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Inferring interactions in complex microbial communities from nucleotide sequence data and environmental parameters

Author

Listed:
  • Yu Shang
  • Johannes Sikorski
  • Michael Bonkowski
  • Anna-Maria Fiore-Donno
  • Ellen Kandeler
  • Sven Marhan
  • Runa S Boeddinghaus
  • Emily F Solly
  • Marion Schrumpf
  • Ingo Schöning
  • Tesfaye Wubet
  • Francois Buscot
  • Jörg Overmann

Abstract

Interactions occur between two or more organisms affecting each other. Interactions are decisive for the ecology of the organisms. Without direct experimental evidence the analysis of interactions is difficult. Correlation analyses that are based on co-occurrences are often used to approximate interaction. Here, we present a new mathematical model to estimate the interaction strengths between taxa, based on changes in their relative abundances across environmental gradients.

Suggested Citation

  • Yu Shang & Johannes Sikorski & Michael Bonkowski & Anna-Maria Fiore-Donno & Ellen Kandeler & Sven Marhan & Runa S Boeddinghaus & Emily F Solly & Marion Schrumpf & Ingo Schöning & Tesfaye Wubet & Franc, 2017. "Inferring interactions in complex microbial communities from nucleotide sequence data and environmental parameters," PLOS ONE, Public Library of Science, vol. 12(3), pages 1-24, March.
    • Handle: RePEc:plo:pone00:0173765
    DOI: 10.1371/journal.pone.0173765
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    References listed on IDEAS

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    1. Steven P. Ellis, 2000. "Singularity and outliers in linear regression with application to least squares, least squares linear regression," Metron - International Journal of Statistics, Dipartimento di Statistica, Probabilità e Statistiche Applicate - University of Rome, vol. 0(1-2), pages 121-129.
    2. Zachary D Kurtz & Christian L Müller & Emily R Miraldi & Dan R Littman & Martin J Blaser & Richard A Bonneau, 2015. "Sparse and Compositionally Robust Inference of Microbial Ecological Networks," PLOS Computational Biology, Public Library of Science, vol. 11(5), pages 1-25, May.
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    Cited by:

    1. Anna S. Weiss & Lisa S. Niedermeier & Alexandra von Strempel & Anna G. Burrichter & Diana Ring & Chen Meng & Karin Kleigrewe & Chiara Lincetto & Johannes Hübner & Bärbel Stecher, 2023. "Nutritional and host environments determine community ecology and keystone species in a synthetic gut bacterial community," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    2. Li, Jie & Shen, Xuzhu & Li, YaoTang, 2021. "Modeling the temporal dynamics of gut microbiota from a local community perspective," Ecological Modelling, Elsevier, vol. 460(C).

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