Metabolomics for Gut Microbiota Research

Metabolomics is the comprehensive analysis of the identification and quantification of all metabolites in biological systems. Fecal sample metabolomics is a new and promising field in the study of intestinal microbial metabolism. The gut microbiota regulates the signaling pathway of intestinal mucosal homeostasis through the production/fermentation of metabolites. Creative Biolabs specializes in custom services of live biotherapeutic products (LBP) development. Our scientists are highly qualified with extensive experience and exceptional skills in the fields of metabolomics for gut microbiota.

Application of Metabolomics in Gut Microbiota

Metabolomics, as an important platform technology, can be used to characterize and quantify small molecular weight compounds in complex biological samples by mass spectrometry (MS) and nuclear magnetic resonance (NMR). Metabolomics has been widely applied to the gut microbiota to understand how the gut microbiota affects the metabolic state of the host through gut microbiota metabolism and host-microbiota co-metabolism. Since the symbiotic gut microbiome may interact with the host to positively or negatively affect disease risk, it is not surprising that metabolomics studies may identify metabolites that can serve as disease biomarkers. In addition, metabolomics studies can be used to interpret the role of gut microbiota in drug metabolism. Metabolomics analysis can also be used to study how diet regulates the gut microbiome and affects host health. There is no doubt that the study of gut microbiota metabolomics has great potential in analyzing the metabolic patterns of gut microbiota and their interactions with the host.

Metabolomic application in human health to improve clinical and nutritional settings.Fig.1 Metabolomic application in human health to improve clinical and nutritional settings. (Vernocchi, 2016)

Workflow of Metabolomics for Investigating Host-gut Microbiota Interactions

1. Sample Collection

Feces, urine, plasma/serum, saliva, exhaled breaths, cerebrospinal fluid (CSF), and tissues from target organs are all potential biological samples for investigating co-metabolism and host-gut microbiome interactions using good experimental designs. In metabolomics studies, careful sample collection and appropriate storage conditions play an important role in reducing the bias of research results. All samples should be kept at a low temperature during transfer. Liquid biological samples can be separated into aliquots to decrease the number of freeze-thaw cycles in future experiments.

2. Analytical Methods

In most metabolomics and microbiota studies, MS is combined with separation methods such as gas chromatography, liquid chromatography, and capillary electrophoresis to provide higher peak volumes and enable qualitative and quantitative analysis.

1) Gas Chromatography-MS

Gas chromatography coupled with MS, including electron impact-quadrupole (GC-EIMS) or time-of flight MS (GC-TOF MS), has been applied to determine metabolites with thermal stability and volatility.

2) Liquid Chromatography-MS

Liquid chromatography-mass spectrometry (LC-MS) is one of the most commonly used analytical platforms for metabolomics studies.

3) Capillary Electrophoresis-MS and Other MS-based Analytical Methods

Capillary electrophoresis (CE) provides a different separation mechanism from conventional chromatography. Metabolites of different molecular weights and charges can be separated in capillary according to their different mobility.

3. Data Preprocessing for MS-based Small Molecule Detection and Analysis

4. Data Analysis

After data preprocessing, the processed data uses mathematical and statistical processing to identify key molecules.

Workflow of MS-based metabolomics study for investigating host-gut microbiota interactions.Fig.2 Workflow of MS-based metabolomics study for investigating host-gut microbiota interactions. (Chen, 2019)

Metabolomics techniques based on MS are powerful for studying key metabolites associated with host-gut microbiome interactions. Metabolomics research has been increasingly applied to the study of intestinal flora in relation to health and disease, with a focus on understanding inflammatory bowel disease. Creative Biolabs is a complete LBP solutions provider. Our expertise shines through our services. If you are interested in our metabolomics services for gut microbiota research, please contact us for more information.


  1. Vernocchi, P.; et al. Gut microbiota profiling: metabolomics based approach to unravel compounds affecting human health. Frontiers in microbiology. 2016, 7: 1144.
  2. Chen, M.X.; et al. Metabolome analysis for investigating host-gut microbiota interactions. Journal of the Formosan Medical Association. 2019, 118: S10-S22.

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