Despite recent advances in metagenomic binning, reconstruction of microbial species from metagenomics data remains challenging. Here we develop variational autoencoders for metagenomic binning (VAMB), a program that uses deep variational autoencoders to encode sequence coabundance and k-mer distribution information before clustering. We show that a variational autoencoder is able to integrate these two distinct data types without any previous knowledge of the datasets. VAMB outperforms existing state-of-the-art binners, reconstructing 29–98% and 45% more near-complete (NC) genomes on simulated and real data, respectively. Furthermore, VAMB is able to separate closely related strains up to 99.5% average nucleotide identity (ANI), and reconstructed 255 and 91 NC Bacteroides vulgatus and Bacteroides dorei sample-specific genomes as two distinct clusters from a dataset of 1,000 human gut microbiome samples. We use 2,606 NC bins from this dataset to show that species of the human gut microbiome have different geographical distribution patterns. VAMB can be run on standard hardware and is freely available at https://github.com/RasmussenLab/vamb.
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The sequence data used in this study are publicly available from either the respective studies or ENA. The semisynthetic MetaHIT dataset was downloaded from https://portal.nersc.gov/dna/RD/Metagenome_RD/MetaBAT/Files/ as the files depth.txt.gz and assembly-filtered.fa.gz. The simulated CAMI High and CAMI2 datasets were downloaded from https://data.cami-challenge.org/participate from ‘Toy Test Dataset High_Complexity’ and ‘2nd CAMI Toy Human Microbiome Project Dataset’, respectively. The de novo assemblies of the Almeida dataset were obtained through personal communication with A. Almeida and R. D. Finn, and the reads downloaded from ENA as specified in their publication. The data and results of binning the MetaHIT, CAMI2 and Almeida datasets, as well as the source data for Figs. 1–3, are available on figshare at https://figshare.com/projects/VAMB/72677. A CodeOcean capsule of VAMB v.3.0.1, including the six training and test datasets for reproducing benchmarking results, is available from https://doi.org/10.24433/CO.2518623.v1. Source data are provided with this paper.
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We thank A. Almeida and R. D. Finn for sharing de novo assemblies of the 1,000 gut microbiome samples that we used for benchmarking VAMB. We thank C. Titus Brown for his source code contribution to the VAMB software package. J.N.N., J.J., R.L.A., L.J.J. and S.R. were supported by the Novo Nordisk Foundation (grant NNF14CC0001). S.R. was supported by the Jorck Foundation Research Award.
H.B.N. is employed at Clinical-Microbiomics A/S. The remaining authors declare no competing interests.
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Figs. 1–33 and Tables 1–10.
Overview of Salmonella spike-in with one to three Salmonella strains in a background of 50 HMP samples.
Results of Salmonella spike-in with one to three genomes in a background of 50 HMP samples.
Results of comparison between multisplit and single-sample binning.
Information on the 1,000 human gut microbiome samples (benchmark set from Almeida et al.18).
Number of NC bins generated by VAMB and MetaBAT2 that are annotated by GTDB to a particular species.
Overview of BLAST hits for alignment of VAMB clusters versus NCBI nonredundant nucleotides.
PERMANOVA analysis of phylogenetic placements and geography.
Results of hyperparameter optimizations of the VAE in VAMB.
CheckM results for all bins produced by VAMB.
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Nissen, J.N., Johansen, J., Allesøe, R.L. et al. Improved metagenome binning and assembly using deep variational autoencoders. Nat Biotechnol 39, 555–560 (2021). https://doi.org/10.1038/s41587-020-00777-4