diff --git a/.gitattributes b/.gitattributes
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diff --git a/LICENSE b/LICENSE
new file mode 100644
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+++ b/LICENSE
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\ No newline at end of file
diff --git a/README.md b/README.md
index 4b4bd9340836ad89c39cb4ef0a2ff0ea84e96c00..a163e51a1e4c5d69b4d3ea99fa66f17c90ddf9ee 100644
--- a/README.md
+++ b/README.md
@@ -1,19 +1,25 @@
-# Abstract for Wippel (2021)
+# Host preference and invasiveness of commensal bacteria in the *Lotus* and *Arabidopsis* root microbiota
+
+## Abstract for Wippel (2021)
Roots of different plant species are colonized by bacterial communities, that are distinct even when hosts share the same habitat. It remains unclear to what extent the host actively selects these communities and whether commensals are adapted to a specific plant species. To address this question, we assembled a sequence-indexed bacterial culture collection from roots and nodules of *Lotus japonicus* that contains representatives of most species previously identified using metagenomics. We analysed taxonomically paired synthetic communities from *L. japonicus* and *Arabidopsis thaliana* in a multi-species gnotobiotic system and detected signatures of host preference among commensal bacteria in a community context, but not in mono-associations. Sequential inoculation experiments revealed priority effects during root microbiota assembly, where established communities are resilient to invasion by latecomers, and that host preference of commensal bacteria confers a competitive advantage in their cognate host. Our findings show that host preference in commensal bacteria from diverse taxonomic groups is associated with their invasiveness into standing root-associated communities.
-
+<img src=./_publication/Wippel_2021_cropped.png width=60%>
## Publication Details
- **DOI**: [10.1038/s41564-021-00941-9](https://doi.org/10.1038/s41564-021-00941-9)
-- **Title**: Host preference and invasiveness of commensal bacteria in the Lotus and Arabidopsis root microbiota
+- **Title**: Host preference and invasiveness of commensal bacteria in the *Lotus* and *Arabidopsis* root microbiota
- **Journal**: Nature Microbiology
- **Published on**: 2021-07-26
## Data Availability
-<Data availability details (if provided by the article)>
+The strains of the *Lj*-SPHERE collection will be deposited at and will be available on request from the Leibniz Institute DSMZ in Braunschweig, Germany. Raw 16S rRNA amplicon reads have been deposited in the European Nucleotide Archive under the accession number PRJEB37695. Similarly, sequencing reads and genome assemblies of the *Lj*-SPHERE core collection have been uploaded to the same database with the accession number PRJEB37696. Source data are provided with this paper.
+
+## Code availability
+
+The scripts used for the computational analyses described in this study are available at http://www.github.com/garridoo/ljsphere, to ensure replicability and reproducibility of these results.
## License
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+# Extended Data
+
+### Extended Data Fig. 1: Flow chart of experimental procedures.
+**a**, Overview of experiments and type of analyses performed on root, rhizosphere, and soil samples, or millifluidic droplets. **b**, Culture collection establishment of *Lotus japonicus* root and nodule bacterial isolates. Image created with BioRender.com.
+
+https://www.nature.com/articles/s41564-021-00941-9/figures/7
+
+### Extended Data Fig. 2 Culture-independent diversity analysis of root-associated bacterial communities from *Lotus* and *Arabidopsis*.
+Rank abundance plot of bacterial communities from *Lotus* or *Arabidopsis* roots, aggregated to the class level, including all families with a mean accumulated relative abundance of > 0.1% on either host. Statistical differences were assessed using a two-sided, non-parametric Mann–Whitney test. Asterisks represent significant values after multiple testing correction using the Benjamini–Hochberg method (*P* < 0.05).
+
+https://www.nature.com/articles/s41564-021-00941-9/figures/8
+
+### Extended Data Fig. 3 Functional overlap of *Lotus* and *Arabidopsis* culture collection genomes.
+PCoA of functional distances of genomes from bacterial isolates of the *Lotus* (*Lj*-SPHERE; n = 294) and the *Arabidopsis* (*At*-SPHERE; n = 194) culture collections.
+
+https://www.nature.com/articles/s41564-021-00941-9/figures/9
+
+### Extended Data Fig. 4 Host-species specific bacterial root communities and commensal host preference is confirmed using independent mixed communities.
+**a** and **c**, Constrained PCoA of Bray-Curtis dissimilarity (constrained by all biological factors and conditioned by all technical variables) of soil, rhizosphere, and root samples from *L. japonicus* wild-type Gifu, *nfr5* mutant, and *A. thaliana* wild type Col-0 plants co-cultivated with the mixed community *LjAt*-SC1 (**a**, experiment C, n = 155, variance explained 53.8%, *P* = 0.001), from Gifu and Col-0 co-cultivated with *LjAt*-SC4 (**b**, experiment D, n = 87, variance explained 60%, *P* = 0.001), or from Gifu and Col-0 co-cultivated with *LjAt*-SC5 (**b**, experiment M, n = 100, variance explained 67%, *P* = 0.001). **d**, **e** and **f**, Aggregated RA of the 16 *Lj*-derived and the 16 *At*-derived strains in the roots of *Lotus* and *Arabidopsis* plants inoculated with *LjAt*-SC1 (**d**; n = 68), *LjAt*-SC4 (**e**; n = 34), or *LjAt*-SC5 (**f**; n = 40). n refers to biologically independent samples.
+
+https://www.nature.com/articles/s41564-021-00941-9/figures/10
+
+### Extended Data Fig. 5 Host preference is retained after in silico removal of individual bacterial families.
+Aggregated relative abundance of *Lotus*- (**a**, n = 20) and *Arabidopsis*-derived (**b**, n = 16) strains in roots from plants inoculated with the mixed community *LjAt*-SC3 (experiment L). Host preference was assessed using a Mann-Whitney non-parametric test after *in silico* removal of each family. The x-axis labels indicate each depleted family. n refers to biologically independent samples.
+
+https://www.nature.com/articles/s41564-021-00941-9/figures/11
+
+### Extended Data Fig. 6 Bacterial abundance in mono-association with host plants.
+Bacterial abundances of commensal bacteria (strain IDs indicated at x-axis) colonizing Col-0, Gifu, and *nfr5* roots, assessed by counting of colony forming units (CFUs) after extraction from root tissue. Plants were grown for two weeks on agar plates in mono-association with the indicated Lj-SPHERE (**a**) and At-SPHERE (**b**) strains (exp. E). n = 6 (3 biologically independent samples × 2 technical replicates). Statistical differences were assessed using a two-sided, non-parametric Mann-Whitney test. Asterisks represent significant values after multiple testing correction using the Benjamini–Hochberg method (*P* < 0.05).
+
+https://www.nature.com/articles/s41564-021-00941-9/figures/12
+
+### Extended Data Fig. 7 Plant performance in mono-associations.
+Shoot fresh weight of Gifu (**a**) and Col-0 (**b**) plants grown for two weeks on agar plates in mono-association with the indicated *Lj*-SPHERE and *At*-SPHERE strains (exp. E). n = 30 (3 biologically independent samples × 10 technical replicates).
+
+https://www.nature.com/articles/s41564-021-00941-9/figures/13
+
+### Extended Data Fig. 8 Sister species of *L. japonicus* and *A. thaliana* establish distinct bacterial root communities.
+Constrained PCoA of Bray-Curtis dissimilarity (constrained by all biological factors and conditioned by all technical variables) of root samples from *L. japonicus* wild type Gifu and *L. corniculatus* (**a**; n = 87; variance explained 58.7%, *P* = 0.001), and or root samples from *A. thaliana* wild type Col-0 and *A. lyrata* MN47 (**b**; n = 86; variance explained 65%, *P* = 0.001), inoculated and grown with the mixed community *LjAt*-SC3, and of the corresponding rhizosphere and bulk soil communities (exp. F).
+
+https://www.nature.com/articles/s41564-021-00941-9/figures/14
+
+### Extended Data Fig. 9 Tested plant immune receptors and signaling pathways do not affect host preference of commensals.
+**a**, Constrained PCoA of Bray-Curtis dissimilarity (constrained by all biological factors and conditioned by all technical variables; n = 98; variance explained 24.6%, *P* = 0.001) of root samples from *L. japonicus* wild type Gifu, *Ljfls2* mutant, *A. thaliana* wild type Col-0, *Atfls2* mutant, and *Atbbc* mutant inoculated and grown with the mixed SynCom *LjAt*-SC1 (exp. G), and of the corresponding bacterial input communities. **b**, Aggregated relative abundance of the 16 *Lj*-derived and the 16 *At*-derived strains in the roots of *Lotus* and *Arabidopsis* plants. n = 21 for Gifu, n = 16 for Col-0, n = 20 for *Ljfls2* and *Atfls2*, n = 18 for *Atbbc*. **c**, Constrained PCoA of Bray-Curtis dissimilarity (constrained by all biological factors and conditioned by all technical variables; n = 64; variance explained 42.2%, *P* = 0.001) of soil and root samples from Gifu, Col-0, and *Atdeps* mutant inoculated and grown with the mixed SynCom *LjAt*-SC3 (exp. H). **d**, Aggregated relative abundance of the 16 *Lj*-derived and the 16 *At*-derived strains in the roots of *Lotus* and *Arabidopsis* plants. n = 14 for Gifu, n = 20 for Col-0 and *Atdeps*. n refers to biologically independent samples.
