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Chemical-Mediated Microbial Interactions Can Reduce the Effectiveness of Time-Series-Based Inference of Ecological Interaction Networks

Author

Listed:
  • Kenta Suzuki

    (BioResource Research Center, RIKEN, Tsukuba 305-0074, Japan)

  • Masato S. Abe

    (Center for Advanced Intelligence Project, RIKEN, Chuo-ku, Tokyo 103-0027, Japan)

  • Daiki Kumakura

    (Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan)

  • Shinji Nakaoka

    (Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
    Laboratory of Mathematical Biology, Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0819, Japan)

  • Fuki Fujiwara

    (Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113–8657, Japan)

  • Hirokuni Miyamoto

    (Graduate School of Horticulture, Chiba University, Matsudo 271-8501, Japan
    RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
    Sermas Co., Ltd., Ichikawa 272-0015, Japan)

  • Teruno Nakaguma

    (Graduate School of Horticulture, Chiba University, Matsudo 271-8501, Japan
    Sermas Co., Ltd., Ichikawa 272-0015, Japan)

  • Mashiro Okada

    (Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113–8657, Japan)

  • Kengo Sakurai

    (Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113–8657, Japan)

  • Shohei Shimizu

    (Center for Advanced Intelligence Project, RIKEN, Chuo-ku, Tokyo 103-0027, Japan)

  • Hiroyoshi Iwata

    (Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113–8657, Japan)

  • Hiroshi Masuya

    (BioResource Research Center, RIKEN, Tsukuba 305-0074, Japan)

  • Naoto Nihei

    (Faculty of Food and Agricultural Sciences, Fukushima University, Fukushima 960-1296, Japan)

  • Yasunori Ichihashi

    (BioResource Research Center, RIKEN, Tsukuba 305-0074, Japan)

Abstract

Network-based assessments are important for disentangling complex microbial and microbial–host interactions and can provide the basis for microbial engineering. There is a growing recognition that chemical-mediated interactions are important for the coexistence of microbial species. However, so far, the methods used to infer microbial interactions have been validated with models assuming direct species-species interactions, such as generalized Lotka–Volterra models. Therefore, it is unclear how effective existing approaches are in detecting chemical-mediated interactions. In this paper, we used time series of simulated microbial dynamics to benchmark five major/state-of-the-art methods. We found that only two methods (CCM and LIMITS) were capable of detecting interactions. While LIMITS performed better than CCM, it was less robust to the presence of chemical-mediated interactions, and the presence of trophic competition was essential for the interactions to be detectable. We show that the existence of chemical-mediated interactions among microbial species poses a new challenge to overcome for the development of a network-based understanding of microbiomes and their interactions with hosts and the environment.

Suggested Citation

  • Kenta Suzuki & Masato S. Abe & Daiki Kumakura & Shinji Nakaoka & Fuki Fujiwara & Hirokuni Miyamoto & Teruno Nakaguma & Mashiro Okada & Kengo Sakurai & Shohei Shimizu & Hiroyoshi Iwata & Hiroshi Masuya, 2022. "Chemical-Mediated Microbial Interactions Can Reduce the Effectiveness of Time-Series-Based Inference of Ecological Interaction Networks," IJERPH, MDPI, vol. 19(3), pages 1-14, January.
  • Handle: RePEc:gam:jijerp:v:19:y:2022:i:3:p:1228-:d:731021
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    References listed on IDEAS

    as
    1. Charles K Fisher & Pankaj Mehta, 2014. "Identifying Keystone Species in the Human Gut Microbiome from Metagenomic Timeseries Using Sparse Linear Regression," PLOS ONE, Public Library of Science, vol. 9(7), pages 1-10, July.
    2. Lori Niehaus & Ian Boland & Minghao Liu & Kevin Chen & David Fu & Catherine Henckel & Kaitlin Chaung & Suyen Espinoza Miranda & Samantha Dyckman & Matthew Crum & Sandra Dedrick & Wenying Shou & Babak , 2019. "Microbial coexistence through chemical-mediated interactions," Nature Communications, Nature, vol. 10(1), pages 1-12, December.
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