Fig. 1
From: Relative abundance data can misrepresent heritability of the microbiome
As relative microbial abundances are interdependent, a heritable signal in one microbe can lead to a spurious heritable signal in a second microbe that is not heritable, or mask a genetic signal in a heritable microbe. A As an example we show three host (mouse) genotypes with two microbes, where one microbe is fully heritable (blue, h2 = 1), and one microbe is not heritable (red, h2 = 0). As a consequence, the average absolute abundance of microbe Blue differs among genotypes, while the average abundance of microbe Red is constant. Using the absolute abundances (and with enough host replicates), heritabilities can correctly be estimated. However, as relative abundances are not independent, a host genetic signal in the abundance of the heritable microbe, will also create a host genetic signal in the second microbe, creating variation in relative abundance among genotypes. This leads to an incorrect heritability estimate \({\widehat{\mathrm{\varphi }}}^{2}=0.5\) for both microbes. B When based on relative abundances, properties of both the focal microbe and of the entire community shape the heritability estimates. Here, we vary the average absolute abundance of the focal microbe (\(\mathrm{\alpha }\)) compared to the absolute abundance of the rest of the community (A) (x-axis shows \(\frac{\mathrm{\alpha }}{\mathrm{\alpha }+\mathrm{A}}\)). Black line: focal microbe has a heritability of 0.5; the background community is not heritable (\(\mathrm{A}=1\); \(\mathrm{z}={\left(\frac{1}{6}\right)}^{2}\); \(\upomega =0\); \({\mathrm{V}}_{\mathrm{P}}={\left(\frac{1}{6}\right)}^{2}\); \({\mathrm{V}}_{\mathrm{G}}=0.5{\left(\frac{1}{6}\right)}^{2}\)). Grey line: focal microbe is not heritable, but the rest of the community has an average heritability of 0.5 (\(\mathrm{A}=1\); \(\mathrm{z}={\left(\frac{1}{6}\right)}^{2}\); \(\upomega =0.5{\left(\frac{1}{6}\right)}^{2}\); \({\mathrm{V}}_{\mathrm{P}}={\left(\frac{1}{6}\right)}^{2}\); \({\mathrm{V}}_{\mathrm{G}}=0\)). C Difference in heritability estimates when based on absolute or relative abundances (y axis) when varying \(\mathrm{\alpha }\) compared to A (x axis). When the focal microbe has a low average absolute abundance compared to the total average abundance of the rest of the community (for instance, in the case of many microbial taxa), the difference between \({\mathrm{\varphi }}^{2}\) and h2 becomes smaller. h2 of the focal taxon i is 0.2, and colored lines show varying heritabilities of the background community (\({h}_{\mathrm{community}}^{2}=\frac{\upomega }{\mathrm{z}}\)). \(\mathrm{A}=100\); \(\mathrm{z}={100\left(\frac{1}{6}\right)}^{2}\); \({\mathrm{V}}_{\mathrm{P}}=\mathrm{\alpha }{\left(\frac{1}{6}\right)}^{2}\). Crosses show results when we estimate heritabilities by fitting a mixed effects model on simulated relative abundance data. To this end, we simulated a population of hosts (500 genotypes × 1000 replicates within each genotype), with microbial communities consisting of 100 taxa (more details in Additional file 1: Appendix S2.1–2.3)