TABLE 1.

FISH probes used in this study and their hybridization conditions

Probe	Target	Sequence (5′-3′)	Formamide (%)	Source or reference
EUB338 Ib	All Bacteria	GCTGCCTCCCGTAGGAGT	0-50	3
EUB338 IIb	Planctomycetales	GCAGCCACCCGTAGGTGT	0-50	14
EUB338 IIIb	Verrucomicrobiales	GCTGCCACCCGTAGGTGT	0-50	14
HHY	Haliscomenobacter hydrossis	GCCTACCTCAACCTGATT	20	51
BAC303	Bacteroidetes	CCAATGTGGGGGACCTT	0	33
PLA886	Planctomycetales	GCCTTGCGACCATACTCCC	35	39
BET42A	Betaproteobacteria	GCCTTCCCACTTCGTTT	35	34
CFB719	Cytophaga-Flavobacterium-Bacteroides	AGCTGCCTTCGCAATCGG	30	53
CF319a	Flavobacteria; some Bacteroidetes; some sphingobacteria	TGGTCCGTGTCTCAGTAC	35	33
CHL1851	Type 1851 filamentous bacterium	AATTCCACAACCTCTCCA	35	6
CFX109	Chloroflexi subgroup 3	CACGTGTTCCTCAGCCGT	30	8
CFX784	Chloroflexi subgroup 1	ACCGGGGTCTCTAATCCC	35	8
CFX1223	All Chloroflexi	CCATTGTAGCGTGTGTGTMG	35	8
GNSB941	All Chloroflexi	AAACCACACGCTCCGCT	35	20
CFX197	Chloroflexi OTU A (clones A26, B1, and B45) (variant A)	TCCCGGAGCGCCTGAACT	40	This study
CFX197comp	Competitor probe against sequences with accession no. ZA3635c and ZA3612c	TCCCGAAGCGCCTGAACTa		This study
CFX223	Chloroflexi OTU B (clone A58) (variant B)	GGTGCTGGCTCCTCCCAG	35	This study
CFX223 H202	Helper probe	AGCGCCTGAGCTTCAGTCATC		This study
CFX223 H241	Helper probe	CGTTACCTTACCAACTAGCTGATGG		This study

^aThe mismatching base of the CFX197comp probe to use with the CFX197 probe is underlined.

^bEUB338 I, II, and III used in equimolar amounts as EUBmix.