Skip to main content
SpringerLink
Log in
Book cover

Hi-C Data Analysis pp 163–181Cite as

Metagenomes Binning Using Proximity-Ligation Data

  • Protocol
  • First Online:

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2301))

Abstract

Microbial communities are key components of all ecosystems, but characterization of their complete genomic structure remains challenging. Typical analysis tends to elude the complexity of the mixes in terms of species, strains, as well as extrachromosomal DNA molecules. Recently, approaches have been developed that bins DNA contigs into individual genomes and episomes according to their 3D contact frequencies. Those contacts are quantified by chromosome conformation capture experiments (3C, Hi-C), also known as proximity-ligation approaches, applied to metagenomics samples. Here, we present a simple computational pipeline that allows to recover high-quality Metagenomics Assemble Genomes (MAGs) starting from metagenomic 3C or Hi-C datasets and a metagenome assembly.

This is a preview of subscription content, log in via an institution.

Protocol
USD   49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   109.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   139.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Springer Nature is developing a new tool to find and evaluate Protocols. Learn more

References

  1. Bork P, Bowler C, de Vargas C, Gorsky G, Karsenti E, Wincker P (2015) Tara oceans studies plankton at planetary scale. Science 348:873–873

    Article  CAS  Google Scholar 

  2. Almeida A, Mitchell AL, Boland M, Forster SC, Gloor GB, Tarkowska A, Lawley TD, Finn RD (2019) A new genomic blueprint of the human gut microbiota. Nature 568:499

    Article  CAS  Google Scholar 

  3. Philippot L, Raaijmakers JM, Lemanceau P, van der Putten WH (2013) Going back to the roots: the microbial ecology of the rhizosphere. Nat Rev Microbiol 11:789–799

    Article  CAS  Google Scholar 

  4. Parks DH, Rinke C, Chuvochina M, Chaumeil P-A, Woodcroft BJ, Evans PN, Hugenholtz P, Tyson GW (2017) Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nat Microbiol 2:1533

    Article  CAS  Google Scholar 

  5. Quince C, Walker AW, Simpson JT, Loman NJ, Segata N (2017) Shotgun metagenomics, from sampling to analysis. Nat Biotechnol 35:833–844

    Article  CAS  Google Scholar 

  6. Olson ND, Treangen TJ, Hill CM, Cepeda-Espinoza V, Ghurye J, Koren S, Pop M (2019) Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes. Brief Bioinform 20(4):1140–1150

    Article  CAS  Google Scholar 

  7. Frank JA, Pan Y, Tooming-Klunderud A, Eijsink VGH, McHardy AC, Nederbragt AJ, Pope PB (2016) Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data. Sci Rep 6:25373

    Article  CAS  Google Scholar 

  8. Beaulaurier J, Zhu S, Deikus G, Mogno I, Zhang X-S, Davis-Richardson A, Canepa R, Triplett EW, Faith JJ, Sebra R et al (2018) Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation. Nat Biotechnol 36:61–69

    Article  CAS  Google Scholar 

  9. Alneberg J, Bjarnason BS, de Bruijn I, Schirmer M, Quick J, Ijaz UZ, Lahti L, Loman NJ, Andersson AF, Quince C (2014) Binning metagenomic contigs by coverage and composition. Nat Methods 11:1144–1146

    Article  CAS  Google Scholar 

  10. Marbouty M, Cournac A, Flot J-F, Marie-Nelly H, Mozziconacci J, Koszul R (2014) Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms. elife 3:e03318

    Article  Google Scholar 

  11. Beitel CW, Froenicke L, Lang JM, Korf IF, Michelmore RW, Eisen JA, Darling AE (2014) Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products. PeerJ 2:e415

    Article  Google Scholar 

  12. Burton JN, Liachko I, Dunham MJ, Shendure J (2014) Species-level deconvolution of metagenome assemblies with Hi-C–based contact probability maps. G3 (Bethesda) 4:1339–1346. https://doi.org/10.1534/g3.114.011825

    Article  Google Scholar 

  13. Džunková M, Low SJ, Daly JN, Deng L, Rinke C, Hugenholtz P (2019) Defining the human gut host–phage network through single-cell viral tagging. Nat Microbiol 4:2192–2203

    Article  Google Scholar 

  14. Alneberg J, Karlsson CMG, Divne A-M, Bergin C, Homa F, Lindh MV, Hugerth LW, Ettema TJG, Bertilsson S, Andersson AF et al (2018) Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes. Microbiome 6:173

    Article  Google Scholar 

  15. Dekker J, Rippe K, Dekker M, Kleckner N (2002) Capturing chromosome conformation. Science 295:1306–1311

    Article  CAS  Google Scholar 

  16. Foutel-Rodier T, Thierry A, Koszul R, Marbouty M (2018) Generation of a metagenomics proximity ligation 3C library of a mammalian gut microbiota. Meth Enzymol 612:183–195

    Article  CAS  Google Scholar 

  17. Flot J-F, Marie-Nelly H, Koszul R (2015) Contact genomics: scaffolding and phasing (meta)genomes using chromosome 3D physical signatures. FEBS Lett 589(20 Pt A):2966–2974

    Article  CAS  Google Scholar 

  18. Marie-Nelly H, Marbouty M, Cournac A, Liti G, Fischer G, Zimmer C, Koszul R (2014) Filling annotation gaps in yeast genomes using genome-wide contact maps. Bioinformatics 30:2105–2113

    Article  CAS  Google Scholar 

  19. Marbouty M, Koszul R (2015) Metagenome analysis exploiting high-throughput chromosome conformation capture (3C) data. Trends Genet 31:673–682

