Representatives of the Xanthomonas group  
Representatives of the Xanthomonas group and the Alphaproteobacteria, Brevundimonas diminuta  
Rhodobacter blasticus  
Rhodobacter, Roseobacter  
Rhodobium marinum, Rhodopseudomonas julia  
Rhodocyclus spp., most member of the Candidatus "Accumulibacter" cluster, Azospira lineage  
Rhodovulum sulfidophilum  
Roseiflexus assemblage  
Roseobacter sp. strain Shippagan group  
Ruminococcus albus, R. flavefaciens  
Ruminococcus productus and relatives  
Salmonella 23S rRNA 
Salmonella spp., Plesiomonas shigelloides  
Saprospira grandis  
Shewanella frigidimarina  
Sphaerotilus natans  
Sphingomonas  
Sphingomonas, Erythrobacter  
spirochete symbiont group of gutless oligochaetes  
spiroplasma-Proteobacteria 
Staphylococcus aureus  
Staphylococcus coagulase-negative 16S rRNA 
Staphylococcus spp. 16S rRNA 
Stenotrophomonas maltophilia  
Streptococcus agalactiae  
Streptococcus oralis  
Streptococcus pneumoniae  
Streptococcus pyogenes  
Streptococcus spp.
subgroup of Bacteriodetes  
subgroup of Betaproteobacteria  
subgroup of Clostridia cluster I and II  
SW5 Psychrobacter/Moraxella 16S rRNA 
Synechococcus (Cyanophyceae)  
Tannerella forsythensis (Bacteroides forsythus)  
Tetrasphaera japonica
Thauera spp. 
Thermoanaerobacterium thermosaccharolyticum  
Thermococcales  
Thermotogales  
Thermus spp.  
Thiobacillus denitrificans  
Thiobacillus denitrificans and Thiobacillus thioparus  
Thiobacillus plumbophilus  
Thiomicrospira denitrificans  
Thiomonas intermedia  
Thioploca spp. 16S rRNA 
Thiothrix eikelboomii, T. nivea, T. unzii, T. fructosivorans, T. defluvii, Eikelboom type 021N group I, II, III  
Thiothrix nivea  
Thioturbo danicus and strain DK4  
Tplasma, Thermoplasma spp.  
Treponema cluster I  
Treponema denticola 16S rRNA 
Treponema maltophilum 16S rRNA 
Treponema phagedenis 16S rRNA 
Treponema vincentii 16S rRNA 
Trichonympha sp. HsTcA  
type I methanotrophs  
type II methanotrophs  
universal Archaea probe 16S rRNA
universal Bacillus probe 
universal Bacteria probe 16S rRNA
universal mesophilic methanogens 
universal non-bacteria probe 16s rRNA 
Urothoe poseidonis clone UP23b  
Vahlkampfiidae  
Veillonella dispar, Veillonella parvula, Veillonella atypica  
Veillonella parvula  
Verrucomicrobiales  
Verrucomicrobium  
Verrucomicrobium, most Prosthecobacter, and uncultured relatives  
Vibrio spp.
Xanthomonas 16S rRNA
Xanthomonas branch  
Yarrowia lipolytica  
Yersinia enterocolitica 16S rRNA 
Yersinia pestis & Yersinia pseudotuberculosis 16S rRNA 
Zoogloea ramigera