Study Data
| Project uploaded by: | Neel Sarovar |
| Project ID: | IMP_100036 |
| Title: | NMR based human gut metabolomic profiling reveals altered metabolites associated with pulmonary and extra-pulmonary tuberculosis |
| Project Description: | Introduction: Tuberculosis remains one of the world's deadliest infectious diseases. The pathophysiology of the two manifestations of Mycobacterium tuberculosis infection, pulmonary TB (PTB) and extrapulmonary TB (EPTB) is still not fully understood. Understanding the metabolic profile of both disease manifestations in patients is important for developing therapeutic approaches and molecular diagnosis. Objective: The current study aimed to elucidate differences in the gut metabolic profile of PTB and EPTB patients compared to healthy controls (HCs). Method: We used an untargeted approach through 1 H Nuclear Magnetic Resonance (NMR) spectroscopy to perform metabolomic profiling of stool samples from 77 TB patients [pulmonary TB (PTB, n = 33), cervical lymph node TB (CrLNTB, n =30), abdominal TB (ATB, n = 14)], and 30 HCs. Multivariate and univariate analyses were performed to identify the differential gut metabolites associated with TB patients. Results: The PTB patients had higher metabolic perturbation than EPTB patients compared to HCs. The top three significantly altered metabolites, namely valine, N-formyl-L- methionine and dimethylsulfone, were used to generate random forest model to distinguish between TB patients and HCs. The receiver operating characteristics curve analysis was used to assess the performance of the model with area under curve score of 0.831, capable to distinguish TB patients from HCs. Thus, our findings offer insights into the gut metabolome of TB patients in India and characterizes for the first time metabolic perturbations in EPTB patients. Conclusion: The study highlights the metabolic disruptions associated with PTB and EPTB patients. |
| Research Area: | Biological Sciences |
| Funding Source: | JC bose fellowship, ICGEB core fund, Insitute of eminence, DU. |
| Project Contributors: | Vishal Sharma , Anoop Singh , Sonam Sharma , Mohita Gaur , Arun Kumar Malaisamy , Deepti Rawat , Anjali Yadav , Bolaji Fatai Oyeyemi , Aarushi Vasudeva , Anil Chaudhry , Ashwani Khanna , Vishal Khanna , Sheelu Lohiya , Reema Arora , Anannya Bandyopadhyay , Neel Sarovar Bhavesh, Yogendra Singh, Richa Misra |
| Study uploaded by: | Neel Sarovar |
| Study ID: | IMS_100030 |
| Title: | NMR based human gut metabolomic profiling reveals altered metabolites associated with pulmonary and extra-pulmonary tuberculosis |
| Summary: | Introduction: Tuberculosis remains one of the world's deadliest infectious diseases. The pathophysiology of the two manifestations of Mycobacterium tuberculosis infection, pulmonary TB (PTB) and extrapulmonary TB (EPTB) is still not fully understood. Understanding the metabolic profile of both disease manifestations in patients is important for developing therapeutic approaches and molecular diagnosis. Objective: The current study aimed to elucidate differences in the gut metabolic profile of PTB and EPTB patients compared to healthy controls (HCs). Method: We used an untargeted approach through 1 H Nuclear Magnetic Resonance (NMR) spectroscopy to perform metabolomic profiling of stool samples from 77 TB patients [pulmonary TB (PTB, n = 33), cervical lymph node TB (CrLNTB, n =30), abdominal TB (ATB, n = 14)], and 30 HCs. Multivariate and univariate analyses were performed to identify the differential gut metabolites associated with TB patients. Results: The PTB patients had higher metabolic perturbation than EPTB patients compared to HCs. The top three significantly altered metabolites, namely valine, N-formyl-L- methionine and dimethylsulfone, were used to generate random forest model to distinguish between TB patients and HCs. The receiver operating characteristics curve analysis was used to assess the performance of the model with area under curve score of 0.831, capable to distinguish TB patients from HCs. Thus, our findings offer insights into the gut metabolome of TB patients in India and characterizes for the first time metabolic perturbations in EPTB patients. Conclusion: The study highlights the metabolic disruptions associated with PTB and EPTB patients. |
| Keywords: | Tuberculosis, diagnosis, pulmonary TB, extra-pulmonary TB, 1H NMR spectroscopy, gut metabolites |
| Publication: | Metabolomics |
| Release Date: | July 22, 2025 |
| Study Type: | Nuclear Magnetic Resonance (NMR) |
| Data Type: | Untargeted |
| IEC/IBSC Approval Number : | 2653/RBIPMT/2019 |
| Sr.No | Sample ID | Sample Name | Organism | Source | Sample Preparation Protocol | Sample Type | Experimental Condition | Time of treatment | Variant/Variety | Gender | Age | Replicates | Storage Conditions | Extraction Protocol | Number of files per sample |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 11 | IMSM_101569 | Exp 82 | Homo sapiens | 9606 | Stool | The frozen stool aliquots were thawed and ~200 mg of the sample was weighed into a sterile microcentrifuge tube. The samples were homogenized in 600μl of autoclaved Milli-Q water for 2-3 minutes before centrifugation at 15,000g for 15 minutes. 400μl of supernatant was transferred to a fresh microcentrifuge tube, and 200μl of 0.1M potassium phosphate buffer pH 7.4 in D 2 O (0.2 M of K 2 HPO 4 and KH 2 PO 4 , containing 10% (w/v) 4,4-dimethyl-4-silapentane-1- sulfonic acid (DSS), a reference compound), was added to each sample. The sample was vortexed, centrifuged, and loaded into the 5 mm NMR tube for 1 H NMR spectra acquisition. | CrLN TB | TB | NA | NA | F | 19 | NA | -80 |
NA |
|
| 12 | IMSM_101570 | Exp 103 | Homo sapiens | 9606 | Stool | The frozen stool aliquots were thawed and ~200 mg of the sample was weighed into a sterile microcentrifuge tube. The samples were homogenized in 600μl of autoclaved Milli-Q water for 2-3 minutes before centrifugation at 15,000g for 15 minutes. 400μl of supernatant was transferred to a fresh microcentrifuge tube, and 200μl of 0.1M potassium phosphate buffer pH 7.4 in D 2 O (0.2 M of K 2 HPO 4 and KH 2 PO 4 , containing 10% (w/v) 4,4-dimethyl-4-silapentane-1- sulfonic acid (DSS), a reference compound), was added to each sample. The sample was vortexed, centrifuged, and loaded into the 5 mm NMR tube for 1 H NMR spectra acquisition. | CrLN TB | TB | NA | NA | M | 24 | NA | -80 |
NA |
|
| 13 | IMSM_101571 | Exp 104 | Homo sapiens | 9606 | Stool | The frozen stool aliquots were thawed and ~200 mg of the sample was weighed into a sterile microcentrifuge tube. The samples were homogenized in 600μl of autoclaved Milli-Q water for 2-3 minutes before centrifugation at 15,000g for 15 minutes. 400μl of supernatant was transferred to a fresh microcentrifuge tube, and 200μl of 0.1M potassium phosphate buffer pH 7.4 in D 2 O (0.2 M of K 2 HPO 4 and KH 2 PO 4 , containing 10% (w/v) 4,4-dimethyl-4-silapentane-1- sulfonic acid (DSS), a reference compound), was added to each sample. The sample was vortexed, centrifuged, and loaded into the 5 mm NMR tube for 1 H NMR spectra acquisition. | CrLN TB | TB | NA | NA | F | 26 | NA | -80 |
