Nav: Home

Scientists develop microbiome search engine to assess microbiome novelty and impact

November 13, 2018

Scientists from the Qingdao Institute of Bioenergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences (CAS), developed a way to objectively evaluate the novelty and impact of plethora of microbiomes in the vast universe of microbiome big-data, based on an innovative tool called Microbiome Search Engine (MSE). These inventions, published in mBio, are the compasses guiding mankind's exploration in the vast universe of microbiome big-data.

Microbiomes, microbial societies that colonize almost every corner of our planet, are pivotal to human health, indoor environment, air, soil, as well as the ocean, and shape these ecosystems' past, today and destiny.

To unravel their secret in benefiting our body and biosphere, a series of large, globally coordinated microbiome sequencing projects have been launched since 2010, such as the Earth Microbiome Project (EMP) and the Human Microbiome Project (HMP). These have led to an ongoing explosion of microbiome sequences (the metagenome data), which describe the structure and function of these microbial societies.

Despite the immense volume of these data, few computational approaches are available to process and integrate them. In particular, it is difficult to relate a new microbiome sample to the huge number of existing microbiome samples.

"MSE to microbiome big-data is like Google or Baidu to webpage big-data. By searching for the most structurally or functionally similar microbiomes in a super-fast manner, MSE offers the first opportunity to relate each microbiome ever published to the microbiome big-data known to mankind so far," said SU Xiaoquan, Lead of the Bioinformatics Group at Single-Cell Center, QIBEBT.

In databases of 100 thousand to 1 million microbiomes, MSE is up to three orders of magnitude faster in searching for the closest neighbors of a microbiome in terms of structure, compared with existing strategies (pairwise comparisons).

"MSE makes comparison of microbiome at the global scale possible, enabling a bird's eye view of microbiome data universe," said SU Xiaoquan.

Taking advantage of MSE, a search-based approach for in-depth mining of microbiome big-data was established. Two innovative evaluation indices including Microbiome Novelty Score (MNS) and Microbiome Attention Score (MAS) were proposed.

MNS evaluates the compositional uniqueness of a microbiome sample at the time of its birth. MAS quantifies the scientific attention devoted to the microbiome by counting the number of close neighbors of the microbiome. Microbiome Focus Index, or MFI, which is derived from MNS and MAS, can measure the impact and contribution of a microbiome sample to mankind's exploration for novel microbiomes.

"Microbiome samples with extraordinary MFI are samples that were born with high novelty and then attracted a lot of follow-up scientific investigation," said XU Jian, director of the Single-Cell Center, QIEBET.

"Therefore, MNS, MAS and MFI serve as one objective way to measure the novelty and impact of a sample, a project, a scientist or a research area; these so called 'alt-metrics', which are based on the 'data' themselves, are fundamentally different from the conventional ways of assessing research impact such as the citation numbers or the Impact Factor, which are subject to human judgments and thus can be biased or skewed."

Using MSE, the team predicts the "sleeping beauty" microbiomes, i.e., published microbiome samples that are still very novel in structure at present yet are destined to attract a lot of scientific attention in the next several years, based on temporal growth of their MAS.

These "sleeping beauties" are mainly from marine environments and mother-baby interactions. Thus, data mining, made possible by MSE, can help the scientific community and the funding agencies decide the research areas with the highest potential in generating high-novelty and high-impact microbiome data.

"We envision that such search against the microbiome database will be an important first step for data analysis at various scales in microbiome studies, just as a BLAST search is essential and universal in sequence analysis studies today," said Rob Knight, Director of Center for Microbiome Innovation, University of California at San Diego.

"This work is of great interest to the microbiome research community and is broadly useful to explore available amplicon datasets," commented by Emiley Eloe-Fadrosh from DOE Joint Genome Institute, who is not related to this study.

As one of the first big-data mining tools introduced by Chinese scientists in the Earth Microbiome Project, MSE will support ongoing mining of the immense datasets being generated by EMP as well as the CAS Microbiome Project.
-end-


Chinese Academy of Sciences Headquarters

Related Microbiome Articles:

A reliable clock for your microbiome
The microbiome is a treasure trove of information about human health and disease, but getting it to reveal its secrets is challenging.
Uncovering drug-like small molecules in the human microbiome
Gene clusters once hidden in the human microbiome, whose products resemble clinically used drugs, are now more discoverable, thanks to a new bioinformatics approach.
Cooking food alters the microbiome
Scientists at UC San Francisco and Harvard University have shown for the first time that cooking food fundamentally alters the microbiomes of both mice and humans, a finding with implications both for optimizing our microbial health and for understanding how cooking may have altered the evolution of the our microbiomes during human prehistory.
Genetic risk is associated with differences in gut microbiome
Children with a high genetic risk of developing type 1 diabetes have different gut microbiomes than children with a low risk, according to a new study from Linköping University in Sweden and the University of Florida in the US.
Genetic census of the human microbiome
Scientists have analyzed the genetic repertoire of bacteria in the human mouth and gut.
More Microbiome News and Microbiome Current Events

Best Science Podcasts 2019

We have hand picked the best science podcasts for 2019. Sit back and enjoy new science podcasts updated daily from your favorite science news services and scientists.
Now Playing: TED Radio Hour

Rethinking Anger
Anger is universal and complex: it can be quiet, festering, justified, vengeful, and destructive. This hour, TED speakers explore the many sides of anger, why we need it, and who's allowed to feel it. Guests include psychologists Ryan Martin and Russell Kolts, writer Soraya Chemaly, former talk radio host Lisa Fritsch, and business professor Dan Moshavi.
Now Playing: Science for the People

#537 Science Journalism, Hold the Hype
Everyone's seen a piece of science getting over-exaggerated in the media. Most people would be quick to blame journalists and big media for getting in wrong. In many cases, you'd be right. But there's other sources of hype in science journalism. and one of them can be found in the humble, and little-known press release. We're talking with Chris Chambers about doing science about science journalism, and where the hype creeps in. Related links: The association between exaggeration in health related science news and academic press releases: retrospective observational study Claims of causality in health news: a randomised trial This...