+
+https://www.nature.com/articles/s41564-021-00941-9/figures/15
+
+### Extended Data Fig. 10 Effect of secreted indole glucosinolates on host preference of commensals.
+**a**, Constrained PCoA of Bray-Curtis dissimilarity (constrained by all biological factors and conditioned by all technical variables; n = 50; variance explained 47.2%, *P* = 0.001) of soil and root samples from *L. japonicus* wild type Gifu, *A. thaliana* wild type Col-0, and *Arabidopsis cyp79b2 cyb79b3* mutant inoculated and grown with the mixed SynCom *LjAt*-SC3 (exp. H). **b**, Aggregated relative abundance of the 16 *Lj*-derived and the 16 *At*-derived strains in the roots of *Lotus* and *Arabidopsis* plants. n = 20 for Col-0, n = 14 for Gifu, n = 6 for *Atcyp79b2b3*. n refers to biologically independent samples.
+
+https://www.nature.com/articles/s41564-021-00941-9/figures/16
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+# Source Data
+
+### Source Data Fig. 1
+Statistical source data.
+
+https://static-content.springer.com/esm/art%3A10.1038%2Fs41564-021-00941-9/MediaObjects/41564_2021_941_MOESM6_ESM.zip
+
+### Source Data Fig. 2
+Statistical source data.
+
+https://static-content.springer.com/esm/art%3A10.1038%2Fs41564-021-00941-9/MediaObjects/41564_2021_941_MOESM7_ESM.zip
+
+### Source Data Fig. 3
+Statistical source data.
+
+https://static-content.springer.com/esm/art%3A10.1038%2Fs41564-021-00941-9/MediaObjects/41564_2021_941_MOESM8_ESM.zip
+
+### Source Data Fig. 4
+Statistical source data.
+
+https://static-content.springer.com/esm/art%3A10.1038%2Fs41564-021-00941-9/MediaObjects/41564_2021_941_MOESM9_ESM.zip
+
+### Source Data Fig. 5
+Statistical source data.
+
+https://static-content.springer.com/esm/art%3A10.1038%2Fs41564-021-00941-9/MediaObjects/41564_2021_941_MOESM10_ESM.zip
+
+### Source Data Fig. 6
+Statistical source data.
+
+https://static-content.springer.com/esm/art%3A10.1038%2Fs41564-021-00941-9/MediaObjects/41564_2021_941_MOESM11_ESM.zip
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+# Supplementary Information
+
+### Supplementary Information
+Supplementary Note, Figs. 1–3 and Tables 1 and 2.
+
+https://static-content.springer.com/esm/art%3A10.1038%2Fs41564-021-00941-9/MediaObjects/41564_2021_941_MOESM1_ESM.pdf
+
+### Reporting Summary
+
+https://static-content.springer.com/esm/art%3A10.1038%2Fs41564-021-00941-9/MediaObjects/41564_2021_941_MOESM2_ESM.pdf
+
+### Supplementary Data 1
+Data and metadata of *Lj*- and *At*-IRLs.
+
+https://static-content.springer.com/esm/art%3A10.1038%2Fs41564-021-00941-9/MediaObjects/41564_2021_941_MOESM3_ESM.zip
+
+### Supplementary Data 2
+Metadata of the *Lj*- and *At*-SPHERE core culture collection.
+
+https://static-content.springer.com/esm/art%3A10.1038%2Fs41564-021-00941-9/MediaObjects/41564_2021_941_MOESM4_ESM.zip
+
+### Supplementary Data 3
+Data and metadata of *LjAt* SynCom experiments.
+
+https://static-content.springer.com/esm/art%3A10.1038%2Fs41564-021-00941-9/MediaObjects/41564_2021_941_MOESM5_ESM.zip
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