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The microbiome ("bacteria") is the existence form of microorganisms in nature, which is ubiquitous in nature, shaping the past, present and future of human society.
Therefore, the in-depth mining of the "big data" of the microbiome is an important tool for the use of microbiota to achieve precise diagnosis, precise care and precise nutrition.
It is also a new means of understanding biological resources, monitoring environmental health, and maintaining national biosecurity.
Recently, the Single Cell Research Center of Qingdao Institute of Bioenergy and Processes, Chinese Academy of Sciences released the second-generation microbiome search engine MSE 2 (http://mse.
ac.
cn) to support more comprehensive, in-depth, and more convenient bacteria Group big data mining.
On January 20, the relevant research results were published in mSystems (Proceedings of the American Society for Microbiology).
In the massive data space of the known human microbiome, the microbiome search engine (MSE) searches for new samples of microbiota with sub-second response times to find structurally similar samples, thereby comprehensively and quickly discovering the characteristics of the new samples.
Therefore, MSE is known as the Google of Microbiome.
MSE 2 has been fully upgraded from three aspects: reference database, search engine kernel and user interface (Figure 1).
Specifically, first, compared to the first-generation MSE database containing 100,000 16S rRNA amplicon sequencing samples, MSE 2 collected, standardized, analyzed, and visualized the most recent types of 16S rRNA amplicons and shotgun metagenomes.
With 270,000 samples, it is one of the standardized metagenome databases with the most comprehensive coverage and the richest number of samples in the domestic and foreign ecosystems.Secondly, the search engine kernel of MSE 2 is fully compatible with both 16S rRNA and shotgun sequencing data.
From OTU[using MSE, researchers have revealed the global characteristics of the known human flora in the structural space and predicted the microbiome The direction with the most scientific potential in the field (Su et al.
, mBio 2018)].
At the same time, MSE represents a new disease detection strategy that relies on big data of flora.
In the diagnosis of chronic diseases based on intestinal flora, it is answering the two questions of "healthy" and "what kind of disease".
The accuracy rate is better than that of commonly used machine learning algorithms, which effectively reduces the probability of "missed diagnosis" and "misdiagnosis" (Su et al.
, mSystems 2020).
In addition, because it covers a comprehensive, multi-dimensional, massive amount of microbiome and its habitat information, MSE has become a powerful tool for evaluating microecological health and evaluating the efficacy of microecological products.
Based on its expanding applications, MSE 2 will become a "compass" for traveling in the microbiome data space, promoting "data-driven" microecological research and large-scale health industry applications.
The research was completed by Qingdao Energy Institute in cooperation with Qingdao University, Chinese Academy of Sciences Literature and Information Center, and Ocean University of China.
Assistant researchers Jing Gongchao and Liu Lu of the Bioinformatics Research Group of the Single Cell Center are the co-first authors of the paper.
Qingdao University professor Su Xiaoquan and Qingdao Energy Institute researcher Xu Jian are the co-corresponding authors of the paper.
The research work was supported by the National Natural Science Foundation of China and the Natural Science Foundation of Shandong Province.
The overall framework of the second-generation microbiome big data search engine MSE 2 Source: Qingdao Institute of Bioenergy and Processes, Chinese Academy of Sciences
Therefore, the in-depth mining of the "big data" of the microbiome is an important tool for the use of microbiota to achieve precise diagnosis, precise care and precise nutrition.
It is also a new means of understanding biological resources, monitoring environmental health, and maintaining national biosecurity.
Recently, the Single Cell Research Center of Qingdao Institute of Bioenergy and Processes, Chinese Academy of Sciences released the second-generation microbiome search engine MSE 2 (http://mse.
ac.
cn) to support more comprehensive, in-depth, and more convenient bacteria Group big data mining.
On January 20, the relevant research results were published in mSystems (Proceedings of the American Society for Microbiology).
In the massive data space of the known human microbiome, the microbiome search engine (MSE) searches for new samples of microbiota with sub-second response times to find structurally similar samples, thereby comprehensively and quickly discovering the characteristics of the new samples.
Therefore, MSE is known as the Google of Microbiome.
MSE 2 has been fully upgraded from three aspects: reference database, search engine kernel and user interface (Figure 1).
Specifically, first, compared to the first-generation MSE database containing 100,000 16S rRNA amplicon sequencing samples, MSE 2 collected, standardized, analyzed, and visualized the most recent types of 16S rRNA amplicons and shotgun metagenomes.
With 270,000 samples, it is one of the standardized metagenome databases with the most comprehensive coverage and the richest number of samples in the domestic and foreign ecosystems.Secondly, the search engine kernel of MSE 2 is fully compatible with both 16S rRNA and shotgun sequencing data.
From OTU[using MSE, researchers have revealed the global characteristics of the known human flora in the structural space and predicted the microbiome The direction with the most scientific potential in the field (Su et al.
, mBio 2018)].
At the same time, MSE represents a new disease detection strategy that relies on big data of flora.
In the diagnosis of chronic diseases based on intestinal flora, it is answering the two questions of "healthy" and "what kind of disease".
The accuracy rate is better than that of commonly used machine learning algorithms, which effectively reduces the probability of "missed diagnosis" and "misdiagnosis" (Su et al.
, mSystems 2020).
In addition, because it covers a comprehensive, multi-dimensional, massive amount of microbiome and its habitat information, MSE has become a powerful tool for evaluating microecological health and evaluating the efficacy of microecological products.
Based on its expanding applications, MSE 2 will become a "compass" for traveling in the microbiome data space, promoting "data-driven" microecological research and large-scale health industry applications.
The research was completed by Qingdao Energy Institute in cooperation with Qingdao University, Chinese Academy of Sciences Literature and Information Center, and Ocean University of China.
Assistant researchers Jing Gongchao and Liu Lu of the Bioinformatics Research Group of the Single Cell Center are the co-first authors of the paper.
Qingdao University professor Su Xiaoquan and Qingdao Energy Institute researcher Xu Jian are the co-corresponding authors of the paper.
The research work was supported by the National Natural Science Foundation of China and the Natural Science Foundation of Shandong Province.
The overall framework of the second-generation microbiome big data search engine MSE 2 Source: Qingdao Institute of Bioenergy and Processes, Chinese Academy of Sciences
