Abstract
In any research field, data access and data integration are major challenges that even large, well-established consortia face. Although data sharing initiatives are increasing, joint data analyses on nutrition and microbiomics in health and disease are still scarce. We aimed to identify observational studies with data on nutrition and gut microbiome composition from the Intestinal Microbiomics (INTIMIC) Knowledge Platform following the findable, accessible, interoperable, and reusable (FAIR) principles. An adapted template from the European Nutritional Phenotype Assessment and Data Sharing Initiative (ENPADASI) consortium was used to collect microbiome-specific information and other related factors. In total, 23 studies (17 longitudinal and 6 cross-sectional) were identified from Italy (7), Germany (6), Netherlands (3), Spain (2), Belgium (1), and France (1) or multiple countries (3). Of these, 21 studies collected information on both dietary intake (24 h dietary recall, food frequency questionnaire (FFQ), or Food Records) and gut microbiome. All studies collected stool samples. The most often used sequencing platform was Illumina MiSeq, and the preferred hypervariable regions of the 16S rRNA gene were V3–V4 or V4. The combination of datasets will allow for sufficiently powered investigations to increase the knowledge and understanding of the relationship between food and gut microbiome in health and disease.
Highlights
Microbiome research has gained popularity over the past 15 years thanks to a reduction in the cost of high-throughput sequencing technology and the increased availability of sophisticated mathematical and computational techniques, allowing for a better quantification of the microbial composition and, an understanding of its impacts on humanNutrients 2021, 13, 3292 health [1,2]
Within the KP-Intestinal Microbiomics (INTIMIC), we identified 23 observational studies conducted in Italy (n = 7), Germany (n = 6), the Netherlands (n = 3), Spain (n = 2), Belgium (n = 1), and France (n = 1), and multinational studies conducted in two or more countries
Of the seven disease-based studies, one had no controls and exclusively recruited diseased individuals with chronic kidney disease (Medika, Italy), whereas the other six primarily recruited disease-based participants and included a non-diseased control group, which was mainly recruited through advertisements
Summary
Microbiome research has gained popularity over the past 15 years thanks to a reduction in the cost of high-throughput sequencing technology and the increased availability of sophisticated mathematical and computational techniques, allowing for a better quantification of the microbial composition and, an understanding of its impacts on humanNutrients 2021, 13, 3292 health [1,2]. Microbiome research has gained popularity over the past 15 years thanks to a reduction in the cost of high-throughput sequencing technology and the increased availability of sophisticated mathematical and computational techniques, allowing for a better quantification of the microbial composition and, an understanding of its impacts on human. Firmicutes and Bacteroidetes are the two dominant phyla. Firmicutes and Bacteroidetes represent approximately 90% of the total community of the adult human gut microbiota. The primary determinants capable of modulating the gut microbial composition are diet and interindividual variations, such as epigenetic variations of the host [2]. A diverse diet leads to a diverse microbiome, which, in turn, is considered a healthy microbiome [5]. Intra- and interindividual variations, as well as the temporal dynamics of the microbiome, preclude a single narrow definition of a healthy human gut microbiome [6]
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