Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Challenges in modeling the human gut microbiome

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Figure 1: The growth simulations for the AGORA and BiGG models.
Figure 2: The blocked reactions and reactions involved in thermodynamically infeasible loops in 100 models.
Figure 3

References

  1. 1

    Magnúsdóttir, S. et al. Nat. Biotechnol. 35, 81–89 (2017).

    Article  Google Scholar 

  2. 2

    Karlsson, F.H. et al. Nat. Commun. 3, 1245 (2012).

    Article  Google Scholar 

  3. 3

    Karlsson, F.H. et al. Nature 498, 99–103 (2013).

    CAS  Article  Google Scholar 

  4. 4

    Qin, J. et al. Nature 490, 55–60 (2012).

    CAS  Article  Google Scholar 

  5. 5

    Forslund, K. et al. Nature 528, 262–266 (2015).

    CAS  Article  Google Scholar 

  6. 6

    Karlsson, F.H., Nookaew, I., Petranovic, D. & Nielsen, J. Trends Biotechnol. 29, 251–258 (2011).

    CAS  Article  Google Scholar 

  7. 7

    Mardinoglu, A. et al. Mol. Syst. Biol. 11, 834 (2015).

    Article  Google Scholar 

  8. 8

    Shoaie, S. et al. Cell Metab. 22, 320–331 (2015).

    CAS  Article  Google Scholar 

  9. 9

    Zomorrodi, A.R. & Maranas, C.D. PLoS Comput. Biol. 8, e1002363 (2012).

    CAS  Article  Google Scholar 

  10. 10

    Harcombe, W.R. et al. Cell Rep. 7, 1104–1115 (2014).

    CAS  Article  Google Scholar 

  11. 11

    King, Z.A. et al. Nucleic Acids Res. 44 D1, D515–D522 (2016).

    Article  Google Scholar 

  12. 12

    Larhlimi, A., David, L., Selbig, J. & Bockmayr, A. BMC Bioinformatics 13, 57 (2012).

    Article  Google Scholar 

  13. 13

    Albenberg, L. et al. Gastroenterology 147, 1055–1063.e8 (2014).

    Article  Google Scholar 

  14. 14

    Espey, M.G. Free Radic. Biol. Med. 55, 130–140 (2013).

    CAS  Article  Google Scholar 

Download references

Acknowledgements

We acknowledge funding from the Novo Nordisk Foundation (NNF10CC1016517) and the Knut and Alice Wallenberg Foundation.

Author information

Affiliations

Authors

Corresponding author

Correspondence to Jens Nielsen.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–11 and Supplementary Tables 1 and 2 (PDF 10901 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Babaei, P., Shoaie, S., Ji, B. et al. Challenges in modeling the human gut microbiome. Nat Biotechnol 36, 682–686 (2018). https://doi.org/10.1038/nbt.4213

Download citation

Further reading

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing