1. Fig. 2 Host genetics explains core microbiome composition with heritable microbes serving as hubs within the microbial interaction networks.
Host genetics explains core microbiome composition with heritable microbes serving as hubs within the microbial interaction networks. The core microbiome is associated with animal genetics as (A) the variance in the core microbiome (y axis) was significantly explained by host genetics. CCA was performed between the matrix of the first 30 microbial (OTU table) principal component scores and host genotype principal component scores based on a common SNP. The analysis was accomplished for the largest Holstein farms in this study (x axis). (B) Heritability analysis based on the genetic relatedness matrix (GRM) showed 39 microbes (x axis) significantly correlating with the animal genotype. Heritability estimate—h2 (y axis; bar plots show mean estimate per microbe), and P values were calculated using genetics complex trait analysis (GCTA) software, followed by a multiple testing correction with Benjamini-Hochberg method. Confidence intervals (CIs; 95%) were estimated on the basis of heritability estimates and the GRM with Fast Confidence IntErvals using Stochastic Approximation (FIESTA) software. (C) Heritable microbes are central to the microbial interaction network, as revealed by the higher mean connectivity (y axis) of these microbes compared to the nonheritable ones. The interaction network was built using Sparse InversE Covariance estimation for Ecological Association and Statistical Inference (SpiecEasi). Results are presented as mean number of microbial interactions with SE. Indicated P values, *P < 0.05, **P < 0.005, ***P <
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).