Metabolomics in Microbiome Research

Metabolomics comprehensively characterizes small polar and lipid metabolites that are uniquely from bacterial processing or shared with the host and modified within the microenvironment of the microbiota. This facilitates the understanding of metabolites and their biological implications in host-microbiota interactions, including their involvement in a multitude of complex diseases, such as cardiovascular disease, metabolic syndromes, and obesity. Furthermore, their involvement in various aspects of these diseases can provide more insights on how to improve current precision medicine approaches, including personalized dietary interventions.

Metabolomics brings us closer to the phenotype of an individual, providing a direct readout of metabolic changes that occur in response to host-microbiota interactions.

HMT’s metabolomics

HMT’s metabolome analysis employs CE-MS & LC-MS platforms. Our technologies are optimized to measure small polar metabolites (including short chain fatty acids, modified indoles, polyamines, etc.), and dipeptides, in many types of samples, from sweat, tears to blood and fecal matter.

Quantitation Quantitation
Over 100 polar metabolites, many of which can be altered by the microbiome, are quantifiable with single- or multi-point calibration.
High resolution High resolution
Good separation of structural isomers, e.g. isobaric fatty acids, oxidative products.
hmt's metabolism_microbiome

Examples of samples that can be analyzed at HMT

Skin (sebum, stratum corneum, tissue biopsy)

  • oxidation, inflammation pathways
  • mechanisms of skin-related disease & conditions
  • metabolic profiles pre-& post-skin treatment

  • correlation between intestinal microbiota & colonic metabolites
  • dysbiosis, IBD-related studies
Sweat, tears, serum, plasma

  • biomarkers for stress, toxicity, inflammation
  • correlation between gut microbiota & systemic metabolites
Fecal matter, urine

  • nutrient, biomass processing, etc.
  • signaling, uremic toxins, transported metabolites
  • antibiotic-induced dysbiosis
Other tissues from target organs

  • interactions between specific tissues & gut flora
  • applicable to a myriad of diseases, such as cancers, CVD, CKD, NAFLD

Recent publications

1. Enteropeptidase inhibition improves obesity by modulating gut microbiota composition and enterobacterial metabolites in diet-induced obese mice.
Sugama et al. Pharmacol Res. 2021. 163:105337.
2. Enriched metabolites that potentially promote age-associated diseases in subjects with an elderly-type gut microbiota.
Yoshimoto et al. Gut Microbes. 2021. 13(1):1-11
3. Bacterial nucleoside catabolism controls quorum sensing and commensal-to-pathogen transition in the Drosophila gut.
Kim et al. Cell Host Microbe. 2020. 27(3): 345-357
4. Improvement of alcohol-poisoning symptoms in mice by the oral administration of live Lactobacillus plantarum SN13T cells.
Noda et al. Int J Mol Sci. 2020. 21(5): 1896
5. Host-microbe-drug-nutrient screen identifies bacterial effectors of metformin therapy.
Pryor et al. Cell. 2019. 178(6): 1299-1312
6. Intestinal luminal putrescine is produced by collective biosynthetic pathways of the commensal microbiome.
Nakamura et al. Gut Microbes. 2019. 10(2): 159-171
7. Commensal-derived metabolites govern Vibrio cholerae pathogenesis in host intestine.
You et al. Microbiome. 2019. 7(1): 132
8. Nrf2-mediated antioxidant effects contribute to suppression of non-alcoholic steatohepatitis-associated hepatocellular carcinoma in murine model.
Yamada et al. J Clin Biochem Nutr. 2018. 63(2): 123-128
9. Gut microbiome and plasma microbiome-related metabolites in patients with decompensated and compensated heart failure.
Hayashi et al. Circ J. 2018. 83(1): 182-192
10. Colonic absorption of low-molecular-weight metabolites influenced by the intestinal microbiome: A pilot study.
Matsumoto et al. PLoS One. 2017. 12(1):e0169207
11. Biotic interactions shape the ecological distributions of Staphylococcus species.
Kastman et al. mBio. 2016. 7(5):e01157-16. doi: 10.1128/mBio.01157-16.
12. Alteration of gut microbiota by vancomycin and bacitracin improves insulin resistance via glucagon-like peptide 1 in diet-induced obesity.
Hwang et al. FASEB J. 2015. 29(6): 2397-411


For more detailed information, visit our Resources page where you can download the following: