Bioinformatics in Metagenomics


Introduction to Metagenomics

Metagenomics research takes the entire microbial community in a specific habitat as the research object. It does not need to be separated and cultivated. It directly extracts environmental sample DNA for sequencing, and studies the community structure, species classification, system evolution, gene function and metabolic network of environmental microbes. It is widely used in the field of microorganisms. The biggest difference between metagenomics research and traditional microbial research methods is that the microorganisms are regarded as a whole, and the steps of cultivating and separating individual microorganisms are eliminated, and all microorganisms in the environment can be directly studied, and then all microorganisms can be analyzed comprehensively. For example, for patients with long-term, recurrent diarrhea, the possible cause may be inflammation of the digestive tract or specific viral or microbial infections caused by the disorder of the intestinal ecosystem. Through the metagenomic sequencing analysis of the patient's stool, the OUT classification analysis can determine whether there is an intestinal ecosystem disorder, and the genome assembly and comparison can determine whether there is a specific pathogen. Metagenomics analysis has been widely used in various fields of biomedical research.

Principal coordinate analysis in the metagenomics analysis of rumen microbial communities.Fig 1. Principal coordinate analysis in the metagenomics analysis of rumen microbial communities. (Stuart E. D, et al. 2015)

Significance of Metagenomics Data Analysis

  1. Directly perform data analysis on the genome of all microbial populations in a specific environment (such as intestinal microbes, skin microbes, etc.).
  2. Environmental microorganisms usually coexist and interact in communities. Metagenomic research can reflect the true living conditions of microorganisms better than individual studies.
  3. In addition to analyzing the diversity and abundance of microbial populations, it can also analyze microbial gene functions and metabolic pathways involved, and discover new genes with specific functions.

Data Analysis Process

Metagenomics data analysis pipeline.Fig 2. Metagenomics data analysis pipeline.

Application of Metagenomic Data in Biomedical Research

Microbial metagenomics data analysis has been widely used in all aspects of microbial research with its significant advantages, such as basic disease research and infectious disease research. Metagenomics research has changed the life of the appointed microbes, providing new solutions to many problems involving microbes:

  • Pathogen discovery: Using bioinformatics methods to analyze human saliva, respiratory tract, blood, excreta, skin and other metagenomics data, it can discover unknown and potential pathogenic microorganisms.
  • Pathogenic microbiome research: Metagenomics analysis of the microbiome in disease and health conditions can study the mechanism of microbial infection on the human body.
  • Public health: Identify pathogens from clinical samples to guide the management and treatment strategies of infected patients, public health microbiology, and monitor the source of infectious disease outbreaks in the community.

What We Offer

As one of the providers of bioinformatics data analysis, CD Genomics offers established, cost-efficient and rapid turnaround analysis services for metagenomics data analysis. The raw input metagenome data can be produced from a range of platforms. In addition, we are able to receive various formats of data for analysis such as raw FastQ/Fasta files, or aligned BAM/SAM files and other intermediate data formats. For data analysis, we will provide you with the following services:

  • Researchers only need to provide raw data and inform us of your analysis needs, and we will provide you with a one-stop data analysis service.
  • We will select the appropriate analysis software or model based on the data and generate high-quality results charts. 
  • It is also worth mentioning that we provide customers with personalized analysis services.

Our workflow

Service Process

CD Genomics is committed to microbiome bioinformatics data analysis services in the field of precision medicine and health, and is committed to becoming the preferred partner of global metagenomics researchers. CD Genomics has an experienced bioinformatics analysis team that can provide high-quality data analysis services for microbiology data of various biological samples (such as skin, saliva, respiratory tract, blood, and excrement). And it has leading bioinformatics data processing software and computing platform, which can perform various statistical and bioinformatics analyses on the collected big data. If you have any questions about the data analysis content, turnaround time and price, please feel free to contact us. We look forward to working with you, and we will provide you with satisfactory services.


  1. Stuart E. D, et al. Metagenomics analysis of the rumen microbial community following inhibition of methane formation by a halogenated methane analog[J]. Front Microbiol. 2015; 6: 1087.

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

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