Fluctuations in butyrate-producing bacteria in ulcerative colitis patients of North India

Table 2 Probes and oligonucleotides employed in the study

Primer or probe	Target (phylogenetic group)	Sequence (5’-3’) from 16S rRNA gene	Used in FISH-flow cytometry or qPCR	Ref.
NON338	No bacteria	ACATCCTACGGGAGGC	Probe1	[21]
EUB338	Most bacteria	GCTGCCTCCCGTAGGAGT	Probe1	[20]
Erec 482	C. coccoides/E.rectale cluster	GCTTCTTAGTCARGTACCG	Probe1	[34]
Clep 1156	Clostridium leptum subgroup	GTTTTRTCAACGGCAGTC	Probe1	[35]
Fpra-655	F. prausnitzii	CGCCTACCTCTGCACTAC	Probe1	[16]
Rint-623	R. intestinalis subcluster	TTCCAATGCAGTACCGGG	Probe1	[16]
Ehal-057	E. halliii L2-7/E. halliii	TTGCACTGCCACCTACGC	Probe1	[16]
Cp1	Competitor 1	GRTTTRTCAYCGGCAGTC	Competitor1	[23]
Cp2	Competitor 1	GTVTTRTCBACGGCAGTC	Competitor1	[23]
H1174	Helper oligonucleotide	TTGACGTCRTCCCCACCTTCCTCC	Helper1	[23]
H1129	Helper oligonucleotide	TAGAGTGMTCTTGCGTA	Helper1	[23]
H1090	Helper oligonucleotide	GGTTGCGCTCGTTGCGGGACTTAA	Helper1	[23]
H750	Helper oligonucleotide	TCGHGCCTCAGCGTCAG	Helper1	[23]
H122	Helper oligonucleotide	GAAGGCAGGTTACTCACGC	Helper1	[23]
Clep FP	C. leptum subgroup	CGTCAGCTCGTGTCGTGAGAT	Primer set2	[36]
Clep RP		CGTCATCCCCACCTTCCTCC
C.cocci FP	C. coccoides subgroup	GCCACATTGGGACTGAGA	Primer set2	[36]
C.cocci RP		GCTTCTTAGTCAGGTACCG
Fpraus FP	F. prausnitzii	GATGGCCTCGCGTCCGATTAG	Primer set2	[37]
Fpraus RP		CCGAAGACCTTCTTCCTC
Rint FP	Roseburia/E. rectale cluster	CKGCAAGTCTGATGTGAAAG	Primer set2	This study
Rint RP		GCGGGTCCCCGTCAATTCC
Ehal FP	E. hallii L2-7/E. hallii members	GCGTAGGTGGCAGTGCAA	Primer set2	[38]
Ehal RP		GCACCGRAGCCTATACGG

¹Respective probe or oligonucleotide was used in fluorescent in situ hybridization (FISH)-flow cytometry;

²Respective primer was used in quantitative polymerase chain reaction (qPCR). FP: Forward primer; RP: Reverse primer; R. intestinalis: Roseburia intestinalis; E. hallii: Eubacterium hallii; F. prausnitzii: Fecalibacterium prausnitzii; C. coccoides: Clostridium coccoides; C. leptum: Clostridium leptum; E. rectale: Eubacterium rectale.