    Article  CAS  Google Scholar 

  20. Marbouty M, Baudry L, Cournac A, Koszul R (2017) Scaffolding bacterial genomes and probing host-virus interactions in gut microbiome by proximity ligation (chromosome capture) assay. Sci Adv 3:e1602105

    Article  Google Scholar 

  21. Stewart RD, Auffret MD, Warr A, Wiser AH, Press MO, Langford KW, Liachko I, Snelling TJ, Dewhurst RJ, Walker AW et al (2018) Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen. Nat Commun 9:870

    Article  Google Scholar 

  22. Baudry L, Foutel-Rodier T, Thierry A, Koszul R, Marbouty M (2019) MetaTOR: a computational pipeline to recover high-quality metagenomic bins from mammalian gut proximity-ligation (meta3C) libraries. Front Genet 10:753. https://www.frontiersin.org/articles/10.3389/fgene.2019.00753/full. Accessed 15 June 2020

    Article  CAS  Google Scholar 

  23. Press MO, Wiser AH, Kronenberg ZN, Langford KW, Shakya M, Lo CC, Mueller KA, Sullivan ST, Chain PSG, Liachko I (2017) Hi-C deconvolution of a human gut microbiome yields high-quality draft genomes and reveals plasmid-genome interactions. bioRxiv, 198713

    Google Scholar 

  24. Stalder T, Press MO, Sullivan S, Liachko I, Top EM (2019) Linking the resistome and plasmidome to the microbiome. ISME J 13:2437–2446

    Article  Google Scholar 

  25. Marbouty M, Baudry L, Cournac A, Koszul R (2017) Scaffolding bacterial genomes and probing host-virus interactions in gut microbiome by proximity ligation (chromosome capture) assay. Sci Adv 3:e1602105. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5315449/. Accessed 21 Mar 2018

    Article  Google Scholar 

  26. Marbouty M, Thierry A, Millot G, Koszul R (in press) MetaHiC phage-bacteria infection network reveals active cycling phages of the healthy human gut. eLife. https://doi.org/10.7554/eLife.60608

  27. Baudry L, Foutel-Rodier T, Thierry A, Koszul R, Marbouty M (2019) MetaTOR: a computational pipeline to recover high-quality metagenomic bins from mammalian gut proximity-ligation (meta3C) libraries. Front Genet 10:753. https://www.frontiersin.org/articles/10.3389/fgene.2019.00753/full. Accessed 29 Aug 2019

    Article  CAS  Google Scholar 

  28. DeMaere MZ, Darling AE (2019) bin3C: exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes. Genome Biol 20:46

    Article  Google Scholar 

  29. Yaffe E, Relman DA (2020) Tracking microbial evolution in the human gut using Hi-C reveals extensive horizontal gene transfer, persistence and adaptation. Nat Microbiol 5(2):343–353

    Article  CAS  Google Scholar 

  30. DeMaere MZ, Darling AE (2016) Deconvoluting simulated metagenomes: the performance of hard- and soft- clustering algorithms applied to metagenomic chromosome conformation capture (3C). PeerJ 4:e2676

    Article  Google Scholar 

  31. Li D, Liu C-M, Luo R, Sadakane K, Lam T-W (2015) MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31:1674–1676

    Article  CAS  Google Scholar 

  32. Nurk S, Meleshko D, Korobeynikov A, Pevzner PA (2017) metaSPAdes: a new versatile metagenomic assembler. Genome Res, gr.213959.116

    Google Scholar 

  33. Kang DD, Froula J, Egan R, Wang Z (2015) MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ 3:e1165

    Article  Google Scholar 

  34. Newman MEJ (2006) Modularity and community structure in networks. Proc Natl Acad Sci U S A 103:8577–8582

    Article  CAS  Google Scholar 

  35. Blondel VD, Guillaume J-L, Lambiotte R, Lefebvre E (2008) Fast unfolding of communities in large networks. J Stat Mech 2008:P10008

    Article  Google Scholar 

  36. Fortunato S, Barthélemy M (2007) Resolution limit in community detection. PNAS 104:36–41

    Article  CAS  Google Scholar 

  37. Marie-Nelly H, Marbouty M, Cournac A, Flot J-F, Liti G, Parodi DP, Syan S, Guillén N, Margeot A, Zimmer C et al (2014) High-quality genome (re)assembly using chromosomal contact data. Nat Commun 5:5695

    Article  CAS  Google Scholar 

  38. Baudry L, Guiglielmoni N, Marie-Nelly H, Cormier A, Marbouty M, Avia K, Mie YL, Godfroy O, Sterck L, Cock JM et al (2020) instaGRAAL: chromosome-level quality scaffolding of genomes using a proximity ligation-based scaffolder. Genome Biol 21:148

    Article  CAS  Google Scholar 

  39. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW (2015) CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25:1043–1055

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This research was supported by funding to R.K. from the European Research Council under the Horizon 2020 Program (ERC grant agreement 771813) and Agence Nationale pour la Recherche JPI-EC-AMR STARCS (ANR-16-JPEC-0003-05).

Author information

Authors and Affiliations

  1. Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS, Paris, France

    Martial Marbouty & Romain Koszul

Authors
  1. Martial Marbouty
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Romain Koszul
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Martial Marbouty or Romain Koszul .

Editor information

Editors and Affiliations

  1. Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy

    Silvio Bicciato

  2. IFOM, The FIRC Institute of Molecular Oncology, Milan, Italy

    Francesco Ferrari

Rights and permissions

Reprints and permissions

Copyright information

© 2022 Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Marbouty, M., Koszul, R. (2022). Metagenomes Binning Using Proximity-Ligation Data. In: Bicciato, S., Ferrari, F. (eds) Hi-C Data Analysis. Methods in Molecular Biology, vol 2301. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1390-0_8

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-1390-0_8

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1389-4

  • Online ISBN: 978-1-0716-1390-0

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation