Table 1.

Studies of the fecal or mucosal microbiota in primary sclerosing cholangitis

Ref.	Population	Sample source	Methods	Taxa depleted in PSC	Taxa enriched in PSC	Diversity in PSC
Adult
Mucosal
Quraishi et al[30], 2020	10 PSC-IBD 10 UC; 10 HC	Mucosal biopsies, sigmoid	16S rRNA; V4 amplified Illumina MiSeq	vs HC: Lachnospiraceae	vs HC: Bacilli, Pseudomonas, Streptococcus, Haemophilus parainfluenzae	Alpha: No difference; Beta: All 3 groups significantly different from each other
				vs UC: 26 taxa, including Lentisphaerae, Gammaproteobac-teria, Enterobacteriaceae, Prevotellaceae, Paraprevotellaceae, Coriobacteriaceae, Erysipelotrichaceae, Desulfovibrionaceae, Myxococcales, Streptococcus, Blautia	vs UC: 24 taxa, including Bacilli, Staphylococcus, Parvimonas sp., Bacteroides fragilis, Roseburia spp., Shewanella spp, Clostridium ramosum, Sphingomonas sp., Actinomyces, Rothia
Quraishi et al[31], 2017 (Letter)	11 PSC-IBD 10 IBD 9 HC	Mucosal biopsies, ascending, transverse, descending colon (results not different by site)	16S rRNA; V3-V4 amplified; Illumina MiSeq	vs HC: Prevotella, Roseburia, Bacteroides	vs HC: Escherichia, Lachnospiraceae, Megasphera	Beta: Different from HC and IBD
Torres et al[27], 2016	13 PSC-UC; 6 PSC-CD; 1 PSC only; 13 UC; 2 CD; 9 HC	Mucosal biopsies from terminal ileum, right and left colon (results not different by site)	16S rRNA; V3-V4 amplified; Illumina MiSeq	vs IBD	vs IBD: Barnesiellaceae, Blautia, Ruminococcus obeum	Alpha: Similar to HC and IBD; Beta: Similar to HC and IBD
Kevans et al[28], 2016	31 PSC-UC; 56 UC; 0 HC	Mucosal biopsies, left colon	16S rRNA; V4 amplified; Illumina MiSeq	Nil after multiple testing adjustment	Nil after multiple testing adjustment	Alpha: ↓ vs UC (in 1 cohort only); Beta: No difference
Rossen et al[29], 2015	8 PSC-UC; 4 PSC-CD; 11 UC; 9 HC	Mucosal biopsies from ileocecum	16S rRNA using HITChip	vs HC: Uncultured Clostridiales II	vs HC	Alpha: ↓ vs HC; Beta: Similar to HC and IBD
				vs UC: Uncultured Clostridiales II	vs UC
Fecal
Lemoinne et al[38], 2019	16 PSC-UC/IBD-U; 11 PSC-CD; 22 PSC only; 33 IBD; 30 HC	Stool	16S rRNA; V3-V4 amplified; Illumina MiSeq	vs HC: Ruminococcus, Faecalibacterium, Lachnoclostridium, Blautia	vs HC: Veillonella, Sphingomonada-ceae, Alphaproteobac-teria, Rhizobiales	Alpha: ↓ vs HC and IBD; Beta: PSC-IBD different from HC and IBD, PSC-IBD similar to PSC only
Rühlemann et al[20], 2019	75 PSC-IBD; 62 PSC only; 118 UC; 133 HC	Stool	16S rRNA; V1-V2 amplified MiSeq	vs HC: Coprococcus Holdemanella, Desulfovibrio, Faecalibacterium, Clostridium IV	vs HC: Veillonella, Streptococcus, Lactobacillus, Enterococcus; Proteobacteria (Gammaproteobacteria), Lactobacillales (Bacilli), Parabacteroides, Bacteroides spp.	Norwegian cohort; Alpha: ↓ vs HC, similar to UC; Beta: Different from HC and IBD; German cohort; Alpha: Similar to HC, ↑ vs UC; Beta: Different from HC and IBD, PSC-IBD similar to PSC only
				vs UC	vs UC: Firmicutes
				PSC-IBD vs PSC only: Bilophila and Bacteroides OTU ↓	PSC-IBD vs PSC only: Nil
Rühlemann et al[25], 2017 (Letter)	38 PSC-UC; 35 PSC only; 88 UC; 98 HC	Stool	16S rRNA; V1-V2		vs HC: Veillonella (no difference compared to UC)	Beta: Different from HC and IBD, PSC-IBD similar to PSC only
Kummen et al[21], 2017	44 PSC-UC; 11 PSC-CD; 30 PSC only; 36 UC; 263 HC	Stool	16S rRNA; V3-V4 amplified; Illumina MiSeq	vs HC: ML615J-28 unknown genus, Succinivibrio, Desulfovibrio, RF32 unknown genus, Phascolarctobacteri-um, Coprococcus, Lachnospiraceae unknown genus, Christensenellaceae unknown genus, Clostridiales unknown genus, YS2 unknown genus, S24.7 unknown genus	vs HC: Veillonella (V. dispar, V. parvula)	Alpha: ↓ vs HC, similar to IBD; Beta: Different from HC and IBD, PSC-IBD similar to PSC only
				vs UC: Dorea, Oscillospira, Citrobacter	vs UC: Veillonella (V. dispar, V. parvula); Akkermansia, Clostridium, Ruminococcaceae
				PSC-IBD vs PSC only: Nil	PSC-IBD vs PSC only: Nil
Bajer et al[22], 2017	32 PSC-IBD; 11 PSC only; 32 UC 31 HC	Stool	16S rRNA; V4 amplified Illumina MiSeq	vs HC: Coprococcus (C. catus), unidentified Lachnospiraceae genera, Faecalibacterium prausnitzii, Ruminococcus gnavus, Prevotella copri (PSC only and PSC-IBD) Phascolarctobacterium (PSC-IBD); Adlercreutzia equolifaciens (PSC only)	vs HC: Rothia, Enterococcus, Streptococcus, Clostridium, Veillonella, Haemophilus (PSC only and PSC-IBD); Staphylococcus, Coprobacillus, Escherichia, Corynebacterium, Lactobacillus (PSC-IBD)	Alpha: Similar to HC and UC; Beta: Different from HC, PSC-IBD different from IBD, PSC-IBD similar to PSC only
				vs UC: Fusobacteriaceae	vs UC: Rothia, Streptococcus, Veillonella, Blautia; Akkermansia muciniphila, Clostridium colinum
Sabino et al[23], 2016	18 PSC only; 27 PSC-UC; 21 PSC-CD; 13 UC; 30 CD; 66 HC	Stool	16S rRNA; V4 amplified; Illumina MiSeq	vs HC: Firmicutes Anaerostipes	vs HC: Bacteroidetes, Fusobacteria, Streptococcus, Enterococcus, Lactobacillus, Fusobacterium, Veillonella1	Alpha: ↓ vs HC; Beta: Different from HC, PSC-UC different from UC, PSC-IBD similar to PSC only
				PSC-IBD vs PSC only: Nil	PSC-IBD vs PSC only: Nil
In a re-analysis by Vieira-Silva et al[24] in 2019, Fusobacterium was associated with intestinal inflammation and Enterococcus with cholangitis/biliary obstruction.
Pediatric
Iwasawa et al[26], 2017 (Letter)	27 PSC; 16 UC; 23 HC	Stool	16S rRNA; 1-V2 amplified	vs HC: Parabacteroides (P distasonis), Anaerostipes hadrus, Blautia obeum	vs HC: Enterococcus faecium, Enterococcus sp. NBRC 107345, Streptococcus parasanguinis, Veillonella sp. 3_1_44	Alpha: ↓ vs HC, ↑ vs IBD; Beta: Different from HC and IBD
				vs UC	vs UC: Faecalibacterium, Ruminococcus, Roseburia

¹Significant only when patients with cirrhosis included. CD: Crohn’s disease; HC: Healthy control; IBD: Inflammatory bowel disease; IBD-U: Inflammatory bowel disease-unclassified; PSC: Primary sclerosing cholangitis; UC: Ulcerative colitis.