Fig. 1 A phylogenetically cohesive core rumen microbiome was found across farms with highly conserved hierarchical structure and tight association to overall.

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Fig. 1 A phylogenetically cohesive core rumen microbiome was found across farms with highly conserved hierarchical structure and tight association to overall microbiome composition. A phylogenetically cohesive core rumen microbiome was found across farms with highly conserved hierarchical structure and tight association to overall microbiome composition. (A) Core microbes are highly represented within individual animals, as a high fraction of them (>50% of the core microbes) are present in >70% of the individuals. (B) The prokaryotic core (blue) was represented by 10 phyla of the 30 found in the overall microbiome (x axis; ochre), including 11 prokaryotic, 2 fungal, and 1 protozoal orders, detected in >50% of the individuals in each farm. *The core microbiome was significantly enriched in Bacteroidetes (enrichment analysis, Fisher exact test, after Benjamini-Hochberg correction, P < 0.0005). SR1, candidate division sulphur river 1. Core prokaryotes (i) consisted of 454 microbes, mainly from the orders Bacteroidales (tree; green) and Clostridiales (tree; maroon). Core heritable taxa are presented as gray bar plots on the tree. (C) The core microbiome composed of a large fraction of the overall microbiome, ranging between three- and two-thirds of the relative abundance, depending on the farm (x axis). Bar plots represent the mean, and error bars represent the SE of the core relative abundance. (D) Core microbiome composition is highly correlated to noncore microbes, as shown by comparing the interanimal dissimilarity (Bray-Curtis) matrix based on core microbes to that based on noncore microbes. Violin plots for each farm (x axis) show the correlation between the two dissimilarity matrices (core and noncore; Mantel R), where the violin (gray) describes the null model (permuted) Mantel R values, and red points depict the actual R. (E) The core microbiome exhibits a clear hierarchical structure, in terms of microbial abundance, which agrees between farms. (i) A highly consistent core microbiome abundance pattern (ranking) across farms (x axis) was revealed by an abundance-ranked color-coded heatmap, where species-level microbial OTUs are ordered by their mean relative abundance across all animals in the cohort (no further clustering or normalization was performed). Color coding reflects the rank abundance of a given OTU in a given individual. (ii) Heatmap showing the degree of correlation in relative abundance profiles between the farms. Color coding reflects the degree of correlation in relative abundance profiles (Spearman r; all P < 0.001). (F) Phylogenetic distances between the core microbes were smaller, showing that they are closer phylogenetically, but also distinct, compared to the overall microbiome, as it was shown by mean pairwise phylogenetic distance (x axis) calculation between core (blue) and 1000 randomly selected noncore microbes (ochre) from the rumen (y axis; P < 0.001). R. John Wallace et al. Sci Adv 2019;5:eaav8391 Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).