Fecal microbiome and bile acid metabolome in adult short bowel syndrome

Abstract

Loss of functional small bowel surface area causes short bowel syndrome (SBS), intestinal failure, and parenteral nutrition (PN) dependence. The gut adaptive response following resection may be difficult to predict, and it may take up to 2 yr to determine which patients will wean from PN. Here, we examined features of gut microbiota and bile acid (BA) metabolism in determining adaptation and ability to wean from PN. Stool and sera were collected from healthy controls and from patients with SBS (n = 52) with ileostomy, jejunostomy, ileocolonic, and jejunocolonic anastomoses fed with PN plus enteral nutrition or who were exclusively enterally fed. We undertook 16S rRNA gene sequencing, BA profiling, and 7α-hydroxy-4-cholesten-3-one (C4) quantitation with LC-MS/MS and serum amino acid analyses. Patients with SBS exhibited altered gut microbiota with reduced gut microbial diversity compared with healthy controls. We observed differences in the microbiomes of patients with SBS with ileostomy versus jejunostomy, jejunocolonic versus ileocolonic anastomoses, and PN dependence compared with those who weaned from PN. Stool and serum BA composition and C4 concentrations were also altered in patients with SBS, reflecting adaptive changes in enterohepatic BA cycling. Stools from patients who were weaned from PN were enriched in secondary BAs including deoxycholic acid and lithocholic aicd. Shifts in gut microbiota and BA metabolites may generate a favorable luminal environment in select patients with SBS, promoting the ability to wean from PN. Proadaptive microbial species and select BA may provide novel targets for patient-specific therapies for SBS.NEW & NOTEWORTHY Loss of intestinal surface area causes short bowel syndrome, intestinal failure, and parenteral nutrition dependence. We analyzed the gut microbiota and bile acid metabolome of a large cohort of short bowel syndrome adult patients with different postsurgical anatomies. We report a novel analysis of the microbiome of patients with ileostomy and jejunostomy. Enrichment of specific microbial and bile acid species may be associated with the ability to wean from parenteral nutrition.

Keywords: FGF19; enterohepatic bile acid cycling; intestinal adaptation; short gut syndrome.

Graphical abstract

Figure 1.

The proportion of genera within the microbiota of healthy controls (NormCrtl, normal control, n = 7), patients with familial adenomatous polyposis coli who have had a total colectomy (NoColon, n = 3), and patients who were fed enterally only (OffTPN, n = 30) or were dependent on parenteral nutrition (OnTPN, n = 22). Stacked bar charts represent the relative abundances of taxa in each sample, with each color representing a different taxon (key on right).

Figure 2.

Shannon diversity indices for healthy control subjects compared with ileostomy (I, n = 16), ileocolonic anastomosis (IC Anast, n = 24), jejunostomy (J, n = 4), and jejunocolonic anastomosis groups (JC Anast, n = 8). **P = 0.002; control vs. whole group (I + IC Anast + J + JC Anast, n = 52). Subgroup analysis revealed reduced α diversity in patients with ileostomy vs. controls (I vs. controls, *P = 0.003) and in patients with ileocolonic anastomosis vs. controls (IC Anast vs. controls *P = 0.003). Patients with jejunostomy vs. controls, P = 0.054. Jejunocolonic anastomosis subgroup showed no significant change in diversity compared with controls (P = 0.122). Horizontal bars represent the median, and box and whiskers show quartiles and the minimum and maximum, respectively.

Figure 3.

LDA analysis of microbiota of normal controls (n = 7) compared with all patients with SBS (n = 52). A: phylum level. B: class level. C: order level. D: family level. E: genus level. Ctrl, control; LDA, linear discriminate analysis; SBS, short bowel syndrome.

Figure 4.

LDA analysis to compare the microbiota of SBS patients with a small bowel ostomy without colon in continuity (n = 20) vs. those with a colon in continuity (n = 32). A–C: SBS ostomy patients (ileostomy + jejunostomy) compared with patients with SBS who have a colon in continuity (ileocolonic and jejunocolonic anastomoses). A: phylum level. B: family level. C: genus level. D and E: comparison of microbiota of SBS patients with ileostomy (n = 16) vs. ileocolonic (IC) anastomosis (n = 24) at phylum (D) and genus (E) levels. F and G: comparison of microbiota of SBS patients with jejunostomy (n = 4) vs. jejunocolonic (JC) anastomosis (n = 8) at phylum (F) and genus (G) levels. LDA, linear discriminate analysis; SBS, short bowel syndrome.

