Research team designs novel Microbiome Search Engine 2

By Danielle Masterson

- Last updated on GMT

Getty Images / metamorworks
Getty Images / metamorworks

Related tags metagenomics Big data microbiome Gut microbiome

When it comes to large-scale mining of microbiome data sets, the process can be complicated, tedious, and downright overwhelming. Given the large volume of data, it is difficult to relate a new microbiome sample to the huge number of existing microbiome samples.

To help streamline the process of correlating newly developed microbiomes with existing data sets, a research team has introduced Microbiome Search Engine 2 (MSE 2), a microbiome database platform for searching query microbiomes against the existing microbiome data sets on the basis of their similarity in taxonomic structure or functional profile. The authors note key improvements such as database extension, data compatibility, a search engine kernel, and a user interface. 

The new tool allows users to search the microbiome space via functional similarity, greatly expanding the scope of search-based mining of the microbiome big data. 

While metagenomic datasets from diverse environments are growing rapidly, the ability to access and reuse the data isn’t an easy process. In order to quickly and informatively correlate new microbiomes with existing ones, researchers developed MSE 2. 

The researcher’s new approach to process and integrate big data is published in mSystems​, a journal of the American Society for Microbiology.

Zoom in

Co-first author Jing Gongchao, Single-Cell Center, CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences (CAS), told NutraIngredients-USA that the development of MSE 2 is a long-term and persistent effort that never ends.

“We first collected all microbiome data from the public database, reorganized them through metadata, and selected samples with relatively high sequencing quality to form a database. Then, we combined with a series of microbiome analysis and comparison algorithms developed by our research group to develop the database,”​ explained Gongchao, adding that the development of MSE 2 is a long-term and continuous project given the high volume of microbiome data.

"Over the past decade we have been passionately collecting published microbiome data—they record the kinds of microbe species and the types of microbial communities that have ever lived on our planet. By collecting and curating them in a minable database, MSE 2 allows these invisible but pivotal creatures on Earth to be 'remembered' by future generations, and those scientists who first discovered them to be recognized,"​ said co-first author Liu Lu, also from Single-Cell Center.

Zoom out

“MSE 2 consists of (i) a well-organized and regularly updated microbiome database that currently contains over 250,000 metagenomic shotgun and 16S rRNA gene amplicon samples associated with unified metadata collected from 798 studies, (ii) an enhanced search engine that enables real-time and fast (<0.5 s per query) searches against the entire database for best-matched microbiomes using overall taxonomic or functional profiles, and (iii) a web-based graphical user interface for user-friendly searching, data browsing, and tutoring,”​ the report, published in January, noted. 

Gongchao said the development of the microbiome data analysis process began back in 2010. Then "in 2016, we released the first version of MSE, which only covered less than 100,000 samples. Today, we have a data capacity of 260,000 samples after the past 10 years. I believe that in the future we will continue to update and release more new versions.”

Game changer

Understanding the complexity of the gut microbiome is still a major challenge for researchers. With a composition unique to each individual which also changes over time, scientists are hoping to unravel the mysteries hiding behind the complex interactions unfolding inside the gut.

Hoping this new tool will help pave the way, Gongchao told us that he believes MSE 2 is a game changer for researchers and the microbiome space.

“With the advent of MSE 2, the microbiome/research world will be changed in terms of both data breadth and depth. It provides researchers with a brand new bird-view of the global microbiome mining, and it also makes it possible to consider the past data and know the future development.”


The microbiome database, including microbiome taxonomy, function, and metadata, are open for download via​. The kernel search engine software is at​ for standalone use with user-defined microbiome databases.


Source: mSystems

Jan 2021, 6 (1) e00943-20; DOI: 10.1128/mSystems.00943-20

“Microbiome Search Engine 2: a Platform for Taxonomic and Functional Search of Global Microbiomes on the Whole-Microbiome Level”

Authors: J. Gongchao et al.


Related topics Research Gut/digestive health

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