Table 3.
Overview of taxonomic alterations in case–control studies on the gut microbiota in PSC
| Reference | Study population | Biological source | Sequencing technique | Enriched in PSC | Depleted in PSC |
|---|---|---|---|---|---|
| Sabino et al., 2016 [111] | 18 PSC only; 27 PSC-UC; 21 PSC-CD; 13 UC; 30 CD; 66 HC | Feces | 16S, V4 |
vs HC: Bacteroidetes, Fusobacteria, Streptococcus, Enterococcus, Lactobacillus, Fusobacterium, Veillonella PSC-IBD vs PSC only: none |
vs HC: Firmicutes Anaerostipes PSC-IBD. vs PSC only: none |
| Bajer et al., 2017 [110] | 32 PSC-IBD; 11 PSC only; 32 UC 31 HC | Feces | 16S, V4 |
vs HC: Rothia, Enterococcus, Streptococcus, Clostridium, Veillonella, Haemophilus (PSC only, and PSC-IBD); Staphylococcus, Coprobacillus, Escherichia, Corynebacterium, Lactobacillus (PSC-IBD) vs UC: Rothia, Streptococcus, Veillonella, Blautia; Akkermansia muciniphila, Clostridium colinum |
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 UC: Fusobacteriaceae |
| Kummen et al., 2017 [109] | 44 PSC-UC; 11 PSC-CD; 30 PSC only; 36 UC; 263 HC | Feces | 16S, V3–V4 |
vs HC: Veillonella (V. dispar, V. parvula) vs UC: Veillonella (V. dispar, V. parvula); Akkermansia, Clostridium, Ruminococcaceae |
vs HC: ML615J-28 unknown genus, Succinivibrio, Desulfovibrio, RF32 unknown genus, Phascolarctobacterium, Coprococcus, Lachnospiraceae unknown genus, Christensenellaceae unknown genus, Clostridiales unknown genus, YS2 unknown genus, S24.7 unknown genus vs UC: Dorea, Oscillospira, Citrobacter |
| Rühlemann et al., 2017 [108] | 38 PSC-UC; 35 PSC only; 88 UC; 98 HC | Feces | 16S, V1–V2 | vs HC: Veillonella (no difference observed compared to UC) | Not investigated |
| Rühlemann et al., 2019 [107] | 75 PSC-IBD; 62 PSC only; 118 UC; 133 HC | Feces | 16S, V1–V2 |
vs HC: Veillonella, Streptococcus, Lactobacillus, Enterococcus; Proteobacteria (Gammaproteobacteria), Lactobacillales (Bacilli), Parabacteroides, Bacteroides spp. vs UC: Firmicutes PSC-IBD vs PSC only: none |
vs HC: Coprococcus, Holdemanella, Desulfovibrio, Faecalibacterium, Clostridium IV PSC-IB.D vs PSC only: Bilophila and Bacteroides OUT |
| Lemoinne et al., 2019 [112] | 16 PSC-UC/IBD-U; 11 PSC-CD; 22 PSC only; 33 IBD; 30 HC | Feces | 16S, V3–V4 | vs HC: Veillonella, Sphingomonadaceae, Alphaproteobacteria, Rhizobiales | vs HC: Ruminococcus, Faecalibacterium, Lachnoclostridium, Blautia |
| Liu et al., 2021 [113] | 37 PSC; 34 IgG4 cholangiopathies; 64 HC | Feces | 16S, V3–V.4 | vs IgG4/HC: Turicibacter, Ruminococcus gnavus group | vs IgG4/HC: Eubacterium sineum group, Oscillospirales, Catenibacterium, Ruminococcaceae UBA 1819 Oscillospiraceae UCG-005, Lachnospiraceae UCG-010, Eubacterium ruminantium group, Eubacterium eligens group, Agathobacter |
| Kummen et al., 2021 [114] | 136 PSC; 93 IBD; 158 HC | Feces | Shotgun metagenomics |
vs HC (meta-analysis; abundance): Clostridium asparagiforme, Escherichia unclassified vs HC (meta-analysis; prevalence): Clostridium clostridioforme, Clostridiales bacterium 1 7 47FAA, Clostridium bolteae, Bifidobacterium bifidum, Clostridium symbiosum, Escherichia unclassified, Eggerthella unclassified, Eggerthella lenta, Clostridium citroniae |
vs HC (meta-analysis; abundance): Coprococcus catus, Roseburia inulinivorans, Ruminococcus obeum, Subdoligranulum unclassified, Eubacterium rectale, Eubacterium siraeum, Bacteroides bacterium ph8, Barnesiella intestinihominis, Alistipesshahii, Bacteroides intestinalis vs HC (meta-analysis; prevalence): Coprobacter fastidiosus, Alistipes senegalensis, Eubacterium ramulus, Eubacterium hallii, Lachnospiraceae bacterium 7 1 58FAA |
| Rossen et al., 2015 [106] | 8 PSC-UC; 4 PSC-CD; 11 UC; 9 HC | Mucosal biopsy, ileocecum | 16S (HITChip) | None |
vs HC: Uncultured Clostridiales II vs UC: Uncultured Clostridiales II |
| Kevans et al., 2016 [105] | 31 PSC-UC; 56 UC; 0 HC | Mucosal biopsy, left colon | 16S, V4 | None | None |
| Torres et al., 2016 [104] | 13 PSC-UC; 6 PSC-CD; 1 PSC only; 13 UC; 2 CD; 9 HC | Mucosal biopsy, terminal ileum, right, and left colon | 16S, V3–V4 | vs IBD: Barnesiellaceae, Blautia, Ruminococcus obeum | None |
| Quraishi et al., 2017 [103] | 11 PSC-IBD 10 IBD 9 HC | Mucosal biopsy, ascending, transverse, descending colon | 16S, V3–V4 | vs HC: Escherichia, Lachnospiraceae, Megasphera | vs HC: Prevotella, Roseburia, Bacteroides |
| Quraishi et al., 2020 [102] | 10 PSC-IBD 10 UC; 10 HC | Mucosal biopsy, sigmoid colon | 16S, V4 |
vs HC: Bacilli, Pseudomonas, Streptococcus, Haemophilus parainfluenzae vs UC: 24 taxa, including Bacilli, Staphylococcus, Parvimonas sp., Bacteroides fragilis, Roseburia spp., Shewanella spp., Clostridium ramosum, Sphingomonas sp., Actinomyces, Rothia |
vs HC: Lachnospiraceae vs UC: 26 taxa, including Lentisphaerae, Gammaproteobacteria, Enterobacteriaceae, Prevotellaceae, Paraprevotellaceae, Coriobacteriaceae, Erysipelotrichaceae, Desulfovibrionaceae, Myxococcales, Streptococcus, Blautia |
CD, Crohn’s disease; HC, healthy control; IBD, inflammatory bowel disease; IBD-U, inflammatory bowel disease—unclassified; IgG4, IgG4-associated cholangiopathy; PSC, primary sclerosing cholangitis; UC, ulcerative colitis.