Microbiome research: the influence of multi-omic databases

By Olivia Brown

- Last updated on GMT

© JONGHO SHIN / Getty Images
© JONGHO SHIN / Getty Images

Related tags Gut microbiome dysbiosis Gut health microbiome Metabolome

The MiMeDB and gutMDisorder v2.0 databases, launched by researchers earlier this year, collate microbiome research to allow for comprehensive multi-omic integration.

The importance of the microbiome for health and disease has been increasingly established over the past decade, with an explosion in research finding significant associations between gut microflora and gastrointestinal disorders, obesity, mood and immunity. These effects are said to result from the production of a variety of metabolites from these microbes, influencing the gut barrier and immunity of the host.

As this research continues, the complexities of the gut microbiome become ever-more evident, with many bacterial species still yet to be discovered. In addition, microbiome compositions vary greatly on an individual level as a result of variations in environmental exposures and factors such as diet, lifestyle and age. This lack of standardisation causes subsequent variation in study results, reducing their reliability.

The creation of databases such as MiMiDB and gutMDisorder v2 have attempted to collate findings from microbiome studies to enable multi-omic integration, to enhance the understanding of the human microbiome.

MiMeDB: the Human Microbial Metabolome Database.

Studies on the microbiome have remained largely focused on the microbes themselves, rather than the metabolites produced that incur the specific health effects. However, with an increased focus on combining metagenomics with metabolomics, the list of produced chemicals is growing exponentially. 

“As a result, the study of the human microbiome has evolved from an almost singular genomic pursuit to a much more holistic, multi-omic enterprise that requires the linking of the microbial (meta)genome, proteome and metabolome to the human exposome—and finally to human health,” ​explained the MiMeDB creators in a paper in Nucleic Acid Research​.

These multi-omic studies now require multi-omic databases and relevant informative tools, yet there appeared to be a shortage of such tools.

“It was also apparent that much of the information needed was scattered in many different journals, books and specialized electronic databases,” ​stated the researchers, highlighting the need for the data connecting human microbiome and produced chemicals to health to be consolidated

Currently MiMeDB contains data on 626 health effects or bioactivities, 1904 microbes, 3112 references, 22 054 reactions, 24 254 metabolites or exposure chemicals, 648 861 MS and NMR spectra, 6.4 million genes and 7.6 billion DNA bases​,” the researchers concluded.

gutMDisorder v2.0: a database for dysbiosis of gut microbiota.

Dysbiosis of the gut microbiota; an imbalance in the composition of microbial communities, can result from health disorders of the host. The gutMDisorder database was developed to facilitate researchers in the investigation of this dysbiosis following occurrence of disorders, as well as therapeutic interventions.

The researchers note that studies have shifted in focus to research dysbiosis under a variety of conditions, without limiting to healthy controls. With compositions of gut microbes varying within the stages of one condition, this is a vital area of attention. Similarly, it has been found that different age groups respond differently to the same condition, as well as to the same probiotic treatment.

Therefore, the gutMDisorder database, reported in a paper also in Nucleic Acid Research,​ may contribute to the important future of personalised nutrition; tailoring specific advice and treatments to increase the health of the population.

Research Influence

The databases “(will allow researchers)​ to exploit multi-omics technologies to define, for example, targets for dietary intervention studies set to improve host health,​” Professor Glenn Gibson, professor of food microbiology at the University of Reading, told NutraIngredients.  “It will make existing research opportunities more reliable and encompassing,” ​he added, explaining the benefits of tallying microbial type to their function.

However, the constant advances in this field may present difficulties in continued data accuracy.

Because both microbiome research and microbial metabolomics are rapidly developing fields, it is also expected that some of the information in MiMeDB will become dated over a relatively short period of time,​” noted the MiMeDB creators, highlighting a need for the databases to be continuously updated. Yet, this process is successfully portrayed by the publishing of gutMDisorder v2.0, with updates taking place earlier this year.

Nucleic Acid Research
Published online, doi: 10.1093/nar/gkac868
“MiMeDB: the Human Microbial Metabolome Database”
Authors: D.S. Wishart, et al.

Nucleic Acids Research
Published online, doi: 10.1093/nar/gkac871s
“gutMDisorder v2.0: a comprehensive database for dysbiosis of gut microbiota in phenotypes and interventions”
Authors: C. Qi, et al.


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