IBD Surgery Effects on Gut Microbiome and Metabolome (UCSD)

Background Many studies have investigated the role of the microbiome in inflammatory bowel disease (IBD), but few have focused on surgery specifically or its consequences on the metabolome that may differ by surgery type and require longitudinal sampling. Our objective was to characterize and contrast microbiome and metabolome changes after different surgeries for IBD, including ileocolonic resection and colectomy. Methods The UC San Diego IBD Biobank was used to prospectively collect 332 stool samples from 129 subjects (50 ulcerative colitis 79 Crohn’s disease). Of these, 21 with Crohn’s disease had ileocolonic resections, and 17 had colectomies. We used shotgun metagenomics and untargeted liquid chromatography followed by tandem mass spectrometry metabolomics to characterize the microbiomes and metabolomes of these patients up to 24 months after the initial sampling. Results The species diversity and metabolite diversity both differed significantly among groups (species diversity: Mann-Whitney U test P value = 7.8e-17 metabolomics, P-value = 0.0043). Escherichia coli in particular expanded dramatically in relative abundance in subjects undergoing surgery. The species profile was better able to classify subjects according to surgery status than the metabolite profile (average precision 0.80 vs 0.68). Conclusions Intestinal surgeries seem to reduce the diversity of the gut microbiome and metabolome in IBD patients, and these changes may persist. Surgery also further destabilizes the microbiome (but not the metabolome) over time, even relative to the previously established instability in the microbiome of IBD patients. These long-term effects and their consequences for health outcomes need to be studied in prospective longitudinal trials linked to microbiome-involved phenotypes.

Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.65. Assay shotgun_dna.

• host run.host_tax_id · “9606”
• host run.scientific_name · “human gut metagenome”
• body site study.description · “332 stool samples from 129 subjects”

382 runs over 382 samples · mean 8.19 Gbp per run (median 8.68 Gbp, total 3,126.76 Gbp; 382 runs with a base count) · layout PAIRED 382 · platform ILLUMINA 382 · models Illumina HiSeq 2500 (382) · 68% of runs with a Sandpiper profile · first public 2021-05-07

Fang X first · Vázquez-Baeza Y · Elijah E · Vargas F · Ackermann G · Humphrey G · Lau R · Weldon KC · Sanders JG · Panitchpakdi M · Carpenter C · Jarmusch AK · Neill J · Miralles A · Dulai P · Singh S · Tsai M · Swafford AD · Smarr L · Boyle DL · Palsson BO · Chang JT · Dorrestein PC · Sandborn WJ · Knight R · Boland BS last

PRJEB38352.csv.gz (12.6 KB) · parquet (88.1 KB) — all 382 samples, every field with route and confidence · PRJEB38352_determinations.csv.gz (30.6 KB) — 4,686 evidence rows