Improved high-molecular-weight DNA extraction, nanopore sequencing and metagenomic assembly from the human gut microbiome

Dylan G. Maghini, Eli L. Moss, Summer E. Vance, Ami S. Bhatt

Published: 2020-12-03 DOI: 10.1038/s41596-020-00424-x

nanopore sequencing

long-read sequencing

DNA extraction

metagenomic assembly

human gut microbiome

AI 解读

Supplementary information

Supplementary Information

Supplementary Fig. 1 and Supplementary Notes 1 and 2.

Reporting Summary

Supplementary Table 1

Summary of HMW DNA extraction methods

Supplementary Table 2

Lytic enzyme activity

Efficient and safe single-cell cloning of human pluripotent stem cells using the CEPT cocktail

Profiling native pulmonary basement membrane stiffness using atomic force microscopy

Genetic circuit design automation with Cello 2.0

Synthesis of siRNA nanoparticles to silence plaque-destabilizing gene in atherosclerotic lesional macrophages

Scalable dual-omics profiling with single-nucleus chromatin accessibility and mRNA expression sequencing 2 (SNARE-seq2)

A practical guide to scanning light-field microscopy with digital adaptive optics

Effective high-throughput isolation of fully human antibodies targeting infectious pathogens

Improved sampling and DNA extraction procedures for microbiome analysis in food-processing environments

MOF-derived nanoporous carbons with diverse tunable nanoarchitectures

Tutorial: a statistical genetics guide to identifying HLA alleles driving complex disease

查看全部

Sections

Figures

References

Supplementary information

Pasolli, E. et al. Extensive unexplored human microbiome diversity revealed by over 150,000 genomes from metagenomes spanning age, geography, and lifestyle. Cell 176, 649–662.e20 (2019).
Almeida, A. et al. A new genomic blueprint of the human gut microbiota. Nature 568, 499–504 (2019).
Nayfach, S., Shi, Z. J., Seshadri, R., Pollard, K. S. & Kyrpides, N. C. New insights from uncultivated genomes of the global human gut microbiome. Nature 568, 505–510 (2019).
Almeida, A. et al. A unified sequence catalogue of over 280,000 genomes obtained from the human gut microbiome. Nat. Biotechnol. Forthcoming (2020).
Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25, 1043–1055 (2015).
Bowers, R. M. et al. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat. Biotechnol. 35, 725–731 (2017).
Vandecraen, J., Chandler, M., Aertsen, A. & Van Houdt, R. The impact of insertion sequences on bacterial genome plasticity and adaptability. Crit. Rev. Microbiol. 43, 709–730 (2017).
Darmon, E. & Leach, D. R. F. Bacterial genome instability. Microbiol. Mol. Biol. Rev. 78, 1–39 (2014).
Yuan, S., Cohen, D. B., Ravel, J., Abdo, Z. & Forney, L. J. Evaluation of methods for the extraction and purification of DNA from the human microbiome. PLoS ONE 7, e33865 (2012).
Moss, E. L., Maghini, D. G. & Bhatt, A. S. Complete, closed bacterial genomes from microbiomes using nanopore sequencing. Nat. Biotechnol. 38, 701–707 (2020).
Ribado, J. V. The impact of environmental exposures on the human and mouse gut microbiome. Dissertation, Stanford University, 2019).
Rang, F. J., Kloosterman, W. P. & de Ridder, J. From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy. Genome Biol. 19, 90 (2018).
Rhoads, A. & Au, K. F. PacBio sequencing and its applications. Genomics Proteomics Bioinformatics 13, 278–289 (2015).
Tamburini, F. B. et al. Short- and long-read metagenomics of South African gut microbiomes reveal a transitional composition and novel taxa. Preprint at http://www.biorxiv.org/content/10.1101/2020.05.18.099820v2.
Wenger, A. M. et al. Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome. Nat. Biotechnol. 37, 1155–1162 (2019).
Wick, R. R., Judd, L. M. & Holt, K. E. Performance of neural network basecalling tools for Oxford Nanopore sequencing. Genome Biol. 20, 129 (2019).
Gorzelak, M. A. et al. Methods for improving human gut microbiome data by reducing variability through sample processing and storage of stool. PLoS One 10, e0134802 (2015).
Flores, R. et al. Collection media and delayed freezing effects on microbial composition of human stool. Microbiome 3, 33 (2015).
Koren, S. et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 27, 722–736 (2017).
Lin, Y. et al. Assembly of long error-prone reads using de Bruijn graphs. Proc. Natl Acad. Sci. USA 113, E8396–E8405 (2016).
Li, H. Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences. Bioinformatics 32, 2103–2110 (2016).
Ruan, J. & Li, H. Fast and accurate long-read assembly with wtdbg2. Nat. Methods 17, 155–158 (2019).
Antipov, D., Korobeynikov, A., McLean, J. S. & Pevzner, P. A. hybridSPAdes: an algorithm for hybrid assembly of short and long reads. Bioinformatics 32, 1009–1015 (2016).
Bertrand, D. et al. Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and elements in human microbiomes. Nat. Biotechnol. 37, 937–944 (2019).
Vaser, R., Sović, I., Nagarajan, N. & Šikić, M. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res. 27, 737–746 (2017).
Walker, B. J. et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE 9, e112963 (2014).
Delcher, A. L., Salzberg, S. L. & Phillippy, A. M. Using MUMmer to identify similar regions in large sequence sets. Curr. Protoc. Bioinformatics Chapter 10, Unit 10.3 (2003).
Köster, J. & Rahmann, S. Snakemake—a scalable bioinformatics workflow engine. Bioinformatics 28, 2520–2522 (2012).
Kurtzer, G. M., Sochat, V. & Bauer, M. W. Singularity: scientific containers for mobility of compute. PLoS ONE 12, e0177459 (2017).
Kang, D. et al. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ 7, e7359 (2019).
Sieber, C. M. K. et al. Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy. Nat. Microbiol. 3, 836–843 (2018).