A research team designs the new Microbiome Search Engine 2


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

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

While metagenomic datasets from diverse environments grow rapidly, the ability to access and reuse the data is not 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 processing and integrating big data is published in mSystems​, a journal of the American Society for Microbiology.


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, persistent effort that never ends.

“We first collected all the microbiome data from the public database, rearranged it using 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,”Gongchao explained, adding that the development of MSE 2 is a long-term and ongoing project given the high volume of microbiome data.

“Over the past decade, we have passionately collected published microbiome data – it records the types of microbe species and the types of microbial communities that have ever lived on our planet. Collecting and storing them in an actionable database, MSE 2 enables these invisible but essential creatures on Earth to be “remembered” by future generations, and the scientists who first discovered them to be recognized”,said co-first author Liu Lu, also of the 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 samples and 16S rRNA gene amplicons associated with unified collected metadata from 798 studies, (ii) an improved search engine that allows fast and fast searches (the report, released in January, noted.

Gongchao said the development of the microbiome data analysis process started 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 last 10 years. future, we will continue to update and release more new versions.

game changer

Understanding the complexity of the gut microbiome remains a major challenge for researchers. With a composition unique to each individual that also changes over time, scientists hope to unravel the mysteries behind the complex interactions that take place inside the gut.

Hoping this new tool will help pave the way, Gongchao told us 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 change in terms of breadth and depth of data. It offers researchers a whole new overview of global microbiome mining, and it enables also to consider the past data and know the future development.


The Microbiome Database, including microbiome taxonomy, function and metadata, can be downloaded via mse.ac.cn​. The kernel search engine software is at github.com/qibebt-bioinfo/meta-storms​for stand-alone use with user-defined microbiome databases.

Source: mSystems

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

“Microbiome Search Engine 2: A Platform for Taxonomic and Functional Search of Global Microbiomes at the Whole Microbiome Level”

Authors: J. Gongchao et al.

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