Summary of Study ST003865
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR002421. The data can be accessed directly via it's Project DOI: 10.21228/M8PV60 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
| Study ID | ST003865 |
| Study Title | Assessment of the effects of Faecal microbiota transplantation with anti-inflammatory diet (FMT-AID) on faecal metabolome in patients with ulcerative colitis. |
| Study Summary | The study aims to understand FMT-AID driven recuperation of faecal metabolome in patients with UC. |
| Institute | All India Institute of Medical Sciences |
| Department | Gastroenterology |
| Laboratory | IBD Research Group |
| Last Name | Bajaj |
| First Name | Aditya |
| Address | AIIMS Campus, Ansari Nagar East, Delhi, Delhi, 110092, India |
| adityabajaj93@gmail.com | |
| Phone | +91-9718405090 |
| Submit Date | 2025-03-28 |
| Num Groups | 3 (Non-IBD Controls, Patients with UC before FMT and Patients with UC after FMT) |
| Total Subjects | 41 (13 Non-IBD controls + 28 patients with UC) |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML, raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-05-01 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002421 |
| Project DOI: | doi: 10.21228/M8PV60 |
| Project Title: | Restoration of mucosal and faecal microbiome and metabolome is associated with response to faecal microbiota transplantation and anti-inflammatory diet in active ulcerative colitis |
| Project Summary: | Background Faecal microbiota transplantation with anti-inflammatory diet (FMT-AID) supports clinical response and deep remission in patients with active ulcerative colitis (UC). The present study aims to assess FMT-associated bacterial, fungal and metabolomic shifts in mucosal and faecal niches in active UC, and to correlate these changes with clinical and endoscopic outcomes of FMT. Study also determines if baseline microbial signatures in UC can determine FMT engraftment and clinical outcomes. We performed a prospective cohort study of patients with UC, recruited as part of the FMT-AID trial, and randomised to receive either 8-week FMT-AID or standard medical therapy (SMT). Non-IBD controls were also recruited in the study. Faecal and mucosal microbiome and mycobiome were characterised in 104 paired pre- and post-intervention samples (n=52, faecal; n=52, mucosal) from 26 patients (16 in FMT-AID arm + 10 in SMT arm) In addition, 48 non-IBD control samples (n=21, faecal; n=27, mucosal) were collected at single time point from 27 subjects. Clinical response (reduction in SCCAI≥3) was the primary outcome. A subset of samples (n=71; 40 paired pre-and post-FMT samples and 31 non-IBD control samples) were used for untargeted metabolomics. Results FMT-AID remodelled mucosal (β-diversity-adonis R2=2.13, p=0.02) and faecal (R2=2.76, p=0.003) bacterial communities and enhanced faecal bacterial diversity (p<0.001). FMT-AID enriched the gut with beneficial bacterial taxa (mucosal-Odoribacter and faecal- Slackia, Agathobaculum and Aldercreutzia) and reduced pathobiont abundances (mucosal- Enterococcus, Veillonella, Malassezia; faecal- Enterococcus, Candida tropicalis). Compared to clinical responders to FMT-AID, the non-responders had a distinct gut microbiome signature, which associated with elevated disease activity (Megasphaera and UCEIS (R=0.77, FDR-q=0.02), Malassezia slooffiae and SCCAI (R=0.81; FDR-q=0.01), UCEIS (R=0.62; FDR-q=0.12) and FCP (R=0.88; FDR-q=0.003)]. FMT-AID also restored mucosal and faecal metabolome with ‘health-associated’ metabolites. Higher pre-intervention abundances of beneficial taxa in mucosa and faeces associated with positive outcomes of FMT-AID. Pre-FMT faecal bacteriome also correlated with post-FMT engraftment of beneficial bacteria. Conclusions Enrichment of specific beneficial bacterial, fungal and metabolomic signatures in faecal and mucosal niches was associated with positive clinical, biochemical and endoscopic outcomes following FMT-AID in patients with UC. Pre-FMT bacteriome was associated with post-FMT engraftment of beneficial bacteria and clinical response. |
| Institute: | All India Institute of Medical Sciences |
| Department: | Gastroenterology |
| Laboratory: | IBD Research Group |
| Last Name: | Bajaj |
| First Name: | Aditya |
| Address: | AIIMS Campus, Ansari Nagar East, Delhi, Delhi, 110092, India |
| Email: | adityabajaj93@gmail.com |
| Phone: | +91-9718405090 |
| Funding Source: | The work has been funded by the Indian Council of Medical Research: Centre for Advanced Research and Excellence in Intestinal Diseases (grant number: 55/4/11/CARE-ID/2018-NCD-II); Science and Engineering Research Board (SERB): Core Research Grant (CRG/2019/005292); and Scheme for Promotion of Academic and Research Collaboration (SPARC P1492). |
| Publications: | Restoration of Mucosal and Fecal Microbiome, Mycobiome and Metabolome is Associated with Response to Fecal Microbiota Transplantation and Anti-Inflammatory Diet in Active Ulcerative Colitis. Available at SSRN: https://ssrn.com/abstract=4953224 or http://dx.doi.org/10.2139/ssrn.4953224 |
| Contributors: | Markandey, Manasvini and Bajaj, Aditya and Kshetrapal, Pallavi and Virmani, Shubi and Singh, Mukesh and Verma, Mahak and Thirunavukkarasu, Ramasamy and Vuyyuru, Sudheer Kumar and Kante, Bhaskar and Kumar, Peeyush and Makharia, Govind and Das, Bhabatosh and Kumar, Dhiraj and Kedia, Saurabh and Ahuja, Vineet, |
Subject:
| Subject ID: | SU003999 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Age Or Age Range: | Non-IBD controls, 36.9 ± 12.64; UC group, 33.28 ± 11.13 |
| Gender: | Male and female |
| Human Ethnicity: | Indian |
| Human Lifestyle Factors: | BMI (kg/m2), Non-IBD controls, 21.17 ± 3.1; UC group, 21.17 ± 4.6 |
| Human Medications: | UC group, Prior 5-ASA course (%) 100; Prior steroid course (%) 6.3; Prior Azathioprine therapy (%) 37.5; Prior biological use (%) 0; Prior methotrexate use (%) 0; Topical 5-ASA use (%) 100; Topical steroid enema use (%) 75 |
| Human Smoking Status: | Smokers (%), Non-IBD controls, 9.5% ; UC group, 11.42% |
| Human Alcohol Drug Use: | Alcohol consumption (%), Non-IBD controls, 0% ; UC group, 2.8% |
| Human Inclusion Criteria: | Age, 20-60 years; Clinical disease activity, Mild-moderate UC (SCCAI 3-9); Endoscopic disease activity, UCEIS >1; Disease extent, Left-sided/pancolitis; Permitted medications, 1.Oral 5-ASA (stable dose for >4 weeks) 2.Azathioprine/6-MP (stable dose for >3 months) 3.Topical 5-ASA or topical steroids (stable dose for >2 weeks) 4.Oral steroids (<20 mg prednisolone with taper of 5 mg/week) 5.Anti-TNF mAb (If used more than 6 months back); Others, 1.Patients who gave written informed consent, 2.Agreement to adhere to diet schedule |
