Sandpiper

Sandpiper profiles taxonomy and relative abundance of microorganisms in shotgun metagenomic datasets by leveraging conserved regions of universal marker genes to estimate community composition of Bacteria and Archaea.

Key Features:

• Novel Species Detection: Detects species lacking genomic representation, including members of novel phyla, by profiling conserved regions of universal marker genes.
• Computational Efficiency: Processes large-scale datasets and has been applied to 248,559 publicly available metagenomes from marine, freshwater, sediment, and soil environments.
• Dominance of Novel Species: Revealed that novel species with no genomic representation can dominate microbial communities, exhibiting a median relative abundance of 75% in analyzed datasets.
• Metagenome-Assembled Genomes (MAGs) Recovery: Identifies metagenomic samples suitable for recovering novel MAGs from lineages of interest to guide targeted genome assembly efforts.
• User-Defined Reference Database Expansion: Supports incorporation of newly recovered genomes into its reference database to improve resolution and accuracy of subsequent community profiling.

Scientific Applications:

• Microbial community profiling: Provides taxonomic and relative abundance profiles of Bacteria and Archaea in shotgun metagenomes using marker-gene signals.
• Novel taxa discovery and biodiversity assessment: Detects and quantifies novel species and underrepresented lineages, including novel phyla, in environmental metagenomes.
• Prioritization for MAG recovery: Pinpoints samples for targeted recovery of metagenome-assembled genomes to expand genomic representation of microbial lineages.

Methodology:

Profiles conserved regions within universal marker genes to estimate community composition, identifies samples for MAG recovery, and supports iterative expansion of the reference database by incorporating newly recovered genomes; the approach was applied to 248,559 publicly available metagenomes from diverse environments.