NA |
|
| 14 | IMSM_101572 | Exp 163 | Homo sapiens | 9606 | Stool | The frozen stool aliquots were thawed and ~200 mg of the sample was weighed into a sterile microcentrifuge tube. The samples were homogenized in 600μl of autoclaved Milli-Q water for 2-3 minutes before centrifugation at 15,000g for 15 minutes. 400μl of supernatant was transferred to a fresh microcentrifuge tube, and 200μl of 0.1M potassium phosphate buffer pH 7.4 in D 2 O (0.2 M of K 2 HPO 4 and KH 2 PO 4 , containing 10% (w/v) 4,4-dimethyl-4-silapentane-1- sulfonic acid (DSS), a reference compound), was added to each sample. The sample was vortexed, centrifuged, and loaded into the 5 mm NMR tube for 1 H NMR spectra acquisition. | CrLN TB | TB | NA | NA | F | 20 | NA | -80 |
NA |
|
| 15 | IMSM_101573 | Exp 198 | Homo sapiens | 9606 | Stool | The frozen stool aliquots were thawed and ~200 mg of the sample was weighed into a sterile microcentrifuge tube. The samples were homogenized in 600μl of autoclaved Milli-Q water for 2-3 minutes before centrifugation at 15,000g for 15 minutes. 400μl of supernatant was transferred to a fresh microcentrifuge tube, and 200μl of 0.1M potassium phosphate buffer pH 7.4 in D 2 O (0.2 M of K 2 HPO 4 and KH 2 PO 4 , containing 10% (w/v) 4,4-dimethyl-4-silapentane-1- sulfonic acid (DSS), a reference compound), was added to each sample. The sample was vortexed, centrifuged, and loaded into the 5 mm NMR tube for 1 H NMR spectra acquisition. | CrLN TB | TB | NA | NA | M | 20 | NA | -80 |
NA |
|
| 16 | IMSM_101574 | Exp 199 | Homo sapiens | 9606 | Stool | The frozen stool aliquots were thawed and ~200 mg of the sample was weighed into a sterile microcentrifuge tube. The samples were homogenized in 600μl of autoclaved Milli-Q water for 2-3 minutes before centrifugation at 15,000g for 15 minutes. 400μl of supernatant was transferred to a fresh microcentrifuge tube, and 200μl of 0.1M potassium phosphate buffer pH 7.4 in D 2 O (0.2 M of K 2 HPO 4 and KH 2 PO 4 , containing 10% (w/v) 4,4-dimethyl-4-silapentane-1- sulfonic acid (DSS), a reference compound), was added to each sample. The sample was vortexed, centrifuged, and loaded into the 5 mm NMR tube for 1 H NMR spectra acquisition. | CrLN TB | TB | NA | NA | F | 24 | NA | -80 |
NA |
|
| 17 | IMSM_101575 | Exp 200 | Homo sapiens | 9606 | Stool | The frozen stool aliquots were thawed and ~200 mg of the sample was weighed into a sterile microcentrifuge tube. The samples were homogenized in 600μl of autoclaved Milli-Q water for 2-3 minutes before centrifugation at 15,000g for 15 minutes. 400μl of supernatant was transferred to a fresh microcentrifuge tube, and 200μl of 0.1M potassium phosphate buffer pH 7.4 in D 2 O (0.2 M of K 2 HPO 4 and KH 2 PO 4 , containing 10% (w/v) 4,4-dimethyl-4-silapentane-1- sulfonic acid (DSS), a reference compound), was added to each sample. The sample was vortexed, centrifuged, and loaded into the 5 mm NMR tube for 1 H NMR spectra acquisition. | CrLN TB | TB | NA | NA | F | 23 | NA | -80 |
NA |
|
