Microbiomics and Metabolomics Analysis

Microbiomics and Metabolomics Analysis

Online Inquiry

Microbiomics takes the microbiome as the object of study, the interaction relationship between internal groups, structure, function, and the interrelationship between microorganisms and the environment or host as the research content. Currently, microbiome research is in a phase of rapid development due to revolutionary breakthroughs in high-throughput sequencing technology and mass spectrometry.

Introduction of Microbiomics and Metabolomics Analysis Services

CD Genomics' microbiome research includes human, plant, and soil, and is dedicated to helping customers solve microbiology-related problems in biomedical, agricultural, and environmental fields. Our microbiomics and metabolomics analysis service focuses on the use of bioinformatics tools to analyze qualitative and quantitative data on low molecular weight metabolites, hormones, and signaling molecules throughout the life cycle or specific physiological cycle of microorganisms, thereby elucidating the relationship between changes in metabolites and microbial physiological activities, and thus revealing the mechanisms of microbial-host interactions.

Mass spectrometry metabolomics approaches for studying the microbiome.Figure 1. Mass spectrometry metabolomics approaches for studying the microbiome. (Bauermeister A, et al., 2022)

Our Routine Microbiomics and Metabolomics Analysis Services Pipelines Include

Our microbiome and metabolome data analysis services are integrated at two main levels. We first analyze the overall correlation between microorganisms and metabolites at the holistic level, and then further analyze the correlation between differential metabolites and microorganisms at the differential level. The specific service pipeline is as follows.

  • Raw data from the analyzed samples are obtained and we pre-process the raw data to obtain a format that can be used for metabolomics studies. The main data preprocessing is mainly used to exclude the influence of factors unrelated to the biological problem on the chromatogram and to normalize or adjust the data set by correction.
  • After obtaining information on microbial community abundance, species, and qualitative and quantitative information on metabolites, we use multivariate data analysis techniques to reveal the information contained in the dataset and to downscale and visualize the coefficients in the dataset to generate scientific hypotheses.
  • Holistic level integration analysis. We compare similarities and variations between microbiomes and metabolomes using procrustes analysis and measure the degree of association between microbes and metabolites using two-way orthogonal partial least squares and correlation analysis.
  • Difference-level integration analysis. We select microorganisms with different genus levels and classify microorganisms based on phylum levels and analyze the relationship between differential metabolites and microorganisms using coinertia analysis. We analyze the distribution characteristics of microbial communities and the relationship between metabolites by considering differential metabolites as environmental factors through canonical correspondence analysis.

Microbiomics and Metabolomics Analysis


We can provide the following analysis results, including but not limited to.

  • Procrustes analysis result graph.
  • Heat map of metabolite-microbial correlations.
  • Chord diagram of metabolite-microbe correlations.
  • Network diagram of metabolite-microbe correlations.
  • Heat map of differential metabolite-differential microbial correlations.
  • Graph of coinertia analysis results.
  • Graph of canonical correspondence analysis results.

How Can We Help You

Choosing our microbiome and metabolome analysis services can help you solve the following problems.

  • Microbial identification. Microorganisms are capable of producing different metabolites, and differences in microbial metabolites can be identified using metabolomic approaches.
  • Antimicrobial mechanism prediction. We can use microbiome metabolic footprint analysis to search for new antimicrobial mechanisms of antimicrobial agents.
  • Gene function elucidation. We are able to determine the function of different unknown genes by analyzing the changes in metabolites under different genetic conditions. For example, by analyzing the differences between the metabolic fluxes of wild-type strains and strains that have undergone genetic manipulation thereby elucidating the function of unknown genes.
  • Fermentation optimization. Many microorganisms can be used as biological chassis for synthetic biology research. We use metabolic flux analysis or metabolic control analysis to elucidate the integrated functions of microbial metabolic pathways and to understand the metabolic state of microorganisms during fermentation, thereby improving the performance of microorganisms and facilitating improvements in industrial fermentation.
  • The relationship between gut flora and disease. We are able to use metabolomics technologies to help our customers explore the gut microbes and metabolites associated with human diseases, thereby advancing diagnostic approaches and therapeutics for these diseases.
  • Soil-plant-microorganism interactions. Normally growing plants have a large and diverse collection of microorganisms on the surface and inside that encode more genes than the host plant. Our microbial metabolomics services can help our customers explore the interrelationships between microbes and their hosts and environments, and thus understand the mechanisms of interactions between organisms.

Can CD Genomics help me generate raw data?

Yes, we can. With advanced instrumentation, a high-coverage self-built database, and experienced metabolomics experts, we can provide you with sequencing services and metabolite detection services.

How should I prepare and send my samples?

If you require our metabolomics testing services, please send samples as requested in the form below and contact us.

Sample Type Minimum requirement per sample Storage and transportation
Serum, Plasma, cerebrospinal fluid 200 ul Snap freeze in liquid nitrogen.
Store at -80 ℃.
Ship with dry ice.
Urine 500 ul
Tissue 200 mg
Cultured Cells 1 x 107 cells
Fecal elements, intestinal contents 1 g
Rumen fluid, fermentation fluid, tissue fluid 1 g of pellet

How to combine microbiomics and metabolomics analysis?

The sequencing results of both 16S amplicon sequencing and metagenomics sequencing can be combined with metabolomics. Metabolomics and 16S amplicon sequencing are mainly used for the association analysis of species classes or abundance with metabolite abundance. However, metagenomics and metabolomics are mainly used for the association analysis of metabolic pathways with gene function and metabolites. There is no fixed method or model for the integration of microbiomics and metabolomics, and we will develop a suitable combined analysis solution for you according to your needs.


  1. Bauermeister A, et al. Mass spectrometry-based metabolomics in microbiome investigations. Nat Rev Microbiol. 2022 Mar; 20(3): 143-160.
  2. Guo R, et al. Microbial Metabolomics: From Methods to Translational Applications. Adv Exp Med Biol. 2021; 1280: 97-113.
* For Research Use Only. Not for use in diagnostic procedures.
Online Inquiry