Microbiome and Metabolome Integration Analysis



In the human intestine, the gut microbes communicate closely with the host. Gut microbes play an important role in metabolism, immunity, and nervous system regulation. Microorganisms can affect the body's weight, digestive function, and resist the risk of infection and autoimmune diseases. In addition, it can also affect the body's response to drugs. These gut microbes interact closely with the host mainly through small molecule metabolites. Microbial metabolomics can discover the key metabolites of gut microbes that change with the pathophysiology of the host, providing clues for the study of the microbiome-host interaction mechanism.

Through microbiome and metabolome integration analysis, the relationship between microorganisms and metabolites can be studied, such as the relationship between microbial flora and its living environment, the influence of metabolites on microbial homeostasis, and the effect of flora changes in complex diseases, as well as the mechanism of action, the interaction between the physiological functions of the microbial flora and its metabolites and their metabolic functions, and the various metabolic regulation pathways that the microbial flora participates in. It has good application prospects in host physiology, disease pathology, and drug pharmacology. At present, the integration analysis of microbiome and metabolome has been widely used in various disease research and made a lot of progress.

Integrated correlation-based network analysis of microbes and metabolites. Pearson’s correlation analysis from the entire network in the CRC group and H group.Figure1. Integrated correlation-based network analysis of microbes and metabolites. Pearson's correlation analysis from the entire network in the CRC group and H group. (Yang Y, et al. 2019)

Application Fields

Microbiome and metabolome integration analysis is used in various fields of biomedical research, such as:

  • Basic disease research: pathological research such as tumors, metabolic diseases, autoimmune diseases, neurological diseases, etc.
  • Clinical research: early marker discovery, clinical diagnosis, disease classification, and personalized treatment.

What We Offer

As one of the experienced bioinformatics analysis service providers, we offer established, cost-efficient and rapid turnaround analysis services for microbiome and metabolome integration analysis. The raw input microbiome and metabolome data can be produced from different sequencing platforms or mass spectrometers. In addition, we can use various formats of data for analysis such as raw data files, or other intermediate data formats. We provide our clients with the following services:

  • Provide integrated analysis of microbiome and metabolomics.
  • According to the different research purposes of the research, we will customize the exclusive analysis plan for you.
  • Use cutting-edge statistical analysis methods to provide you with accurate co-expression data analysis.
  • A complete and practical report, in addition to displaying analysis methods and results, also includes interpretation of biological significance.
  • The fast analysis cycle accelerates the pace of your research.

Data Analysis Technical Route

Flow chart showing microbiome and metabolome integration analysis. - CD Genomics.Fig 2. Flow chart showing microbiome and metabolome integration analysis.

Analysis Content Includes:

Based on the microbiome (metagenomic sequencing / amplicon sequencing) and metabolome (non-targeted / targeted metabolome) omics data, we first screen the different strains and metabolites between the groups from the microbial and metabolic levels, and then conduct joint analysis based on the correlation between the expression levels of the two. The angle reveals the correlation between specific flora and specific metabolites (groups), and screens the key strains that cause changes in the metabolic state of the flora or functional metabolic small molecules.

  • Correlation analysis heat map of microorganisms and metabolites.
  • Microbial and metabolite association network diagram.
  • Scatter plot analysis of typical microorganisms or metabolites.
  • Differential metabolic pathway and function analysis.
  • Correlation analysis between the function of different strains and metabolites.

Data Ready

Before data analysis, the first thing is to get your data ready. The input data can be obtained from the following channels:

Channels of moicrobiome and metabolome input data. - CD Genomics.In order to process data more efficiently, we prefer to receive data files in the raw format, but we can also accept pre-normalized files.

What's More

For microbiome and metabolome integration analysis, if you have not generated the raw data, CD Genomics can help by arranging for the generation of your data. Alternatively, we are able to provide services for obtaining and mining data from available databases. If you have any questions about the data analysis cycle, analysis content and price, please click online inquiry. For more questions, please feel free to contact us. We have a professional technical support team to serve you.


  1. Yachida S ,et al. Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer[J]. Nature Medicine, 2019, 25(6):968-976.
  2. Yang Y ,et al. Integrated microbiome and metabolome analysis reveals a novel interplay between commensal bacteria and metabolites in colorectal cancer[J]. Theranostics, 2019, 9(14).

* For research use only. Not for use in clinical diagnosis or treatment of humans or animals.

Online Inquiry

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