| 18 | IMSM_101576 | Exp 206 | Homo sapiens | 9606 | Stool | The frozen stool aliquots were thawed and ~200 mg of the sample was weighed into a sterile microcentrifuge tube. The samples were homogenized in 600μl of autoclaved Milli-Q water for 2-3 minutes before centrifugation at 15,000g for 15 minutes. 400μl of supernatant was transferred to a fresh microcentrifuge tube, and 200μl of 0.1M potassium phosphate buffer pH 7.4 in D 2 O (0.2 M of K 2 HPO 4 and KH 2 PO 4 , containing 10% (w/v) 4,4-dimethyl-4-silapentane-1- sulfonic acid (DSS), a reference compound), was added to each sample. The sample was vortexed, centrifuged, and loaded into the 5 mm NMR tube for 1 H NMR spectra acquisition. | CrLN TB | TB | NA | NA | F | 27 | NA | -80 |
NA |
|
| 19 | IMSM_101577 | Exp 209 | Homo sapiens | 9606 | Stool | The frozen stool aliquots were thawed and ~200 mg of the sample was weighed into a sterile microcentrifuge tube. The samples were homogenized in 600μl of autoclaved Milli-Q water for 2-3 minutes before centrifugation at 15,000g for 15 minutes. 400μl of supernatant was transferred to a fresh microcentrifuge tube, and 200μl of 0.1M potassium phosphate buffer pH 7.4 in D 2 O (0.2 M of K 2 HPO 4 and KH 2 PO 4 , containing 10% (w/v) 4,4-dimethyl-4-silapentane-1- sulfonic acid (DSS), a reference compound), was added to each sample. The sample was vortexed, centrifuged, and loaded into the 5 mm NMR tube for 1 H NMR spectra acquisition. | CrLN TB | TB | NA | NA | F | 32 | NA | -80 |
NA |
|
| 20 | IMSM_101578 | Exp 215 | Homo sapiens | 9606 | Stool | The frozen stool aliquots were thawed and ~200 mg of the sample was weighed into a sterile microcentrifuge tube. The samples were homogenized in 600μl of autoclaved Milli-Q water for 2-3 minutes before centrifugation at 15,000g for 15 minutes. 400μl of supernatant was transferred to a fresh microcentrifuge tube, and 200μl of 0.1M potassium phosphate buffer pH 7.4 in D 2 O (0.2 M of K 2 HPO 4 and KH 2 PO 4 , containing 10% (w/v) 4,4-dimethyl-4-silapentane-1- sulfonic acid (DSS), a reference compound), was added to each sample. The sample was vortexed, centrifuged, and loaded into the 5 mm NMR tube for 1 H NMR spectra acquisition. | CrLN TB | TB | NA | NA | M | 25 | NA | -80 |
NA |
| Sr.No | NMR Exp ID | Sample Name/ID | Reference Standard | NMR Instrument Name | NMR Instrument Type | NMR Experiment Type | NMR Spectrometer Frequency | NMR Probe | NMR Probe temperature | NMR Solvent | NMR tube size | Data Transformation (Software/s Used) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 21 | IME_100824 | Exp 212 / IMSM_101579 | DSS | Bruker Avance III 500MHz | Solution NMR | 1D 1H | 500 | 5 mm triple-resonance CPTCI cryogenic cooled probehead equipped with z-gradient | 298k | D2O | 5 mm | NA |
| 22 | IME_100825 | Exp 210 / IMSM_101580 | DSS | Bruker Avance III 500MHz | Solution NMR | 1D 1H | 500 | 5 mm triple-resonance CPTCI cryogenic cooled probehead equipped with z-gradient | 298k | D2O | 5 mm | NA |
| 23 | IME_100826 | Exp 216 / IMSM_101581 | DSS | Bruker Avance III 500MHz | Solution NMR | 1D 1H | 500 | 5 mm triple-resonance CPTCI cryogenic cooled probehead equipped with z-gradient | 298k | D2O | 5 mm | NA |
| 24 | IME_100827 | Exp 217 / IMSM_101582 | DSS | Bruker Avance III 500MHz | Solution NMR | 1D 1H | 500 | 5 mm triple-resonance CPTCI cryogenic cooled probehead equipped with z-gradient | 298k | D2O | 5 mm | NA |
| 25 | IME_100828 | Exp 228 / IMSM_101583 | DSS | Bruker Avance III 500MHz | Solution NMR | 1D 1H | 500 | 5 mm triple-resonance CPTCI cryogenic cooled probehead equipped with z-gradient | 298k | D2O | 5 mm | NA |
