Summary of Study ST003868
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 PR002424. The data can be accessed directly via it's Project DOI: 10.21228/M89N9N 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 | ST003868 |
| Study Title | Commensal Human Gut Microbes Produce Unique Patterns of Neuro-active Compounds |
| Study Type | Basic Research - Therapeutic Microbes (Neurotransmitters Production) |
| Study Summary | The human gut microbiota communicates with multiple organs in the human body, including the enteric and central nervous systems, through the production of neuroactive molecules. However, the specific neuroactive compounds produced by commensal gut bacteria remain unclear. In this study, we investigated the capacity of diverse human commensal gut bacteria to produce neurotransmitters, neurotransmitter precursors, and short-chain fatty acids (SCFAs) using targeted and non-targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. |
| Institute | Medical University of South Carolina |
| Department | Regenerative & Cellular Medicine |
| Laboratory | Melinda Engevik Lab |
| Last Name | Engevik |
| First Name | Mindy |
| Address | 96 Jonathan Lucas St. Ste. 601, MSC 617, Charleston, SC 29425 |
| engevik@musc.edu | |
| Phone | 843-792-3148 |
| Submit Date | 2025-04-07 |
| Num Groups | 8 different strains of bacteria (grown as biological triplicates) + 3 blank ZMBI controls |
| Total Subjects | 24 cultures + 3 blanks |
| Num Males | N/A |
| Num Females | N/A |
| Publications | iScience Submission under review |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML, raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-06-02 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002424 |
| Project DOI: | doi: 10.21228/M89N9N |
| Project Title: | Commensal Human Gut Microbes Produce Unique Patterns of Neuro-active Compounds |
| Project Type: | Basic Research - Therapeutic Microbes |
| Project Summary: | The human gut microbiota communicates with multiple organs in the human body, including the enteric and central nervous systems, through the production of neuroactive molecules. However, the specific neuroactive compounds produced by commensal gut bacteria remain unclear. In this study, we investigated the capacity of diverse human commensal gut bacteria to produce neurotransmitters, neurotransmitter precursors, and short-chain fatty acids (SCFAs) using targeted and non-targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. We examined eight bacterial species, including the Gram-positive Lactococcus lactis, Enterococcus faecalis, Blautia producta, Clostridium symbiosum, and Streptococcus thermophilus, and the Gram-negative Prevotella copri, Bacteroides fragilis, and Escherichia coli Nissle. Our results demonstrated that these bacteria differentially consumed glutamine, glutamate, and tryptophan, with several species producing neuroactive metabolites. Notably, E. coli Nissle and B. producta produced significant levels of gamma-aminobutyric acid (GABA), while P. copri was the sole producer of tryptamine from tryptophan. Interestingly, none of the tested bacteria produced serotonin or its intermediates, despite consuming tryptophan. In the tyrosine pathway, E. faecalis generated tyramine and dopamine, while L. lactis, B. producta, and E. coli Nissle synthesized L-DOPA. In addition to neurotransmitters, we identified the production of SCFAs by multiple bacterial strains. Of the bacterial species, B. producta exhibited the broadest range of SCFAs produced. These findings suggest that commensal gut microbes have the potential to influence host neurological processes through the production of neuroactive compounds and SCFAs, underscoring the therapeutic possibilities of modulating the gut microbiota to treat neurological disorders. |