Figure 5.

LDA analysis of the microbiota of SBS patients with jejunocolonic (n = 8) compared with ileocolonic anastomoses (n = 24; A), or jejunostomy (n = 4) vs. ileostomy (n = 16; B), at genus level. LDA, linear discriminate analysis; SBS, short bowel syndrome.

Figure 6.

LDA analysis of the microbiota of SBS patients with jejunocolonic anastomoses and who are fed with parenteral nutrition (OnTPN, n = 4) vs. patients with SBS who have weaned from PN (OffTPN, n = 4). A: phylum level. B: family level. C: class level. D: genus level. LDA, linear discriminate analysis; PN, parenteral nutrition; SBS, short bowel syndrome.

Figure 7.

Plasma C4 and FGF19 levels in normal healthy subjects (n = 50) and in patients with SBS (n = 33). A: C4 vs. FGF19 correlation in patients with SBS (red dots) and normal subjects (black dots). B: normal subjects. C: patients with SBS. Comparison of mean C4 plasma levels (D) and FGF19 levels (E) in normal subjects vs. patients with SBS. F: FGF19 levels in normal subjects compared with patients with SBS with ileostomy, ileocolonic, or jejunocolonic anastomoses. For normal compared with ileostomy, *P = 0.014; normal compared with ileocolonic, **P = 0.028; normal compared with jejunocolonic, #P = 0.032. P = NS for all other comparisons. C4, 7α-hydroxy-4-cholesten-3-one; FGF19, fibroblast growth factor 19; NS, not significant; SBS, short bowel syndrome.

Figure 8.

Stool bile acid concentrations in normal healthy subjects (n = 7) compared with patients with SBS who had jejunocolonic or ileocolonic anastomosis (colon, n = 33 samples) or who had ileostomy or jejunostomy and no colon in continuity (no colon, n = 21 samples). A: Cholic acid (CA), **P = 0.013; ***P = 0.026; B: chenodeoxycholic acid (CDCA), *P = 0.030; C: glycocholic acid (GCA), ***P = 0.004, ****P < 0.00001; D: taurocholic acid (TCA), **P = 0.012, ***P < 0.0001; E: taurochenodeoxycholic acid (TCDCA), *P = 0.03, ****P = 0.0002; F: glycochenodeoxycholic acid (GCDCA), *P = 0.030, ****P = 0.0004.

Figure 9.

Stool bile acid concentrations in healthy subjects (n = 7) compared with SBS patients with residual colon in continuity (colon, n = 33 samples) and to patients with small bowel ostomy (no colon, n = 21 samples). A: total bile acid stool concentration, *P = 0.049 healthy vs. colon; *P = 0.03 healthy vs. no colon. B: conjugated/unconjugated ratio: colon vs. no colon, ***P = 0.0007. C: primary bile acid/secondary bile acid ratio: healthy vs. no colon, ****P < 0.0001; colon vs. no colon, ****P < 0.0001. SBS, short bowel syndrome.

Figure 10.

Stool bile acid concentrations in normal healthy subjects and in patients with SBS who are fed with parenteral nutrition (“on”) vs. patients with SBS who are fed with enteral nutrition (“off”). A: total bile acids in normal healthy subjects (n = 7) compared with patients with SBS on (n = 12; *P = 0.04) or off (n = 20;*P = 0.028) PN. B: LCA concentration in healthy subjects (n = 7) vs. patients with jejunocolonic anastomosis who are on PN (n = 6) or off PN (n = 6); LCA, **P = 0.003; *P = 0.015. C: DCA concentration in healthy subjects (n = 7) or patients with jejunocolonic anastomoses who are on PN (n = 6) or off PN (n = 6); DCA, **P = 0.004. D–F: GCA, GCDCA, and conjugated/unconjugated ratio in healthy subjects (n = 7) vs. SBS patients with ileocolonic anastomosis on PN (n = 7) or off PN (n = 14). GCA, *P = 0.037; GCDCA, *P = 0.045; conjugated/unconjugated, *P = 0.040. DCA, deoxycholic acid; GCA, glycocholic acid; GCDCA, glycochenodeoxycholic acid; LCA, lithocholic acid; PN, parenteral nutrition; SBS, short bowel syndrome.