| 26 | IME_100829 | Exp 229 / IMSM_101584 | DSS | Bruker Avance III 500MHz | Solution NMR | 1D 1H | 500 | 5 mm triple-resonance CPTCI cryogenic cooled probehead equipped with z-gradient | 298k | D2O | 5 mm | NA |
| 27 | IME_100830 | Exp 230 / IMSM_101585 | DSS | Bruker Avance III 500MHz | Solution NMR | 1D 1H | 500 | 5 mm triple-resonance CPTCI cryogenic cooled probehead equipped with z-gradient | 298k | D2O | 5 mm | NA |
| 28 | IME_100831 | Exp 231 / IMSM_101586 | DSS | Bruker Avance III 500MHz | Solution NMR | 1D 1H | 500 | 5 mm triple-resonance CPTCI cryogenic cooled probehead equipped with z-gradient | 298k | D2O | 5 mm | NA |
| 29 | IME_100832 | Exp 232 / IMSM_101587 | DSS | Bruker Avance III 500MHz | Solution NMR | 1D 1H | 500 | 5 mm triple-resonance CPTCI cryogenic cooled probehead equipped with z-gradient | 298k | D2O | 5 mm | NA |
| 30 | IME_100833 | Exp 233 / IMSM_101588 | DSS | Bruker Avance III 500MHz | Solution NMR | 1D 1H | 500 | 5 mm triple-resonance CPTCI cryogenic cooled probehead equipped with z-gradient | 298k | D2O | 5 mm | NA |
| Sr.No | First name | Last name | Organization | Designation | |
|---|---|---|---|---|---|
| 1 | Richa | Misra | richamisra@svc.ac.in | University of Delhi | principal_investigator |
| 2 | Yogendra | Singh | ysinghdu@gmail.com | University of Delhi | co_principal_investigator |
| 3 | Neel Sarovar | Bhavesh | neelsb@icgeb.res.in | ICGEB | co_principal_investigator |
| 4 | Anannya | Bandyopadhyay | anannya@zoology.du.ac.in | University of Delhi | research_scholar |
| 5 | Reema | Arora | arorareema1569@gmail.com | Lok Nayak Hospital | research_scholar |
| 6 | Sheelu | Lohiya | drsheelulohiya@gmail.com | Lok Nayak Hospital | research_scholar |
| 7 | Vishal | Khanna | dr.vishalkhanna@reddif.com | Lok Nayak Hospital | research_scholar |
| 8 | Ashwani | Khanna | dr.vishalkhanna@reddif.com | Lok Nayak Hospital | research_scholar |
| 9 | Anil | Chaudhry | dranilchaudhry@gmail.com | Rajan Babu Institute of Pulmonary Medicine and Tuberculosis | research_scholar |
| 10 | Aarushi | Vasudeva | aarushi_vasudeva@yahoo.com | University of Delhi | research_scholar |
| 11 | Bolaji Fatai | Oyeyemi | bolajioyeyemi@gmail.com | ICGEB | research_scholar |
| 12 | Anjali | Yadav | anniey2411@gmail.com | University of Delhi | research_scholar |
| 13 | Deepti | Rawat | deeptirawat0397@gmail.com | University of Delhi | research_scholar |
| 14 | Arun Kumar | Malaisamy | makias191@gmail.com | ICGEB | research_scholar |
| 15 | Mohita | Gaur | m.mohitagaur@gmail.com | University of Delhi | research_scholar |
| 16 | Sonam | Sharma | sonamsharmamr@gmail.com | ICGEB | research_scholar |
| 17 | Anoop | Singh | anoop.singh.du@gmail.com | University of Delhi | research_scholar |
| 18 | Vishal | Sharma | s.vishalzoology@gmail.com | University of Delhi | research_scholar |
| Sr.No | ftprun ID | NMR Exp ID | NMR Data Files |
|---|---|---|---|
| 91 | IMR_101493 | IME_100894 | 220.zip |
| 92 | IMR_101494 | IME_100895 | 221.zip |
| 93 | IMR_101495 | IME_100896 | 226.zip |
| 94 | IMR_101496 | IME_100897 | 227.zip |
| 95 | IMR_101497 | IME_100898 | 219.zip |
| 96 | IMR_101498 | IME_100899 | 218.zip |
| 97 | IMR_101499 | IME_100900 | 235.zip |
| 98 | IMR_101500 | IME_100901 | 236.zip |
| 99 | IMR_101501 | IME_100902 | 237.zip |
| 100 | IMR_101502 | IME_100903 | 238.zip |