Biology subjects

Kraaij, R.

Publications and source records attributed to Kraaij, R..

3 recordsLinked to original sources

bioRxiv2025

A comprehensive quality control pipeline in human microbiome research for large population studies

The widespread application of high-throughput Next Generation Sequencing (NGS) technologies has made microbiome research an emerging field in public health and biomedical sciences. However, there are still many challenges that need to be addressed in this field. Pipelines available to generate microbiome data across cohorts are diverse, and sources of variation to be recorded and evaluated during microbiome profiling have not been standardized. Moreover, meticulous quality control of the microbiome data processing, from collection to computational quantification is still challenging, especially in large population studies. Innovative approaches are required to handle samples and to minimize the potential bias introduced by logistic hurdles in biobanking. In this paper, we describe the methodological steps surrounding the optimization of the 16S rRNA gut microbiome profiling in two large prospective cohorts the Generation R Study (mean age 9.83 {+/-} 0.32 years) and the Rotterdam Study (mean age 62.67 {+/-} 5.66 years). This paper also highlights potential solutions to sample mislabeling in large-scale microbiome analysis. To summarize, our study addresses common problems in human microbiome research. It aims to improve the research quality and reliability by integrating more stringent quality control standards into microbiome research.

bioinformatics↗

bioRxiv2022

The gut microbiome and child mental health: a population-based study

The link between the gut microbiome and the brain has gained increasing scientific and public interest for its potential to explain psychiatric risk. While differences in gut microbiome composition have been associated with several mental health problems, evidence to date has been largely based on animal models and human studies in small sample sizes. Here, we aimed to systematically characterize associations of the gut microbiome with overall psychiatric symptoms as well as with specific domains of emotional and behavioral problems, assessed via the maternally rated Child Behavior Checklist in 1,784 ten-year-old children from the multi-ethnic, population-based Generation R Study. While we observe lower gut microbiome diversity in case of more overall and specific mental health problems, associations were not significant. Likewise, we did not identify any taxonomic feature associated with mental health problems after multiple testing correction, although nominally significant findings indicated depletion of genera previously associated with psychiatric disorders, including Anaerotruncus, Anaeroplasma, and Hungatella. The identified compositional abundance differences were found to be similar across all mental health problems. Finally, we did not find any specific microbial functions that were enriched in relation to children with mental health problems. In conclusion, based on the largest sample examined to date, we found no clear evidence of associations between gut microbiome diversity, taxonomies or functions and mental health problems in the general pediatric population. In future, the use of longitudinal designs with repeated measurements microbiome and psychiatric outcomes will be critical to clarify any emerging associations between the gut microbiome and mental health from early life to adulthood.

microbiology↗

bioRxiv2019

Relationship between gut microbiota and circulating metabolites in population-based cohorts

Gut microbiota has been implicated in major diseases affecting the human population and has also been linked to triglycerides and high-density lipoprotein levels in the circulation. As recent development in metabolomics allows classifying the lipoprotein particles into more details, we aimed to examine the impact of gut microbiota on circulating metabolites measured by Nuclear Magnetic Resonance (1H-NMR) technology in 2,309 individuals from the Rotterdam Study and the LifeLines-DEEP cohort in whom gut microbiota was profiled using 16S rRNA gene sequencing. The relationship between gut microbiota and metabolites was assessed by linear regression analysis while adjusting for age, sex, body-mass index, technical covariates, medication use, and multiple testing. Our analysis revealed association of 32 microbial families and genera with very-low-density and high-density subfractions, serum lipid measures, glycolysis-related metabolites, amino acids, and acute phase reaction markers. These observations provide novel insights into the role of microbiota in host metabolism and support the potential of gut microbiota as a target for therapeutic and preventive interventions.

epidemiology↗