Influence of 16S rRNA reference databases in amplicon-based environmental microbiome research

Area of Science:

• Microbiology
• Bioinformatics
• Environmental Science

Background:

• Reference databases are crucial for amplicon microbiome research.
• Existing databases vary in sequence content and taxonomic data.
• Previous studies highlighted database choice issues in human health microbiome research.

Purpose of the Study:

• To evaluate the influence of different 16S rRNA reference databases on environmental microbiome inference.
• To illustrate the impact of database selection on soil microbiome studies.
• To compare the effects of Genome Taxonomy Database (GTDB), Ribosomal Database Project (RDP), SILVA, and Consensus Taxonomy (ConTax) databases.

Main Methods:

• Analysis of amplicon (V1V3, V3V4, V4V5, V6V8) data from 128 soil samples.
• Evaluation of four distinct 16S rRNA reference databases: GTDB, RDP, SILVA, and ConTax.
• Statistical assessment of differences in microbiome inference across datasets.

Main Results:

• Significant differences in observed amplicon sequence variant distribution (P < 2.647e-12) were found across datasets generated by different databases.
• Beta diversity metrics were altered by the choice of reference database.
• Microbiome composition inferred by various databases differed significantly (P = 0.001), regardless of the amplicon region used.

Conclusions:

• The selection of a reference database demonstrably influences the outcomes of environmental microbiome research.
• Database choice affects core microbiome structure in environmental studies.
• Researchers must carefully consider reference database selection for accurate soil microbiome analysis.