add host preference assay and protocol

assays/HostPreferenceAndInvasivenessIndices/protocols/HostPreferenceAndInvasivenessIndicesProtocol.md

+## Host preference and invasiveness indices
+
+To quantify the strength of the host preference of each bacterial strain individually, we calculated the ratio between the mean relative abundance of a given SynCom member in root samples of their cognate host and its mean relative abundance in root samples of the other plant species. The host preference indices depicted in Fig. 5a were calculated independently for each experiment. To avoid obtaining very high ratios due to small denominator values, strains with mean relative abundances below 0.1% in either of the two hosts were removed from the analysis. Similarly, an invasiveness index was calculated by obtaining the ratio between mean relative abundance of a strain when invading resident communities on roots of their cognate host, compared to the other plant species. The invasiveness index was calculated using samples from the sequential inoculation experiment (experiment L, Fig. 4). The direct comparison between the two indices shown in Fig. 5b,c were calculated using samples from experiment L only, where invasion and competition treatments were performed in parallel. To test whether a SynCom member was significantly more abundant in the roots of their cognate host (that is, significant host preference), we used the non-parametric Wilcoxon test controlling for false-discovery rate with α = 0.05.
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