FlowSoFine - an analyzing tool for microbial pattern changes detected by flow cytometry

The gut-liver axis is important in the pathogenesis of many liver diseases. An essential part of this axis is the gut microbiota. Detection of changes in microbial composition is therefore of high interest. Currently, deep sequencing methods are gold-standard to assess the bacterial microbiome. However, there are alternative methods available. Recently, flow cytometric profiling has been described, where bacteria are discriminated based on DNA-content and size, creating unique and robust microbial fingerprints for each sample. The advantages of this method are its low-cost, fast sample preparation and measuring. Unfortunately, the subsequent data processing and statistical analysis can be a challenge due to the lack of easily accessible analysis tools. Our aim is to develop a bioinformatics tool for statistical readout and visualization of microbial pattern changes measured by flow cytometry.

All flow cytometry data files of the experiment are merged into a single data set, on the basis of which a template in form of a multi-dimensional grid is created. This template is then laid over the scatter plots of the individual samples one by one. In this way, a data set is created which contains the proportion of the measured events for each grid section. This information is used for nonparametric statistics to explore differences between and characteristic features within sample groups. We implemented this bioinformatic approach in the web-application called FlowSoFine.FlowSoFine is a freely accessible, user-friendly analyzing tool, enabling scientists without in-depth programming knowledge to process data from data collection to statistical evaluation. Additionally, a non-metric multidimensional scaling plot is used for visualization of differences in microbial patterns between groups (e.g. treatment). Automated heatmap clustering is applied to the samples and highlights areas with similarities within groups. Furthermore, a series of plots is created to identify bacterial populations of interest

With FlowSoFine, we provide researchers the option to quickly follow the heterogeneity and dynamic changes in the gut microbiome after experimental interventions.

FlowSoFine approach: https://github.com/AG-ESSER/HexTemplatesFCS/

Publication History

Article published online:
07 September 2021