TABLE 2

FISH probes used in this study

ProbeFluorophore(s)Target organismSequence (5′→3′)Target positionReference
Exptl probe set
    Eub338-IAlexa 555 or
Rhodamine Red-X
Most bacteriaGCTGCCTCCCGTAGGAGT338–355 (16S)53
    Vib1749Texas Red-XVibrionaceae familyAGCCACCTGGTATCTGCGACT1749–1769 (23S)Unpublished dataa
    Vib2300Texas Red-XVibrionaceae familyTAACCTCACGATGTCCAACCGTG2299–2321 (23S)Unpublished dataa
    Alf968Atto 620 or Dy490AlphaproteobacteriaGGTAAGGTTCTGCGCGTT968–985 (16S)54
    Gam42aAtto 647N or Cy5GammaproteobacteriaGCCTTCCCACATCGTTT1027–1043 (23S)55
Nontarget control
probes
    Vei488Alexa 555VeillonellaCCGTGGCTTTCTATTCCG488–505 (16S)56
    PorTan34Texas Red-XPorphyromonas and
Tannerella
GTTAAGCCTATCGCTAGC34–51 (16S)Unpublished datab
    Fus714Atto 620FusobacteriumGGCTTCCCCATCGGCATT714–731 (16S)57
    Lep568Atto 647NLeptotrichiaGCCTAGATGCCCTTTATG568–585 (16S)57
Nontarget probe
    Hhaem1007Rhodamine Red-XHaemophilus
haemolyticus
AGGCACTCCCATATCTCTACAG1007–1028 (16S)Unpublished datab
  • a C. Schlundt, J. L. Mark Welch, E. R. Zettler, and L. A. Amaral-Zettler.

  • b J. L. Mark Welch and G. G. Borisy.