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Microbiome niche modification drives diurnal rumen community assembly, overpowering individual variability and diet effects

The ISME Journalvolume 12pages24462457 (2018) | Download Citation


Niche modification is a process whereby the activity of organisms modifies their local environment creating new niches for other organisms. This process can have a substantial role in community assembly of gut microbial ecosystems due to their vast and complex metabolic activities. We studied the postprandial diurnal community oscillatory patterns of the rumen microbiome and showed that metabolites produced by the rumen microbiome condition its environment and lead to dramatic diurnal changes in community composition and function. After feeding, microbiome composition undergoes considerable change in its phylogenetic breadth manifested as a significant 3–5-fold change in the relative abundance of methanogenic archaea and main bacterial taxa such as Prevotella, in a manner that was independent of individual host variation and diet. These changes in community composition were accompanied by changes in pH and methane partial pressure, suggesting a strong functional connection. Notably, cross-incubation experiments combining metabolites and organisms from different diurnal time points showed that the metabolites released by microbes are sufficient to reproduce changes in community function comparable to those observed in vivo. These findings highlight microbiome niche modification as a deterministic process that drives diurnal community assembly via environmental filtering.

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The research described here was supported by grants from Israel Science Foundation (1313/13) and by the European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreement 640384).

Author information


  1. Department of Life Sciences & the National Institute for Biotechnology in the Negev, 7 Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel

    • Yoav Shaani
    • , Tamar Zehavi
    • , Stav Eyal
    •  & Itzhak Mizrahi
  2. Department of Cattle Husbandry, Extension Service, Ministry of Agriculture, PO Box 28, Bet-Dagan, 50250, Israel

    • Yoav Shaani
  3. Department of Ruminant Science, Institute of Animal Science, Agricultural Research Organization, PO Box 6, Bet-Dagan, 50250, Israel

    • Joshuah Miron


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The authors declare that they have no conflict of interest.

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Correspondence to Itzhak Mizrahi.

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