Big Data for a Small World: A Review on Databases and Resources for Studying Microbiomes

Area of Science:

• Microbiology
• Bioinformatics
• Ecology

Background:

• Microorganisms form complex communities influenced by environmental factors.
• Rapid advancements in sequencing enable diverse microbiome exploration.
• Inconsistent data processing methods hinder cross-study comparisons and data reuse.

Purpose of the Study:

• To catalogue databases of system-specific microbiomes.
• To discuss challenges in metagenomics data analysis and comparison.
• To emphasize the need for standardized biome-specific annotations.

Main Methods:

• Literature review of publicly available common and specialized microbiome databases.
• Analysis of current challenges in metagenomics data preprocessing and annotation.
• Discussion of strategies for future data standardization.

Main Results:

• Identification and categorization of various microbiome databases.
• Highlighting the heterogeneity in metagenomics data processing pipelines.
• Demonstrating the impact of inconsistent annotations on data comparability.

Conclusions:

• Standardized, biome-specific annotations are essential for robust metagenomics data analysis.
• Improved data standardization will facilitate cross-biome research and data integration.
• Future datasets should prioritize comprehensive, biome-specific metadata for enhanced usability.