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. 2019 Aug 23;20:172. doi: 10.1186/s13059-019-1786-0

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© The Author(s). 2019

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Fig. 5 — Proposed host-microbial interactions and their regulatory mechanisms in the developing rumen. Early rumen microbiota alters the rumen development via direct and indirect (miRNAs) interactions with the transcriptome. Microbial-derived VFAs are associated with genes involved in ruminal tissue metabolism (M10 gene module), non-coding RNA processing (M2 gene module), and epigenetic modifications (M18 gene module) as well as miRNAs regulating epithelial morphogenesis (R7 miRNA module). miRNAs regulate the host transcriptome either in response to microbial metabolites/rumen microbiota or directly during the early rumen development