Biology subjects

Vancuren, S. J.

Publications and source records attributed to Vancuren, S. J..

3 recordsLinked to original sources

bioRxiv2026

Diet-derived Microbial Metabolites Modulate Stress-Responsive Gene Expression in Germ-free Zebrafish

The gut microbiome plays a pivotal role in overall host health, yet the extent at which diet-derived microbial metabolites affect neurodevelopment and inflammation remains unclear. Here, we employed the robogut bioreactor system seeded with fecal samples from two healthy pediatric donors to generate microbial communities exposed to four different diets: low fiber Western (LFW), high fiber Western (HFW), Mediterranean (MED), and Yanomami (YAN), as well as three fiber supplements: fruit and vegetable fiber (FVF), cereal fiber (CRF), and resistant starch fiber (RSF). Metabolites produced by these microbial communities were isolated and applied to germ-free zebrafish (Danio rerio) embryos to assess their effects on neurodevelopment and inflammatory gene expression under basal and stress-induced conditions. Despite minimal changes in microbial composition across diets and fiber sources, significant differences in short-chain fatty acid concentrations were observed. Metabolite treatments had limited effects on the expression of neural and inflammatory genes under basal conditions. Under stress conditions, metabolites from any diet mitigated stress-induced bdnf expression, suggesting a possible modulatory role of microbial metabolites on stress responses. Overall, these findings highlight the resilience of microbial communities to dietary changes and underscore the importance of microbial metabolite output and its donor-specific nature in influencing host neurodevelopment and immune responses.

developmental biology↗

bioRxiv2020

A generalist lifestyle allows rare Gardnerella spp. to persist at low levels in the vaginal microbiome

Gardnerella spp. are considered a hallmark of bacterial vaginosis, a dysbiosis of the vaginal microbiome. There are four cpn60 sequence-based subgroups within the genus (A, B, C, and D), and thirteen genome species have been defined recently. Gardnerella spp. co-occur in the vaginal microbiome with varying abundance, and these patterns are shaped by a resource-dependent, exploitative competition, which affects the growth rate of subgroup A, B, and C negatively. The growth rate of rarely abundant subgroup D, however, increases with the increasing number of competitors, negatively affecting the growth rate of others. We hypothesized that a nutritional generalist lifestyle and minimal niche overlap with the other, more abundant Gardnerella spp. facilitate the maintenance of subgroup D in the vaginal microbiome through negative-frequency dependent selection. Using 40 whole genome sequences from isolates representing all four subgroups we found that they could be distinguished based on content of their predicted proteomes. Proteins associated with carbohydrate and amino acid uptake and metabolism were significant contributors to the separation of subgroups. Subgroup D isolates had significantly more of their proteins assigned to amino acid metabolism than the other subgroups. Subgroup D isolates were also significantly different from others in terms of number and type of carbon sources utilized in a phenotypic assay, while the other three could not be distinguished. Overall, the results suggest that a generalist lifestyle and lack of niche overlap with other Gardnerella spp. leads to subgroup D being favoured by negative-frequency dependent selection in the vaginal microbiome.

microbiology↗

bioRxiv2019

Variant calling for cpn60 barcode sequence-based microbiome profiling

Amplification and sequencing of conserved genetic barcodes such as the cpn60 gene is a common approach to determining the taxonomic composition of microbiomes. Exact sequence variant calling has been proposed as an alternative to previously established methods for aggregation of sequence reads into operational taxonomic units (OTU). We investigated the utility of variant calling for cpn60 barcode sequences and determined the minimum sequence length required to provide species-level resolution. Sequence data from the 5 region of the cpn60 barcode amplified from the human vaginal microbiome (n=45), and a mock community were used to compare variant calling to de novo assembly of reads, and mapping to a reference sequence database in terms of number of OTU formed, and overall community composition. Variant calling resulted in microbiome profiles that were consistent in apparent composition to those generated with the other methods but with significant logistical advantages. Variant calling is rapid, achieves high resolution of taxa, and does not require reference sequence data. Our results further demonstrate that 150 bp from the 5 end of the cpn60 barcode sequence is sufficient to provide species-level resolution of microbiota.

bioinformatics↗