Table 1.

Changes in Gut Microbiota and Bile Acids Profile in Patients with Inflammatory Bowel Disease.

Publication	Patients	Samples and Methods	Major Findings
Duboc et al., 2013 [9]	12 with CD, 30 with UC and 29 HCs	Fecal samples (real-time qPCR and HPLC) Serum samples (HPLC)	Firmicutes (e.g., Clostridium leptum and Faecalibacterium prausntizii) was reduced and Escherichia coli was enriched in IBD. Microbial deconjugation, transformation and desulphation capability were depleted in IBD. Fecal conjugated and 3-OH-sulfated BAs were increased, whilst serum and fecal secondary BAs were reduced in IBD.
Sinha et al., 2020 [10]	17 with UC and seven with FAP	Stool samples (metagenomic sequencing and metabolomic analysis)	α-Diversity was reduced and phylum Firmicutes and Ruminococcaceae (in Clostridium cluster XIVa) were decreased in UC. Secondary BAs (LCA and DCA) were remarkably reduced and CDCA was remarkably increased in UC. CA levels were also increased but not significant in UC.
Franzosa et al., 2019 [15]	88 with CD, 76 with UC and 56 non-IBD	Stool samples (metagenomic sequencing and metabolomic analysis)	Roseburia hominis and Ruminococcus obeum were reduced in IBD. Ruminococcus gnavus and Escherichia coli were increased in CD. Cholate and CDCA were increased in IBD, whilst secondary BAs (LCA and DCA) were decreased in CD.
Jacobs et al., 2016 [16]	26 with CD, 10 with UC and 54 healthy first-degree relatives	Stool samples (16S rRNA sequencing and HPLC)	Microbial diversity was reduced in CD. Bifidibacterium adolescentis and Parabacteroides distasonis were enriched, whilst Faecalibacterium prausntizii and Bacteroides fragilis were reduced in CD. CA, 7-keto-DCA, CDCA sulphate and 3-sulfo-DCA were increased in CD.
Lloyd-Price et al., 2019 [18]	67 with CD, 38 with UC and 27 non-IBDs	Stool samples (metagenomic sequencing and metabolomic analysis)	α-Diversity was decreased and Faecalibacterium prausnitzii and Roseburia hominis were depleted, whilst Escherichia coli was enriched in CD. Primary BA cholate and conjugated BAs (CA, GCA, TCA and GCDCA) were increased, whilst secondary BAs (LCA and DCA) were reduced in IBD.
Wang et al., 2021 [19]	29 pediatric patients with CD and 20 HCs	Fecal samples (16S rRNA sequencing and UPLC-MS)	No significant difference was found in α-diversity between CD and HC. The genera Bifidobacteria and Clostridium (clusters IV and XI) were decreased in CD. CD showed an increased level of conjugated and primary BAs and a decreased level of unconjugated and secondary BAs (DCA, LCA and hyodeoxycholic acid).
Weng et al., 2019 [37]	173 with CD, 107 with UC and 42 HCs	Fecal samples (metagenomic sequencing and metabolomic analysis) Mucosal biopsy samples (16S rRNA sequencing)	α-Diversity was remarkably reduced in CD. Enterococcus and Hydrogenophilus were enriched in fecal and mucosal samples of IBD. Proteobacteria was enriched in mucosal samples of IBD. LCA, CDCA and tauro-LCA were remarkably decreased in IBD.
Murakami et al., 2018 [38]	Six with CD, six with UC and 26 HCs	Fecal samples (T-RFLP analysis and HPLC) Serum samples (HPLC)	The proportion of fecal Clostridium cluster XIVa was remarkably reduced in IBD. Fecal and serum DCA/(DCA + CA) in IBD were reduced compared with those in healthy subjects.
Diederen et al., 2020 [39]	43 pediatric patients with CD and 18 HCs	Fecal samples (16S rRNA sequencing and HPLC)	OTU richness was reduced in CD but the diversity did not remarkably differ between CD and HC. Eubacterium rectale, Bifidobacterium longum and Ruminococcus bromii were increased, whilst Escherichia coli was decreased in CD. The relative concentration of primary BAs was increased in CD.
Yang et al., 2021 [22]	32 patients with UC and 23 HCs	Fecal samples (16S rRNA sequencing and UPLC-MS)	Faecalibacterium, Roseburia, Butyricicoccus and Clostridium were reduced, whilst Enterobacteriaceae, Enterobacteriales, and Escherichia_Shigella were enriched in UC. The secondary BAs, such as LCA, DCA and tauro-LCA were decreased significantly, whilst primary and conjugated BAs (CA, TCA and G/TCDCA) were increased in UC.

Abbreviations: HPLC, high-performance liquid chromatography; T-RFLP, terminal restriction fragment length polymorphism analysis; UPLC-MS, ultraperformance liquid chromatography coupled with mass spectrometry; OTU, operational taxonomic unit; IBD, inflammatory bowel disease; UC, ulcerative colitis; CD, Crohn’s disease; HC, healthy controls; FAP, familial adenomatous polyposis; BA, bile acid; CA, cholic acid; CDCA, chenodeoxycholic acid; DCA, deoxycholic acid; LCA, lithocholic acid; GCA, glycocholic acid; TCA, taurocholic acid; GCDCA, glycochenodeoxycholic acid.