Kelder, A. | Search bioRxiv

bioRxiv2025

CytoScan: Automated detection of technical anomalies for cytometry quality control

Studies evaluating cellular phenotypes by cytometry techniques are increasingly facing analytical challenges due to the multitudes of samples and parameters that are evaluated concurrently. Spurious technical effects resulting from a lack of standardization can affect marker distributions and further complicate multi-sample analyses. User-friendly tools for exploratory data analysis to identify such technical effects in large datasets are lacking. To fill this gap, we present a novel R package, CytoScan, that evaluates inter-measurement variation in cytometry datasets and allows for detecting anomalous measurements after data acquisition. CytoScan can detect two types of anomalies: files with limited similarity to others within a dataset (outliers) and files with limited similarity to previously acquired high-quality reference data (novelties). Using simulations of skewed marker distributions and real-life technical effects we demonstrate that CytoScan can accurately detect such anomalies. CytoScan can be applied to large cytometry datasets on consumer-grade hardware with informative visualizations, providing accessible quality-control for more reliable analyses.

bioinformatics↗

bioRxiv2025

Uncovering differences in rye and wheat degradation by human gut microbiota applying a quantitative multi-metaOmics in vitro approach

While wheat is the most common grain used in bread-making worldwide, rye is popular in many European countries too. Rye is associated with several health benefits, which is attributed to its comparatively higher fiber content (primarily fructans and arabinoxylans) that promote production of short chain fatty acids (SCFA) by gut microbiota, in particular butyrate. Intervention studies revealed bacterial alterations upon rye administration, however, the detailed mechanisms involved in its degradation are not understood. We grew fecal communities (n=20) on pre-digested rye and wheat, respectively, demonstrating that rye was yielding higher cell and SCFA concentrations in almost all samples along with distinct abundances of many taxa. A multi metaOmics (metagenomics/metatranscriptomics) approach (n=5 donors) showed higher bacterial growth rates for most taxa on rye compared to wheat. The higher growth rate of rye was accompanied by increased expression of genes involved in growth and energy generation suggesting higher carbon substrate accessibility. The carbohydrate active enzyme repertoire was greatly distinct between communities growing on the two substrates with several specific glycoside hydrolases increasingly expressed in rye containing cultures. Agathobacter faecis was revealed as the key butyrogenic species for rye degradation and its expression pattern based on metagenome assembled genomes showed adaptation to growth on rye via expression of genes involved in arabinoxylan degradation and fructose (major monomer of fructans) uptake. Our study verifies higher SCFA production from rye over wheat and gives detailed insights into molecular mechanisms involved. It supports that the observed health benefits of rye are mediated by gut microbiota.

microbiology↗