Biology subjects

Collij, V.

Publications and source records attributed to Collij, V..

4 recordsLinked to original sources

bioRxiv2023

The gut microbiome across the cardiovascular risk spectrum

RationaleDespite significant progress in treatment strategies, cardiovascular disease remains a leading cause of death worldwide. Identifying new potential targets is crucial for enhancing preventive and therapeutic strategies. The gut microbiome has been associated with the development of coronary artery disease (CAD), however our understanding of the precise changes in the gut microbiome occurring during CAD development remains limited. ObjectiveTo investigate microbiome changes in participants without clinically manifest CAD with different cardiovascular risk levels and in patients with ST-elevation myocardial infarction (STEMI). Methods and ResultsIn this cross-sectional study we characterized the gut microbiome using metagenomics of 411 fecal samples from individuals with low (n=130), intermediate (n=130) and high (n=125) cardiovascular risk based on the Framingham score, and STEMI patients (n=26). We analyzed alpha and beta diversity of the gut microbiome and differential abundance of species and functional pathways among the different groups while accounting for confounders including medication and technical covariates. Abundances of Collinsella stercoris, Flavonifractor plautii and Ruthenibacterium lactatiformans showed a positive trend with cardiovascular risk, while Streptococcus thermophilus was negatively associated. Furthermore, in the differential abundance analysis we identified eight species and 49 predicted metabolic pathways that were differently abundant among the groups. These species included species linked to inflammation. Starch biosynthesis and phenolic compound degradation pathways were enriched in the gut microbiome of STEMI patients, while pathways associated with vitamin, lipid and amino-acid biosynthesis were depleted. ConclusionsWe identified four microbial species that demonstrated a gradual trend in their abundance from low risk individuals to those with STEMI, and species and pathways that were differently abundant in STEMI patients compared to groups without clinically manifest CAD. Further investigation is warranted to gain deeper understanding of their precise role in CAD progression and potential implications, with the ultimate goal of identifying novel therapeutic targets. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=142 HEIGHT=200 SRC="FIGDIR/small/546971v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@f7f0b1org.highwire.dtl.DTLVardef@1db0c8eorg.highwire.dtl.DTLVardef@154adeorg.highwire.dtl.DTLVardef@1e64c74_HPS_FORMAT_FIGEXP M_FIG C_FIG Created with BioRender.com

genomics↗

bioRxiv2022

The faecal metabolome and its determinants in inflammatory bowel disease

ObjectiveInflammatory bowel disease (IBD) is a multifactorial immune-mediated inflammatory disease of the intestine, comprising Crohns disease and ulcerative colitis. By characterising metabolites in faeces, combined with faecal metagenomics, host genetics and clinical characteristics, we aimed to unravel metabolic alterations in IBD. DesignWe measured 1,684 different faecal metabolites and 8 short-chain and branched-chain fatty acids in stool samples of 424 IBD patients and 255 non-IBD controls. Regression analyses were used to compare concentrations of metabolites between cases and controls and determine the relationship between metabolites and each participants lifestyle, clinical characteristics and gut microbiota composition. Moreover, genome-wide association analysis was conducted on faecal metabolite levels. ResultsWe identified over 300 molecules that were differentially abundant in the faeces of patients with IBD. The ratio between a sphingolipid and L-urobilin could discriminate between IBD and non-IBD samples (AUC = 0.85). We found changes in the bile acid pool in patients with dysbiotic microbial communities and a strong association between faecal metabolome and gut microbiota. For example, the abundance of Ruminococcus gnavus was positively associated with tryptamine levels. In addition, we found 158 associations between metabolites and dietary patterns, and polymorphisms near NAT2 strongly associated with coffee metabolism. ConclusionIn this large-scale analysis, we identified alterations in the metabolome of patients with IBD that are independent of commonly overlooked confounders such as diet and surgical history. Considering the influence of the microbiome on faecal metabolites, our results pave the way for future interventions targeting intestinal inflammation.

microbiology↗

bioRxiv2020

Effect of host genetics on the gut microbiome in 7,738 participants of the Dutch Microbiome Project

Host genetics are known to influence the gut microbiome, yet their role remains poorly understood. To robustly characterize these effects, we performed a genome-wide association study of 207 taxa and 205 pathways representing microbial composition and function within the Dutch Microbiome Project, a population cohort of 7,738 individuals from the northern Netherlands. Two robust, study-wide significant (p<1.89x10-10) signals near the LCT and ABO genes were found to affect multiple microbial taxa and pathways, and were replicated in two independent cohorts. The LCT locus associations were modulated by lactose intake, while those at ABO reflected participant secretor status determined by FUT2 genotype. Eighteen other loci showed suggestive evidence (p<5x10-8) of association with microbial taxa and pathways. At a more lenient threshold, the number of loci identified strongly correlated with trait heritability, suggesting that much larger sample sizes are needed to elucidate the remaining effects of host genetics on the gut microbiome.

genetics↗

bioRxiv2020

The Dutch Microbiome Project defines factors that shape the healthy gut microbiome

The gut microbiome is associated with diverse diseases, but the universal signature of an (un)healthy microbiome remains elusive and there is a need to understand how genetics, exposome, lifestyle and diet shape the microbiome in health and disease. To fill this gap, we profiled bacterial composition, function, antibiotic resistance and virulence factors in the gut microbiomes of 8,208 Dutch individuals from a three-generational cohort comprising 2,756 families. We then correlated this to 241 host and environmental factors, including physical and mental health, medication use, diet, socioeconomic factors and childhood and current exposome. We identify that the microbiome is primarily shaped by environment and cohousing. Only [~]13% of taxa are heritable, which are enriched with highly prevalent and health-associated bacteria. By identifying 2,856 associations between microbiome and health, we find that seemingly unrelated diseases share a common signature that is independent of comorbidities. Furthermore, we identify 7,519 associations between microbiome features and diet, socioeconomics and early life and current exposome, of which numerous early-life and current factors are particularly linked to the microbiome. Overall, this study provides a comprehensive overview of gut microbiome and the underlying impact of heritability and exposures that will facilitate future development of microbiome-targeted therapies.

microbiology↗