Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

By Donovan H. Parks, Christian Rinke, Maria Chuvochina, Pierre-Alain Chaumeil, Ben J. Woodcroft, P. Evans, Philip Hugenholtz, Gene W. Tyson. 2017

1,634 citations recorded by the source corpus.

Challenges in cultivating microorganisms have limited the phylogenetic diversity of currently available microbial genomes. This is being addressed by advances in sequencing throughput and computational techniques that allow for the cultivation-independent recovery of genomes from metagenomes. Here, we report the reconstruction of 7,903 bacterial and archaeal genomes from >1,500 public metagenomes. All genomes are estimated to be ≥50% complete and nearly half are ≥90% complete with ≤5% contamination. These genomes increase the phylogenetic diversity of bacterial and archaeal genome trees by >30% and provide the first representatives of 17 bacterial and three archaeal candidate phyla. We also recovered 245 genomes from the Patescibacteria superphylum (also known as the Candidate Phyla Radiation) and find that the relative diversity of this group varies substantially with different protein marker sets. The scale and quality of this data set demonstrate that recovering genomes from metagenomes provides an expedient path forward to exploring microbial dark matter. The recovery of 7,903 bacterial and archaeal metagenome-assembled genomes increases the phylogenetic diversity represented by public genome repositories and provides the first representatives from 20 candidate phyla.

Subfields: Ecology, Molecular Biology

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Citations in the corpus

IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes (2018, background): “Recent large-scale recovery of metagenome-assembled genomes (MAGs) from diverse environments has provided significant insights into evolutionary and metabolic properties of uncultivated bacteria and archaea (39,40).”
GToTree: a user-friendly workflow for phylogenomics (2019, background): “The number of sequenced genomes is increasing rapidly, largely through the recovery of metagenome-assembled genomes (MAGs) (e.g. Hug et al. 2016; Parks et al. 2017) and through the generation of single-cell amplified genomes (SAGs) (e.g. Kashtan et al. 2014; Berube et al. 2018).”
A computational framework to explore large-scale biosynthetic diversity (2019, neutral): “…developments in high-throughput sequencing, genome mining efforts are now expanding to large-scale pan-genomic mining of entire bacterial genera 4,22,23 , strain collections 24 and metagenomic datasets from which thousands of metagenome-assembled genomes (MAGs) can be extracted at once 25-28 .”
Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle (2019, neutral): “…et al., 2015; Brooks et al., 2017; Ferretti et al., 2018; Human Microbiome Project Consortium, 2012; Raveh-Sadka et al., 2015; Sharon et al., 2013), but systematic cross-study cataloging of metagenomically assem-bledgenomesfocusedsofaronnon-humanenvironments(Oyama et al., 2017; Parks et al., 2017).”
A genomic catalog of Earth’s microbiomes (2020, methodology): “We compared the MAGs from the GEM catalogue to MAGs from the UBA dataset [1] for 440 samples analyzed by both studies and represented by a single sequencing experiment in the NCBI SRA.”
MGnify: the microbiome sequence data analysis resource in 2023 (2022, background): “Since then there has been a paradigm shift, as a result of the now routine large-scale recovery of genomes from metagenomes (so called metagenome assembled genomes, MAGs) (7,8).”
Dynamic Phosphate Uptake in Arbuscular Mycorrhizal Roots Under Field Conditions (2019, background): “The drop in sequencing costs and the advances in informatics offer new opportunities for the reconstruction of individual microbial genomes (Parks et al., 2017), which may enable us to understand the genomic structures (e.”