Stool substitute transplant therapy for the eradication of Clostridium difficile infection: ‘RePOOPulating’ the gut

Microbiome

Table 1 Composition of stool substitute (RePOOPulate)

Closest species match, inferred by alignment of 16S rRNA sequence to GreenGenes database^a	% identity to closest match	Relative abundance (by biomass) in RePOOPulate formulation
Acidaminococcus intestinalis	100	+++
Bacteroides ovatus	99.52	+
Bifidobacterium adolescentis (two different strains)	99.79	++
	99.79	++
Bifidobacterium longum (two different strains)	99.86	+++
	99.16	+++
Blautia producta	96.43	+
Clostridium cocleatum	91.92	+
Collinsella aerofaciens	98.73	+
Dorea longicatena (two different strains)	99.62	+
	99.60	+
Escherichia coli	99.80	+
Eubacterium desmolans	94.90	+
Eubacterium eligens	98.15	+++++
Eubacterium limosum	97.05	+
Eubacterium rectale (four different strains)	99.59	+++++
	99.60	+++++
	99.19	+++++
	99.53	+++++
Eubacterium ventriosum	100	++
Faecalibacterium prausnitzii	99.17	+++++
Lachnospira pectinoshiza	95.22	+
Lactobacillus casei/paracasei	99.47	+
Lactobacillus casei	99.74	+
Parabacteroides distasonis	99.45	++
Raoultella sp.	99.40	+
Roseburia faecalis	99.65	++
Roseburia intestinalis	100	++
Ruminococcus torques (two different strains)	99.15	+++
	99.29	+++
Ruminococcus obeum (two different strains)	94.89	+
	94.69	+
Streptococcus mitis ^b	99.79	+

List of cultured isolates from the healthy donor, with favorable antibiotic resistance profiles (defined as vancomycin and/or imipenem sensitive, with further sensitivity to at least three of piperacillin, amoxicillin/clavulanic acid, ceftazidime, ceftriaxone, moxifloxacin and metronidazole) that were included in the stool substitute preparation. ^aClosest species match was inferred by alignment of the 16S rRNA sequence to the GreenGenes database[7]; note that in some cases 16S rRNA gene sequences could not resolve identity beyond genus, and that closest match does not infer definitive speciation. Shaded boxes indicate strains that are possibly novel species (and, in some cases, genera). Note that some representative strains identify with the same species by 16S rRNA gene sequence alignment, but we believe them to be different strains based on differences in colony morphology, antibiotic resistance patterns and growth rates. ^bIdentifies with S. mitis but is not β-hemolytic.