Kepler Microbiome Analysis: Tools & Applications

The Kepler metagenomic profiler is a host-agnostic  pipeline focused on taxonomic and functional profiling. Powered by Cosmos-Hub, Kepler is accessible via a graphical user interface purpose-built for microbiome analysis and extensible to other scientific domains.

The pipeline enables users to execute computational tools and connect pertinent analytical components with minimal effort, helping researchers and programmers create scientific workflows, compose structured sets of input parameters, and integrate a broad range of analytical and statistical database management processes.

In this article, we'll look at how the Kepler Workflow combines curated genomic databases, phylogenetic biomarkers, and a 2-phase computational pipeline to deliver high-precision, multi-kingdom microbiome profiling—covering bacteria, viruses, fungi, and protists—alongside functional and resistome analysis for applications in clinical, environmental, and population health research.

Read the complete Kepler Whitepaper for technical details

What is the Kepler Workflow?

Kepler is a multi-kingdom taxonomic profiling pipeline engineered for microbiome research. It utilizes a meticulously curated database and advanced computational algorithms to accurately identify bacteria, viruses, fungi, and protists from metagenomic data.

Kepler’s approach leverages high-completeness genome references and unique k-mer biomarkers, delivering robust results even from challenging, low-biomass, or host-contaminated samples. The Kepler project supports researchers to benefit from sensitivity, precision, and broad applicability across diverse domains—including clinical diagnostics, environmental science, and population health.

Core Kepler Methodologies & Workflow

Kepler pipeline integrates a range of specialized steps that streamline the microbiome analysis workflow. The comprehensive algorithm consists of three interwoven pipelines:

Pre-computational Stage for Curating and Building a Comprehensive Biomarker Database (GenBook™)

At the foundation of GenBook™, our pre-computational curation process ensures you are working with the most accurate and comprehensive microbial genome database available. We begin by selecting only the highest quality microbial genomes, filtering out contamination, redundant assemblies, and low-complexity sequences to maintain signal integrity. 

This results in a database of more than 180,000 genes and genomes covering 30,000 species across bacteria, viruses, protists, fungi, and phages—built to provide researchers with a trusted and diverse reference library for microbiome profiling.

K-mer based Taxonomic Classification/Identification

The first stage of classification applies k-mer based identification, where millions of sequencing reads are broken into k-mer sets and compared against GenBook™ biomarkers. 

This process rapidly filters out 99% of irrelevant genomes and delivers a shortlist of the most likely reference strains. By working at the sub-species level with exceptional sensitivity, this stage offers precise taxonomic resolution and ensures that researchers can quickly zero in on the organisms that matter most in their samples.

Probabilistic Smith-Waterman based Abundance Estimation and Classification Refinement

To refine accuracy further, we deploy a probabilistic Smith-Waterman algorithm for abundance estimation and classification. This step evaluates the remaining candidate strains in detail, resolving ambiguous reads and proportionally allocating them across taxa using maximum likelihood estimation. The result is highly accurate, variance-reduced abundance data that researchers can rely on for confident decision-making. 

Together, these staged comparators allow Kepler to deliver the most precise and reliable microbial classification and quantification available.

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Kepler Functional & Resistome Profiling

Kepler extends core taxonomic capabilities with functional and resistome profiling modules. The platform links microbial pathway annotation, gene function mapping, and antimicrobial resistance detection within a unified analysis path, via:

• Functional Microbiome Mapping: Kepler also has an integrated functional pipeline to annotate translated reads against curated functional databases including MetaCyc, EnzymeCommission, Pfam, CAZy, and GeneOntology. This mapping supports comprehensive metabolic and biochemical potential analysis, essential for understanding host and environmental processes.
• Resistome Analysis: Direct queries against databases like Res-Finder for antimicrobial resistance and VFDB for virulence factors to enable detection of antimicrobial resistance genes/classes (ARGs) and virulent signatures. The pipeline quantifies ARGs by class and species, assesses horizontal gene transfer risks, and crafts pathogenicity profiles vital for public health surveillance.

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Applications of Kepler Analysis in Microbiome Research

• Clinical Diagnostics: Detects pathogens and maps AMR genes for actionable insights into infectious disease management.
• Environmental Research: Profiles soil, plant, and animal microbiomes, enabling ecological monitoring and tracking of antibiotic resistance spread.
• Probiotic Development: Supports precision strain detection, powering therapeutic research and next-gen probiotic development.
• Livestock and Companion Animal Health: Facilitates large-scale studies with high sensitivity and recall, effective even in low-biomass, complex, or host-contaminated samples.

Kepler Analysis Benefits

Key benefits include:

• Delivers unmatched species and sub-species sensitivity—even in low-biomass samples
• Enables host-agnostic profiling for human, plant, soil, and animal microbiomes
• Quantifies antimicrobial resistance genes and gene abundance accurately
• Profiles bacteria, viruses, fungi, and protists in a unified workflow

• Provides functional annotation, uncovering the mechanistic potential of microbiome community changes

• Integrates user-friendly, automated analysis and interpretation via Cosmos-Hub’s platform

Cited by

The papers have cited the Cosmos-Hub in their methodology. Consult these for direct examples:

• Microbiome diversity protects against pathogens by nutrient blocking
• Multi-omic approach to decipher the impact of skincare products with pre/postbiotics on skin microbiome and metabolome

• Mobile phones are hazardous microbial platforms warranting robust public health and biosecurity protocols

• Microbiome Analysis for Wastewater Surveillance during COVID-19

Comparison Table: Kepler vs. Other Workflows

Kepler in Scientific Workflows

Kepler provides host-agnostic profiling and multi-kingdom detection, connecting pertinent analytical components for comprehensive workflow analysis. The extensible system allows integration of computational tools, database management, and automation, empowering large-scale data execution across scientific and engineering disciplines.

Applications span diagnostics, environmental research, animal health studies, and population health studies, supported by accurate scientific workflows, statistical database management, and robust computational tools.

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Kepler Scientific Workflow System FAQs

How does Kepler differ from other microbiome analysis tools?

Kepler combines exact k-mer match profiling with probabilistic alignment and a unique phylogenetic biomarker tree, achieving superior species and sub-species sensitivity, lower false positives, and multi-kingdom detection—covering viruses and fungi, not just bacteria.

Is Kepler suitable for environmental, not just animal or human samples?

Absolutely. Kepler supports host-agnostic profiling, excelling in environmental microbiome mapping (soil, plants, animals) as well as clinical contexts.

Does Kepler support resistome and AMR profiling?

Yes. The Kepler software package integrates direct resistome analysis via ResFinder and VFDB, quantifying ARGs and mapping virulence factors for surveillance and research.