SingleM and Sandpiper: Robust microbial taxonomic profiles from metagenomic data

Abstract

Determining the taxonomy and relative abundance of microorganisms in metagenomic data is a foundational problem in microbial ecology. To address the limitations of existing approaches, we developed ‘SingleM’, which estimates community composition using conserved regions within universal marker genes. SingleM accurately profiles complex communities of known microbial species, and is the only tool that detects species without genomic representation, even those representing novel phyla. Given SingleM’s computational efficiency, we applied it to 248,559 publicly available metagenomes and show that the vast majority of samples from marine, freshwater, sediment and soil environments are dominated by novel species lacking genomic representation (median relative abundance 75.0%). SingleM also provides a way to identify metagenomes for the recovery of novel metagenome-assembled genomes from lineages of interest, and can incorporate user-recovered genomes into its reference database to improve profiling resolution. Quantifying the full diversity of Bacteria and Archaea in metagenomic data shows that microbial genome databases are far from saturated.

Age, metabolisms, and potential origin of dominant anammox bacteria in the global oxygen-deficient zones

“…1A and B ). When searching in the sandpiper database [ 82 ], members of this genus are present with >0.01% relative abundances in 36 globally distributed marine sediment samples ( Table S3 ). They are present in sediments not only beneath ODZs (ETNP and Arabian Sea), but also in areas without ODZs (e.g.…”

“…We also investigated the presence of the sedimentary relatives of Ca. Scalindua praevalens by searching the distribution of GTDB species Scalindua sp022570935 in the Sandpiper database [ 82 ], which employs SingleM ( https://github.com/wwood/singlem ) to search against all public metagenome datasets listed in the NCBI SRA database.…”

Profiling trace organic chemical biotransformation genes, enzymes and associated bacteria in microbial model communities

“…Draft MAGs were then polished based on the clusters with one round of Racon v1.4.22 (https://github.com/isovic/racon) and one round of medaka v1.4.3 (https://github.com/nanoporetech/medaka) to generate high-quality final MAGs. The relative abundance of each MAG was evaluated by SingleM v0.16.0 32 . The taxonomies of all MAGs derived from 24 model communities were classified by GTDB-Tk v2.3.2 33 .…”

Quantifying microbial DNA in metagenomes improves microbial trait estimation

“…All data and code to reproduce the analyses and figures are available at the following GitHub repository: https://github.com/EisenRa/2024_soil_dark_matter_reply. To estimate the average genome sizes of samples from Piton et al 2 , datasets corresponding to each run accession were sourced from Sandpiper 10 . SingleM v0.17.0 “Archive OTU tables” of each sample were generated by merging those of the corresponding runs, and then re-assigned taxonomy using SingleM “renew” with a GTDB R214 reference metapackage (DOI: 10.5281/zenodo.11123537).…”

“…This was likely because their approach only considered reads aligning to bacterial reference genomes, overlooking bacterial sequences not represented in databases 8,9 . We estimate that, as is common for soil metagenomes 10 , only a small fraction of the microbial communities are represented by genomes at the species level (mean 0.5 ± 1.0% s.d. ).…”