Metagenomics for Gut Microbiota Research

Metagenomics is an extremely powerful tool for describing the genetic potential of microorganisms present in a given environment. Creative Biolabs has been focusing on live biotherapeutic products (LBP) for more than 10 years and has accumulated a lot of research experience in gut microbiota projects. Now, we have established a mature metagenomics technical platform.

Workflow of Metagenomics for Gut Microbiota Research

Metagenomic studies on the human gut microbiome generally comprise four experimental steps: (1) collection of fecal samples, (2) metagenomic DNA extraction, (3) massive DNA sequencing, and (4) data analyses with bioinformatics. Each of the experimental steps can affect the quality and bias of the sample and the resulting output data.

1. Sample Collection and Storage

Depending on the duration of storage and the sampling method used for collecting the fecal sample, the profile of the microorganism can alter with respect to microbial growth. The most widely recommended protocol in microbiome research is to immediately freeze the sample on dry ice or in liquid nitrogen and then stored at -80℃ until DNA extraction.

2. DNA Extraction

DNA extraction is one of the key steps in microbiome research. Therefore, errors in DNA extraction should be kept to a minimum to accurately estimate the diversity of microbial communities

3. Massive DNA Sequencing

Two main platforms have been developed for NGS studies: (1) the Genome Sequencer 454 FLX system, which generally produces around 400,000 reads with average lengths of 250-350 bp; and (2) the Illumina Genomic Analyzer system typically produce more than 10 times as many reads per run as 454 FLX system with an average length of 35-75 bp.

4. Bioinformatics

Overview of analytical tools for human gut microbiome research.Fig.1 Overview of analytical tools for human gut microbiome research. (Song, 2018)

Metagenomic Approaches

  • Whole-community Shotgun Sequencing

Using this technology, DNA is extracted from environmental samples, shotgun sequenced, and the resulting DNA sequence data is spliced together using an assembly algorithm, or the unassembled data is analyzed to monitor the functional capabilities of entire communities.

  • Single Cell Genomics

In this way, individual microbial cells are isolated from samples. Their DNA is extracted and then amplified using multiple displacement amplification (MDA) techniques. The amplified DNA was then shotgun sequenced.

  • Targeted Approaches

By targeting specific genes, a lot of information about complex microbial communities can be obtained, often in a very cost-effective way.

  • Functional Metagenomic Screening

The ability to screen metagenomic libraries of DNA fragments encoding critical functions will provide a powerful method for the discovery of new genes, as it extends functional screening to the genomes of uncultured organisms in microbial communities.

  • Global Analyses of Gene Expression

Important functional information can be obtained from the emerging fields of metatranscriptomics and metaproteomics. Metatranscriptomics has been applied to the study of intestinal microbiota in recent years.

Application of Metagenomics for Gut Microbiota

When studying the human gut microbiome, metagenomic analysis has the potential to provide sufficient information in the following areas of research: microbial composition and diversity, novel genes, microbial pathways, functional dysbiosis, detection of antibiotic resistance genes, and the identification of microbiome and host interactions and coevolution.

Application of metagenomics in the human gut microbiome.Fig.2 Application of metagenomics in the human gut microbiome. (Wang, 2015)

The microbiome is known to have a significant influence on the maintenance of human health and the occurrence of diseases. Therefore, it is expected that data from the microbiome will provide important information necessary for dispensing therapeutic directions for the treatment of various diseases in the future, thereby contributing to the development of personalized health care regimes in the future. At Creative Biolabs, delivering the best probiotic strains and services is just the start; we make sure each client gets our utmost attention and each project benefits from a customized service plan. If you are interested in our metagenomics services for gut microbiota research, please contact us to get started.


  1. Song, E.J.; et al. Progress of analytical tools and techniques for human gut microbiome research. J Microbiol. 2018 Oct;56(10): 693-705.
  2. Wang, W.L.; et al. Application of metagenomics in the human gut microbiome. World journal of gastroenterology: WJG. 2015, 21(3): 803.

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