| Institute: | Baylor College of Medicine |
| Department: | Pathology & Immunology |
| Laboratory: | Horvath Lab |
| Last Name: | Horvath |
| First Name: | Thomas |
| Address: | 1 Baylor Plaza, Houston, TX, 77030, USA |
| Email: | thomas.horvath2@bcm.edu |
| Phone: | 832-824-0904 |
| Funding Source: | T32GM132055-01, T32DK124191-01A1, K01DK123195, K01DK121869, P30DK123704, P20GM120457, S10OD036416 |
| Publications: | iScience Submission currently under Review |
| Contributors: | Anna M. Tingler1, Charulekha Packirisamy1, Alyssa Guterriez1, Adelaide E. Horvath1,2,3, Makenna Grozis1, Sigmund J. Haidacher4,5, Kathleen M. Hoch4,5, Anthony M. Haag4,5, Numan Oezguen4,5, Kristen A. Engevik1, Amy Engevik1, Thomas D. Horvath4,5*, Melinda A. Engevik1* |
Subject:
| Subject ID: | SU004002 |
| Subject Type: | Bacteria |
| Subject Species: | Bacteroides fragilis; Blautia producta; Clostridium symbiosum; Escherichia coli Nissle; Enterococcus faecalis Symbioflor; Lactococcus lactis; Prevotella copri; Streptococcus thermophilus |
| Taxonomy ID: | 817; 1121114; C. symbiosum no TaxID; 316435; S. thermophilis no TaxID; P. copri no TaxID; L. lactus no TaxID; E. faecalis no TaxID |
| Genotype Strain: | Bacteroides fragilis (ATCC 23745); Blautia producta (ATCC 27340D); Clostridium symbiosum (DSZM 14940); Escherichia coli Nissle (1917); Enterococcus faecalis Symbioflor (DSZM 16431); Lactococcus lactis (CB1); Prevotella copri (DSZM 18205); Streptococcus thermophilus (ATCC 491 ) |
Factors:
Subject type: Bacteria; Subject species: Bacteroides fragilis; Blautia producta; Clostridium symbiosum; Escherichia coli Nissle; Enterococcus faecalis Symbioflor; Lactococcus lactis; Prevotella copri; Streptococcus thermophilus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Gram Stain |
|---|---|---|---|
| SA424712 | ZMBI_3 | Blank Media | Blank Media |
| SA424713 | ZMBI_2 | Blank Media | Blank Media |
| SA424714 | ZMBI_1 | Blank Media | Blank Media |
| SA424715 | Escherichia coli Nissle_3 | Microbial Culture | negative |
| SA424716 | Prevotella copri_4 | Microbial Culture | negative |
| SA424717 | Prevotella copri_3 | Microbial Culture | negative |
| SA424718 | Prevotella copri_2 | Microbial Culture | negative |
| SA424719 | Bacteroides fragilis_2 | Microbial Culture | negative |
| SA424720 | Bacteroides fragilis_1 | Microbial Culture | negative |
| SA424721 | Escherichia coli Nissle_2 | Microbial Culture | negative |
| SA424722 | Clostridium symbiosum_2 | Microbial Culture | negative |
| SA424723 | Bacteroides fragilis_3 | Microbial Culture | negative |
| SA424724 | Escherichia coli Nissle_1 | Microbial Culture | negative |
| SA424725 | Clostridium symbiosum_1 | Microbial Culture | negative |
| SA424726 | Clostridium symbiosum_3 | Microbial Culture | negative |
| SA424727 | Lactococcus lactis_1 | Microbial Culture | positive |
| SA424728 | Lactococcus lactis_2 | Microbial Culture | positive |
| SA424729 | Prevotella copri_1 | Microbial Culture | positive |
| SA424730 | Enterococcus faecalis Symbioflor_2 | Microbial Culture | positive |
| SA424731 | Blautia producta_3 | Microbial Culture | positive |
| SA424732 | Streptococcus thermophilus_1 | Microbial Culture | positive |
| SA424733 | Streptococcus thermophilus_2 | Microbial Culture | positive |
| SA424734 | Streptococcus thermophilus_3 | Microbial Culture | positive |
| SA424735 | Blautia producta_2 | Microbial Culture | positive |
| SA424736 | Blautia producta_1 | Microbial Culture | positive |
| SA424737 | Enterococcus faecalis Symbioflor_1 | Microbial Culture | positive |
| SA424738 | Enterococcus faecalis Symbioflor_3 | Microbial Culture | positive |
| Showing results 1 to 27 of 27 |
Collection:
| Collection ID: | CO003995 |
| Collection Summary: | After incubation, the bacteria were examined by microscopy and the cultures were centrifuged at 5,000 x g for 5 minutes to pellet the bacteria. The supernatant was sterile filtered by passing the supernatant through a 0.2 μm-pore polyvinylidene difluoride (PVDF) membrane filter using 1 mL volume syringes and the cell-free conditioned growth media samples were examined by LC-MS/MS, similar to our other studies. |
| Sample Type: | Media |
Treatment:
| Treatment ID: | TR004011 |
| Treatment Summary: | Prevotella copri DSZM 18205, Lactococcus lactis CB1, Enterococcus faecalis Symbioflor DSZM 16431, Blautia producta ATCC 27340D, Clostridium symbiosium DSZM 14940, Bacteroides fragilis ATCC 23745, Escherichia coli Nissile 1917, and Streptococcus thermophilus ATCC 491 were cultured in brain heart infusion medium supplemented with 2% yeast extract and 0.2% cysteine in an AS150 anaerobic chamber (Anaerobe Systems, Morgan Hill, CA USA) overnight at 37°C. The following day, the growth and purity of the bacteria were examined by microscopy using an AE2000 microscope at 40x magnification (Motic, Kowloon, Hong Kong). The optical density at 600nm (OD600nm) of the cultures was obtained using a SmartSpec Plus UV/Visible Spectrophotometer (Bio-Rad Laboratories, Hercules, CA USA). The bacteria were sub-cultured in a chemically defined media (ZMB1)34 at OD600nm of 0.1 and incubated for 20 hrs anaerobically at 37°C. There were no additional treatments other than letting the microbes grow in the fully-defined ZMBI culture media |
Sample Preparation:
| Sampleprep ID: | SP004008 |
| Sampleprep Summary: | After incubation, the bacteria were examined by microscopy and the cultures were centrifuged at 5,000 x g for 5 minutes to pellet the bacteria. The supernatant was sterile filtered by passing the supernatant through a 0.2 μm-pore polyvinylidene difluoride (PVDF) membrane filter using 1 mL volume syringes and the cell-free conditioned growth media samples were examined by LC-MS/MS, similar to our other studies. Sample Preparations for Reverse-Phase Non-Targeted Metabolomics A 10 µL volume of each cell-free conditioned bacterial media sample was diluted in a 50-µL volume of pure methanol and the sample was vortex-mixed briefly and centrifuged at 17,000g for 5 minutes. Then, a 40 µL volume of the extract supernatant was diluted 1:1 with a 40 µL volume of pure water in an autosampler vial, and the sample mixture was vortex-mixed briefly, and a 5-µL sample volume was injected onto the high-resolution LC-MS/MS system for bioanalysis. Sample Preparations for HILIC-based Non-Targeted Metabolomics A 10 µL volume of each cell-free bacterial conditioned media sample was diluted in a 90-µL volume of acetonitrile that contained 1% formic acid and the sample was vortex-mixed briefly and centrifuged at 17,000g for 5 minutes. Then, the extract supernatant was transferred to an autosampler vial, and a 5-µL sample volume was injected onto the high-resolution LC-MS/MS system for bioanalysis. |
Chromatography:
| Chromatography ID: | CH004822 |
| Chromatography Summary: | RP - NT-Metabolomics Method |
| Instrument Name: | Shimadzu Nexera X2 |
| Column Name: | Phenomenex Luna C18(2) (150 x 1 mm, 3 µm, 100 Å) |
| Column Temperature: | ambient |
| Flow Gradient: | The gradient elution program was specified as follows: 0-0.5 min, 5% B; 0.5-14 min, 5-50% B; 14-14.6 min, 50-90% B; 14.6-14.9 min, 90% B; 14.9-15.0 min, 90-5% B; 15.0-20 min 5%B; and at 20.01 min a Stop command is specified, and there is a 20.4 min duty cycle for each injection |
| Flow Rate: | 0.080 mL/min |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
Analysis:
| Analysis ID: | AN006357 |
| Analysis Type: | MS |
| Chromatography ID: | CH004822 |
| Num Factors: | 3 |
| Num Metabolites: | 120 |
| Rt Units: | Minutes |
| Units: | Abundance (Counts) |
