CCMP: software-as-a-service approach for fully-automated microbiome profiling

Area of Science:

• Microbiology
• Bioinformatics
• Computational Biology

Background:

• Microbiome profiling is crucial for discovering disease biomarkers and therapeutics.
• Next-generation sequencing is standard for microbiome data, but analysis tools have high entry barriers.
• Existing pipelines require specialized hardware, software installation, and command-line expertise, limiting accessibility.

Purpose of the Study:

• To develop a user-friendly, cloud-based web tool for microbiome profiling.
• To simplify the analysis of 16S ribosomal RNA gene sequencing data.
• To make complex bioinformatics analyses accessible to a wider research community.

Main Methods:

• Created Cloud Computing for Microbiome Profiling (CCMP), a free Software-as-a-Service (SaaS) web tool.
• Integrated cloud computing, fast file transfer, and established microbiome analysis tools.
• Automated the process from raw sequencing data upload to comprehensive analysis reporting.

Main Results:

• CCMP processes 16S ribosomal RNA gene sequence data, performing taxonomic annotation, abundance profiling, and statistical tests.
• The tool successfully analyzed 125 GB of data from 1052 specimens in 21 hours.
• Generated figures and tables for taxonomic annotations, statistical tests, alpha and beta diversity, and principal coordinate analyses.

Conclusions:

• CCMP provides a fully-automated, accessible platform for large-scale microbiome data analysis.
• The tool overcomes traditional bioinformatics barriers, democratizing microbiome research.
• CCMP facilitates the identification of microbiota signatures associated with diseases or experimental conditions.