Database Commons

a catalog of worldwide biological databases

Metabolites produced by the gut microbiota play an important role in the cross-talk with the human host. Many microbial metabolites are biologically active and can pass the gut barrier and make it into the systemic circulation, where they form the gut microbial exposome, i.e. the totality of gut microbial metabolites in body fluids or tissues of the host. A major difficulty faced when studying the microbial exposome and its role in health and diseases is to differentiate metabolites solely or partially derived from microbial metabolism from those produced by the host or coming from the diet. Our objective was to collect data from the scientific literature and build a database on gut microbial metabolites and on evidence of their microbial origin. Three types of evidence on the microbial origin of the gut microbial exposome were defined: (1) metabolites are produced in vitro by human faecal bacteria; (2) metabolites show reduced concentrations in humans or experimental animals upon treatment with antibiotics; (3) metabolites show reduced concentrations in germ-free animals when compared with conventional animals. Data was manually collected from peer-reviewed publications and inserted in the Exposome-Explorer database. Furthermore, to explore the chemical space of the microbial exposome and predict metabolites uniquely formed by the microbiota, genome-scale metabolic models (GSMMs) of gut bacterial strains and humans were compared. A total of 1848 records on one or more types of evidence on the gut microbial origin of 457 metabolites was collected in Exposome-Explorer. Data on their known precursors and concentrations in human blood, urine and faeces was also collected. About 66% of the predicted gut microbial metabolites (n = 1543) were found to be unique microbial metabolites not found in the human GSMM, neither in the list of 457 metabolites curated in Exposome-Explorer, and can be targets for new experimental studies. This new data on the gut microbial exposome, freely available in Exposome-Explorer ( http://exposome-explorer.iarc.fr/ ), will help researchers to identify poorly studied microbial metabolites to be considered in future studies on the gut microbiota, and study their functionalities and role in health and diseases.

Exposome-Explorer (http://exposome-explorer.iarc.fr) is the first database dedicated to biomarkers of exposure to environmental risk factors. It contains detailed information on the nature of biomarkers, their concentrations in various human biospecimens, the study population where measured and the analytical techniques used for measurement. It also contains correlations with external exposure measurements and data on biological reproducibility over time. The data in Exposome-Explorer was manually collected from peer-reviewed publications and organized to make it easily accessible through a web interface for in-depth analyses. The database and the web interface were developed using the Ruby on Rails framework. A total of 480 publications were analyzed and 10 510 concentration values in blood, urine and other biospecimens for 692 dietary and pollutant biomarkers were collected. Over 8000 correlation values between dietary biomarker levels and food intake as well as 536 values of biological reproducibility over time were also compiled. Exposome-Explorer makes it easy to compare the performance between biomarkers and their fields of application. It should be particularly useful for epidemiologists and clinicians wishing to select panels of biomarkers that can be used in biomonitoring studies or in exposome-wide association studies, thereby allowing them to better understand the etiology of chronic diseases. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.