Metaproteomics for Gut Microbiota Research

Proteomics provides comprehensive identification and quantification of proteins in a sample, while metaproteomics is a comprehensive characterization of proteins expressed in a microbial community at a given point in time. Metaproteomics has been used to investigate microbiomes in humans and animals as well as in environmental communities such as soil, sludge, food, and the ocean. Creative Biolabs has 10+ years of experience providing CRO services with a skilled team of scientists in the live biotherapeutics products (LBP) development, we have accumulated a wealth of project experience in the study of gut microbiota.

Experimental Workflow of Metaproteomics

1. Stool Sample Preparation

The gut microbiota metaproteome was studied mainly by fecal samples. However, faeces contain a complex environmental matrix that can interfere with protein characterization studies. The performance of metaproteomic analysis of human intestinal microbiota depends on sample preparation. Storage conditions can affect the samples and, therefore, a strict stool storage procedure is required after defecation, usually at -80℃. Many studies have reported that the use of SDS combined with mechanical disruption methods, provided better cell lysis yields than other buffers, in the case of gut microbial protein extraction. The extracted proteins are usually enzymatically digested into peptides before or after the pre-separation step. After protein extraction, additional pre-concentration steps are often performed to obtain more concentrated peptides samples.

2. Pre-fractionation and Mass Spectrometry

1) Pre-fractionation

The pre-fractionation of the sample allows the analysis of less complex mixtures to detect more peptides. However, the number of analysis steps for a single sample is increased, which greatly prolongs the overall analysis time and increases the cost.

2) Mass spectrometry

Tandem mass spectrometry is currently the preferred technique for peptide detection, which monitors the quality of peptides and their induced fragments.

3. Metaproteomics Data Computation

1) Conventional sequence database search

2) Customized iterative database approach

3) De novo sequencing search

Representation of a workflow in a metaproteomic analysis of fecal sample extracted from the gut.Fig.1 Representation of a workflow in a metaproteomic analysis of fecal sample extracted from the gut. (Petriz, 2017)

Metaproteomics for The Human Gut Microbiota

The human gastrointestinal microbiome is arguably the best-studied host-associated microbiome. Metaproteomic approaches have also been developed for studying the microbial mucosa-lumen interface of different intestinal sites and have been applied in a cohort study of inflammatory bowel disease.

  • Exploration of The Gut Metaproteome

In the field of microbial ecology, macroproteomics provides valuable data for in-depth analysis of microbial community responses to human and microbial changes.

Applications of human gut metaproteomic study.Fig.2 Applications of metaproteomics in the study of the gut microbiota (Xiao, 2017)

  • Gut Microbiota in Health and Diseases

It is now thought that pathologies associated with immune or metabolic disorders can be triggered or exacerbated by our host's bacteria. For example, the altered gut microbiota has been linked to metabolic diseases such as obesity and diabetes. Recently, a study looked at the relationship between intestinal flora and cirrhosis. The scientists used metaproteomics to detect proteome changes in the case of affected patients. These specific proteins can be used as potential biomarkers and therapeutic targets. In addition, metaproteomic analysis of the gut microbiome has increasingly been used to identify specific proteins as therapeutic targets. The gut metaproteome is a key factor in maintaining the relationship between host and microbiota. Therefore, it is necessary to focus on the identification of human intestinal biomarkers. This could lead to the implementation of new clinical diagnostic tests and treatments to cure microbial-related diseases.

Macroproteomics of the human gut microbiota has revealed a new and powerful method that can be used to describe and better understand the human gut environment. Metaproteomics is the cornerstone in the study of microbial ecosystems. It has great potential to become a valuable tool for routine diagnosis in clinical microbiology laboratories. Creative Biolabs has established a growing list of technology platforms for gut microbiota research. If you are interested in our metaproteomics services, please contact us for more.


  1. Petriz, B.A.; Franco, O.L. Metaproteomics as a complementary approach to gut microbiota in health and disease. Frontiers in chemistry. 2017, 5: 4.
  2. Xiao, M.; et al. Metaproteomic strategies and applications for gut microbial research. Applied microbiology and biotechnology. 2017, 101(8): 3077-3088.

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