Microbiome Search Engine 2 helps researchers explore microbiome space

January 22, 2021

Metagenomics - the study of genetic material from an environmental sample - is growing as species evolve or are discovered across the globe. To correlate the newly developed microbiomes with existing data sets, a team of researchers based in China has developed the Microbiome Search Engine 2 (MSE 2). It was published on Jan. 19 in mSystems, a journal of the American Society for Microbiology.

"Here, we introduce MSE 2, a microbiome database platform for searching query microbiomes in the global metagenome data space based on taxonomic or functional similarity of the whole microbiome," said 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).

The previous version of the search engine limited queries to taxonomical similarities, meaning the functional genes had to match. There was not a way for researchers to compare different samples that performed the same function in various microbiomes. The ability to study how the same function may have evolved in different microbes could offer guidance in identifying and treating diseases, according to JING.

"A search-based strategy is useful for large-scale mining of microbiome datasets, providing a bird's eye view of the microbiome data space and disease diagnosis via microbiome big data," JING said.

"The new ability to search the microbiome space via functional similarity greatly expands the scope of search-based mining of the microbiome big data," JING added. "By adding a function-based dimension for these and related applications, MSE 2 should accelerate large-scale mining of the ever-expanding metagenome data space."

MSE 2 includes an extended database with meta data from 819 studies, updated data compatibility to better incorporate newly available data sets and a user-friendly interface. A single query takes less than half of a second to search against the entire database of more than 260,000 samples.

"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.
-end-
MSE 2 was developed by a team led by SU Xiaoquan from College of Computer Science and Technology, Qingdao University, and XU Jian from Single-Cell Center, QIBEBT, CAS. The Natural Science Foundation of China and the Shandong Natural Science Foundation supported this work.

Chinese Academy of Sciences Headquarters

Related Microbiome Articles from Brightsurf:

The microbiome of Da Vinci's drawings
The microbiome study of seven drawings from Leonardo Da Vinci reveals that conservation work, geographical location, and past contaminations leave invisible traces on drawings despite their optimal storage conditions: a novel aspect of art objects that could be monitored to establish a bioarchive of our artistic heritage.

Managing the microbiome raises new hope for autism
Analysis of 619 plasma metabolites in a new study show a distinctive metabolic profile in autistic children prior to microbial transfer therapy The procedure helps modify gut microbiota, improving symptoms gastrointestinal and behavioral symptoms of the disease.

Discoveries reshape understanding of gut microbiome
The findings redefine how the so-called gut microbiome operates and how our bodies coexist with some of the 100 trillion bacteria that make it up.

A new tool for modeling the human gut microbiome
MIT engineers designed a device that replicates the lining of the colon.

How viruses and bacteria balance each other in the gut microbiome
A tiny arms race between bacteria and the viruses that attack them inside the gut could eventually offer a new way to treat out-of-balance microbiomes.

Microbiome confers resistance to cholera
Many parts of the world are in the midst of a deadly pandemic of cholera, an extreme form of watery diarrhea.

Parasites and the microbiome
In a study of ethnically diverse people from Cameroon, the presence of a parasite infection was closely linked to the make-up of the gastrointestinal microbiome, according to a research team led by Penn scientists.

Gut microbiome influences ALS outcomes
Harvard University scientists have identified a new gut-brain connection in the neurodegenerative disease ALS.

The microbiome controls immune system fitness
Working alongside colleagues in Mainz, Bern, Hannover and Bonn, researchers from Charité -- Universitätsmedizin Berlin, the Berlin Institute of Health (BIH) and the German Rheumatism Research Center Berlin (DRFZ) were able to show how the microbiome helps to render the immune system capable of responding to pathogens.

Researchers uncover the moscow subway microbiome
Recently, a group of ITMO University researchers has looked into the microbiome of the Moscow Subway.

Read More: Microbiome News and Microbiome Current Events
Brightsurf.com is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to Amazon.com.