| Human Exclusion Criteria: | Disease activity, Patients with severe disease activity or acute severe colitis; Prohibited medications, 1.Topical steroids (if used within 2 weeks), 2.Antibiotics and Probiotics (if used within 4 weeks of randomization); Others, 1.History of bowel surgery, 2.Pregnancy/lactation, 3.Presence of co-morbid illnesses, 4.Concomitant gastrointestinal infection |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Factor |
|---|---|---|
| SA424633 | 10-C-F | Control |
| SA424634 | 02-C-F | Control |
| SA424635 | 16-C-F | Control |
| SA424636 | 14-C-F | Control |
| SA424637 | 13-C-F | Control |
| SA424638 | 12-C-F | Control |
| SA424639 | 01-C-F | Control |
| SA424640 | 08-C-F | Control |
| SA424641 | 06-C-F | Control |
| SA424642 | 05-C-F | Control |
| SA424643 | 04-C-F | Control |
| SA424644 | 07-C-F | Control |
| SA424645 | 03-C-F | Control |
| SA424646 | 05-B-F | Post-FMT |
| SA424647 | 13-B-F | Post-FMT |
| SA424648 | 12-B-F | Post-FMT |
| SA424649 | 11-B-F | Post-FMT |
| SA424650 | 09-B-F | Post-FMT |
| SA424651 | 06-B-F | Post-FMT |
| SA424652 | 08-B-F | Post-FMT |
| SA424653 | 03-B-F | Post-FMT |
| SA424654 | 02-B-F | Post-FMT |
| SA424655 | 01-B-F | Post-FMT |
| SA424656 | 05-A-F | Pre-FMT |
| SA424657 | 17-A-F | Pre-FMT |
| SA424658 | 28-A-F | Pre-FMT |
| SA424659 | 27-A-F | Pre-FMT |
| SA424660 | 26-A-F | Pre-FMT |
| SA424661 | 25-A-F | Pre-FMT |
| SA424662 | 24-A-F | Pre-FMT |
| SA424663 | 23-A-F | Pre-FMT |
| SA424664 | 22-A-F | Pre-FMT |
| SA424665 | 21-A-F | Pre-FMT |
| SA424666 | 20-A-F | Pre-FMT |
| SA424667 | 19-A-F | Pre-FMT |
| SA424668 | 18-A-F | Pre-FMT |
| SA424669 | 14-A-F | Pre-FMT |
| SA424670 | 16-A-F | Pre-FMT |
| SA424671 | 15-A-F | Pre-FMT |
| SA424672 | 06-A-F | Pre-FMT |
| SA424673 | 01-A-F | Pre-FMT |
| SA424674 | 13-A-F | Pre-FMT |
| SA424675 | 12-A-F | Pre-FMT |
| SA424676 | 02-A-F | Pre-FMT |
| SA424677 | 10-A-F | Pre-FMT |
| SA424678 | 03-A-F | Pre-FMT |
| SA424679 | 09-A-F | Pre-FMT |
| SA424680 | 08-A-F | Pre-FMT |
| SA424681 | 07-A-F | Pre-FMT |
| SA424682 | 04-A-F | Pre-FMT |
| SA424683 | 11-A-F | Pre-FMT |
| Showing results 1 to 51 of 51 |
Collection:
| Collection ID: | CO003992 |
| Collection Summary: | Fecal samples were collected at a single time point from non-IBD controls and twice from patients with UC, once before the commencement of FMT-AID (Pre-FMT) and once after 7 weekly FMT sessions (Post-FMT). Fecal samples were collected in sterile stool vials, homogenized manually and distributed in 50mg aliquots in sterile 2ml cryovials. The aliquots were flash-frozen in liquid nitrogen and stored at -80°C for metabolite extraction. |
| Sample Type: | Feces |
| Collection Location: | IBD Clinic, All India Institute of Medical Sciences, New Delhi |
| Collection Frequency: | Faecal samples were collected at a single time point from non-IBD controls and twice from patients with UC, once before the commencement of FMT-AID (Pre-FMT) and once after 7 weekly FMT sessions (Post-FMT). |
| Volumeoramount Collected: | Stored two aliquots of 50mg each. |
| Storage Conditions: | -80℃ |
| Collection Vials: | Sterile stool vials |
| Storage Vials: | Cryovials |
| Collection Tube Temp: | 4°C |
| Additives: | None |
Treatment:
| Treatment ID: | TR004008 |
