Product Update : Introducing VITAprok v1.0 & VITAeuk v1.0 — A Complete Single-Cell Transcriptome Toolkit from Prokaryotes to Eukaryotes

Singapore, May 2025 – Bioinformatics analysis is a critical component of single-cell research. As a biotechnology company deeply rooted in the field of single-cell transcriptomics, M20 Genomics is committed to providing researchers with robust and reliable data analysis solutions.

In March 2025, we launched a major upgrade to the VITAseer platform, introducing the foundational analysis module VITAbasic v1.4. Now, the platform has been further expanded with the release of two dedicated downstream tools—VITAprok v1.0 for prokaryotic and VITAeuk v1.0 for eukaryotic single-cell transcriptomic data (Figure 1). With this update, VITAseer delivers a truly end-to-end analysis pipeline, enabling standardized, modular, and flexible workflows across a broad range of sample types and research scenarios.

Figure 1. Structure of VITAseer

Highlights

Streamlined Installation: Users can effortlessly deploy the analysis environment by simply extracting the VITAprok or VITAeuk package and executing the environment setup script—no complex configuration required.

Highly Configurable Parameters: Each module is accompanied by comprehensive documentation detailing all parameters, including functional descriptions and default values, enabling users to tailor the analysis workflow to specific experimental designs.

First-in-Class Compatibility: VITAprok is the first single-cell transcriptome analysis software globally that supports both individual microbial isolates and complex microbiome communities, offering unprecedented versatility.

Comprehensive Microbial Functional Profiling: VITAprok enables in-depth investigation of functional heterogeneity and redundancy within microbial populations, delivering a robust framework for deciphering microbial activity and metabolic potential at single-cell resolution.

VITAprok v1.0

VITA Single-Cell Full-Length Transcriptome Sequencing Platform is the first commercialized platform to support both single-species bacterial samples and complex microbiome sample like the human gut microbiome. As the field rapidly evolves, standardized analysis tools are in high demand.

Leveraging insights from over 7,000 prokaryotic single-cell datasets, M20 Genomics developed VITAprok v1.0—a streamlined and standardized downstream analysis tool designed to work seamlessly with VITAbasic v1.4. The core analysis modules of VITAprok, summarized in Table 1, include quality control, functional subcluster analysis, and differential gene expression, among others.

Table 1. Analysis modules of VITAprok

As an example, we present the analysis of a single-species bacterial sample of Acinetobacter baumannii using VITAprok v1.0. Figure 2A shows the results of dimensionality reduction and clustering, revealing distinct functional subpopulations within the species. Follow-up analyses identified differentially expressed genes (Figure 2B) and functionally enriched pathways (Figure 2C) across these subclusters, providing deeper insights into intraspecies functional heterogeneity at the single-cell level.

Figure 2. Representative analysis results of an Acinetobacter baumannii sample using VITAprok. A. UMAP plot showing distinct functional subpopulations within the sample. B. Bubble plot of top differentially expressed genes across subpopulations. C. Bubble plot of pathway enrichment results for each functional subpopulation.

We further demonstrate the application of VITAprok v1.0 on a human fecal sample. In this analysis, dominant species were first clustered, and taxonomically annotated (Figure 3A). We then performed functional enrichment analysis on the one of the dominant species Enterocloster bolteae (Figure 3B). In addition, we conducted differential gene expression (Figure 3C) and pathway enrichment analyses (Figure 3D) for the dominant species, offering insights into their species-specific functional profiles within the microbial community.

Figure 3. Representative analysis results of a human fecal sample using VITAprok. A. UMAP plot highlighting dominant species within the sample. B. Barplot showing functional enrichment results for the dominant species Enterocloster bolteae. C. Bubble plot of differentially expressed genes in dominant species. D. Heatmap of pathway enrichment analysis for dominant species.

VITAeuk v1.0

In addition to prokaryotic samples, M20 Genomics has gained extensive experience in eukaryotic single-cell transcriptome analysis. VITAeuk v1.0, the dedicated downstream analysis module for VITAbasic v1.4, offers a customized pipeline for eukaryotic single-cell data. It includes comprehensive modules for quality control, cell clustering, automated cell type annotation, differential gene expression analysis, functional enrichment, cell–cell communication, and lncRNA analysis (Table 2), empowering researchers to investigate molecular mechanisms and biological pathways at single-cell resolution.

Table 2. Analysis modules of VITAeuk

Here, we present the application of VITAeuk for analyzing a lung tissue sample, starting with dimensionality reduction and cell type annotation (Figure 4A). The subsequent cell–cell interaction analysis revealed the predicted communication events between various cell types (Figure 4B). Furthermore, VITAeuk facilitates in-depth profiling of both mRNA-based differential gene expression (Figure 4C) and lncRNA signatures across distinct cell populations (Figure 4D), offering valuable insights into cellular functions and regulatory dynamics at single-cell resolution.

Figure 4. Representative analysis results of a lung tissue sample using VITAeuk. A. UMAP plot showing cell clustering and annotation results. B. Cell–cell communication analysis. C. Heatmap of mRNA-based differentially expressed genes across cell types. D. Heatmap of lncRNA-based differentially expressed genes across cell types.

An Integrated Platform for Comprehensive Single-Cell Analysis of Both Prokaryotic and Eukaryotic Samples

The VITAseer platform unifies prokaryotic and eukaryotic single-cell analysis into a streamlined, modular framework—from raw sequencing reads to biological pathway insights. It fills a critical gap in microbial transcriptomics and empowers researchers to uncover functional heterogeneity, intercellular interactions, and beyond.

For more details, please do not hesitate to contact us via info@m20genomics.com