Table 1 Computational tools to assess microbiome composition.
From: Omics-based decoding of molecular and metabolic crosstalk in the skin barrier ecosystem
Sequencing Methodology | Tool | Primary function | Biological question | Microbiome Input Data | Distinctive Features | Output | References |
|---|---|---|---|---|---|---|---|
Shotgun | MetaPhlAn | Species-level taxonomic profiling using clade-specific markers. | What species are present and how do they vary across conditions? | Shotgun metagenomics | High-resolution and robust species-level profiles; widely adopted. | Relative abundance tables, species heatmaps. | Blanco-Míguez et al., [89] |
Kraken | Ultra-rapid taxonomic classification of metagenomic reads. | Which microbes are present in large datasets? | Shotgun metagenomics | Extremely fast and scalable; suited for high-throughput datasets. | Classification reports, abundance tables. | Lu et al., [90] | |
EasyMetagenome | Pipeline for multiple analysis methods, including quality control (QC), host read removal, assembly. | How can I perform a complete metagenome workflow of shotgun data with minimal coding? | Shotgun metagenomics | User-friendly pipeline; integrates multiple analytical steps. | QC reports, contig/bin assemblies, abundance tables. | Bai et al., [97] | |
QIIME2 | Provides complete and integrated workflow from raw sequencing reads to publication-quality visualizations and statistics analysis, focusing on diversity and taxonomy. | How do microbial communities differ across different conditions? | 16S rRNA, shotgun | Community-driven and extensible; ensures reproducibility through provenance tracking and standardized outputs; ideal for comparative microbiome studies. | OTU/ASV tables, alpha/beta diversity plots, taxonomic summaries. | Bolyen et al., [91] | |
16S | Phyloseq | R package for statistical analysis and visualization. | How can I statistically compare microbial communities? | 16S rRNA, shotgun | Powerful visualization and statistical integration in R. | Rich graphics, ordination plots, diversity statistics. | McMurdie & Holmes, [92] |
MGX (Microbiome Genomics) | Workflow for 16S, shotgun metagenomics and amplicon sequencing data. It integrates taxonomic profiling, functional annotation, and statistical analysis. | How do taxonomy and function change in the microbiome? | 16S rRNA, shotgun | Flexible platform that combines taxonomic and functional metagenome analysis within one environment. It offers ready-to-use workflows, interactive visualizations, and the possibility to add custom pipelines or data. | Combined taxonomic + functional profiles. | Jaenicke et al., [95] | |
Greengenes2 | A 16S rRNA database that offers tools for taxonomic classification and microbial profiling. | Which microbes can be reliably classified in 16S datasets? | 16S rRNA | Updated and curated; improves classification accuracy. | Taxonomic reference tree, annotated taxa. | McDonald et al., [94] | |
RDP (Ribosomal Database Project) Classifier | Naive Bayes–based classifier for taxonomic and phylogenetics assignment of rRNA sequences. | Which taxa are present in my 16S data? | 16S rRNA | One of the earliest and most widely validated classifiers for microbial taxonomy; supports local use, and the RDP Classifier (v2.14, 2023) remains actively maintained and integrated into major microbiome pipelines. | Taxonomic labels with bootstrap confidence scores. | Cole et al., [98]; RDP Classifier v2.14, 2023 | |
SILVA Database | Curated, high-quality reference database of small and large subunit rRNA sequences for taxonomic assignment and phylogenetic analysis. | Which taxa are present in my 16S rRNA data? | 16S rRNA | Provides one of the most comprehensive rRNA sequence collections across all domains of life. Continuously updated and curated. Offers QC alignments and standardized taxonomy. Considered a gold-standard reference in microbial ecology studies. | Reference taxonomy, annotated alignments. | Quast et al., [93] | |
EasyMap | Web tool for 16S taxonomic assignment + functional prediction. | How can I perform a complete metagenome workflow of 16S data with minimal coding? | 16S rRNA | User-friendly and interactive platform; Offers complete microbiome analysis (QC, taxonomy assignment, microbial composition, alpha and beta diversity, differential abundance analysis and functional prediction. | Taxonomic tables, diversity plots, functional predictions. | Dahan et al., [96] |