| Treatment Summary: | FMT-AID arm received seven consecutive weekly, multi-donor pooled faecal microbiota transplantations (FMT), administered colonoscopically with an anti-inflammatory diet (AID). The AID was enriched in components supporting the expansion of T-regulatory cells, healthy gut microbiota and improvement of gut barrier integrity. AID suggested avoidance of gluten-based grains, meat, refined sugars, food additives and dairy products and promoted the consumption of fresh fruits and vegetables (especially cruciferous vegetables as a source of AhR ligands), fermented foods and polyphenols. |
| Treatment: | Faecal microbiota transplantation with anti-inflammatory diet |
| Treatment Compound: | Pooled, multi-donor faecal suspension |
| Treatment Route: | Colonoscopic infusion of FMT |
| Treatment Dose: | 50 g of stool homogenized with 200-250 mL of 0.9% normal saline till liquid consistency. |
| Treatment Dosevolume: | 200-250 mL of fecal suspension |
| Treatment Vehicle: | 0.9% normal saline |
| Human Fasting: | Not required |
| Human Endp Clinical Signs: | The primary outcome measure for the present study is clinical response (reduction in SCCAI score by 3 or more points), and secondary outcomes are clinical remission (SCCAI <2), endoscopic remission (UCEIS <1), and endoscopic response (decline in UCEIS by 2 or more points). |
Sample Preparation:
| Sampleprep ID: | SP004005 |
| Sampleprep Summary: | For fecal metabolome extraction, 100 μL of 50% methanol was added to each Precellys homogenization tube containing ~50 mg stool sample, followed by homogenization in the Precellys 24 tissue homogenizer. Homogenized samples were subjected to 90-second heat shock treatment at 37°C. 150 μL of 100% methanol was then added per sample, followed by a 10 min incubation on ice. Samples were centrifuged at 1400rpm for 15 min at 4°C, and 200uL of supernatant from each sample was mixed with 200uL of methyl-tert-butyl-ether (MTBE). This mixture was vortexed for 1 hour at RT, followed by centrifugation at 14000 rpm for 15 min at 4°C. 80 μL from each of the aqueous and organic phases were pooled together in a fresh tube from each sample and vacuum dried overnight in a Speed Vac. Metabolite extracts were reconstituted in 15% acetonitrile for reverse phase chromatography and run on the Orbitrap Fusion Tibrid Mass Spectrometer (Thermofisher Scientific) for an untargeted LCMS-based metabolomic screening. |
| Sampleprep Protocol Filename: | fecal-metabolite-extraction-protocol.pdf |
| Processing Storage Conditions: | -20℃ |
| Extract Storage: | -80℃ |
Chromatography:
| Chromatography ID: | CH004818 |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | Waters ACQUITY UPLC CSH C18 (100 x 1 mm, 1.7 μm) |
| Column Temperature: | 40°C |
| Flow Gradient: | 0 min, 0.1% B; 2.5 min, 5% B; 7 min, 20% B; 15 min, 99% B; 19 min, 0% B |
| Flow Rate: | 0.3 mL/min |
| Retention Time: | 0.01 to 14.0 min |
| Sample Injection: | 5 µL |
| Solvent A: | 100% Water; 0.1% Formic acid |
| Solvent B: | 100% Methanol; 0.1% Formic acid |
| Chromatography Type: | Reversed phase |
Analysis:
| Analysis ID: | AN006352 |
| Analysis Type: | MS |
| Chromatography ID: | CH004818 |
| Has Mz: | 1 |
| Has Rt: | 1 |
| Rt Units: | Seconds |
| Results File: | ST003865_AN006352_Results.txt |
| Units: | Peak intensity |
| Analysis ID: | AN006353 |
| Analysis Type: | MS |
| Chromatography ID: | CH004818 |
| Has Mz: | 1 |
| Has Rt: | 1 |
| Rt Units: | Seconds |
| Results File: | ST003865_AN006353_Results.txt |
| Units: | Peak Intensity |
