A conserved genetic basis for commensal-host specificity through live imaging of colonization dynamics
Data files
Oct 10, 2024 version files 2.34 MB
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aSec-phylogeny-based-on-the-core-genes-aln-gb.fasta
33.02 KB
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aSec-phylogeny-based-on-the-core-genes-MappingFile.txt
1.78 KB
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aSec-phylogeny-based-on-the-core-genes-rooted.tree
1.03 KB
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aSecTree1-rooted.tree
326 B
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aSecTree1.fasta
11 KB
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aSecTree2-rooted.tree
127 B
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aSecTree2.fasta
4.59 KB
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aSecTree3-rooted.tree
65 B
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aSecTree3.fasta
2.75 KB
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aSecTree4-rooted.tree
155 B
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aSecTree4.fasta
5.50 KB
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Cluster1-aBSREL.json
498.64 KB
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Cluster1-pal2nal.fasta
12.53 KB
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Cluster2-aBSREL.json
268.92 KB
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Cluster2-pal2nal.fasta
6.67 KB
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Cluster3-aBSREL.json
332.16 KB
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Cluster3-pal2nal.fasta
7.04 KB
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Fig3-SpeciesTree-36Org-rooted.tree
2.29 KB
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Fig3-SpeciesTree-36Org.fasta
589.85 KB
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Phylogeny_of_colonization_island-containing_strains-MappingFile.txt
14.89 KB
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Phylogeny_of_colonization_island-containing_strains.fasta
100.10 KB
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Phylogeny_of_colonization_island-containing_strains.tree
8.60 KB
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README.md
2 KB
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SpeciesTree1-rooted.tree
792 B
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SpeciesTree1.fasta
199.92 KB
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SpeciesTree2-rooted.tree
288 B
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SpeciesTree2.fasta
83.27 KB
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SpeciesTree3-rooted.tree
165 B
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SpeciesTree3.fasta
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SpeciesTree4-rooted.tree
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SpeciesTree4.fasta
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Abstract
Animals throughout the metazoa selectively acquire specific symbiotic gut bacteria from their environment that aid host fitness. Current models of colonization suggest these bacteria use weakly specific receptors to stick to host tissues and that colonization results when they stick in a region of the host gut that overlaps with their nutritional niche. An alternative model is that unique receptor-ligand binding interactions provide specificity for target niches. Here we use live imaging of individual symbiotic bacterial cells colonizing the gut of living Drosophila melanogaster to show that Lactiplantibacillus plantarum specifically recognizes a distinct physical niche in the host gut. We find that recognition is controlled by a colonization island that is widely conserved in commensals and pathogens from the Lactobacillales to the Clostridia. Our findings indicate a genetic mechanism of host specificity that is broadly conserved.
README: A conserved genetic basis for commensal-host specificity through live imaging of colonization dynamics
https://doi.org/10.5061/dryad.80gb5mkzw
Alignments and all the trees used to construct all the figures are available in this public repository. For further information related to the code and programs used to generate the figures, please visit:
Gutierrez-Garcia, K., Aumiller, K., Dodge, R., Obadia, B., Deng, A., Agrawal, S., Yuan, X., Wolfe, R., Garud, N., & Ludington, W. B. (2024). A conserved genetic basis for commensal-host specificity through live imaging of colonization dynamics. Zenodo. https://doi.org/10.5281/zenodo.13115916
Or
https://github.com/K-Gutierrez/LpColonizationIsland/)
Files related to Figure 3:
- Fig3-SpeciesTree-36Org-rooted.tree
- Fig3-SpeciesTree-36Org.fasta
Files related to aSec tree:
- aSec-phylogeny-based-on-the-core-genes-aln-gb.fasta
- aSec-phylogeny-based-on-the-core-genes-MappingFile.txt
- aSec-phylogeny-based-on-the-core-genes-rooted.tree
Files related to dN/dS analysis:
- Cluster1-pal2nal.fasta
- Cluster1-aBSREL.json
- Cluster2-pal2nal.fasta
- Cluster2-aBSREL.json
Cluster3-pal2nal.fasta
Cluster3-aBSREL.json
Files for the core genome tree:
- Phylogeny_of_colonization_island-containing_strains-MappingFile.txt
- Phylogeny_of_colonization_island-containing_strains.fasta
- Phylogeny_of_colonization_island-containing_strains.tree
Files to perform the Co-phylogenetic analysis
- aSecTree1-rooted.tree
- aSecTree1.fasta
- SpeciesTree1-rooted.tree
- SpeciesTree1.fasta
- aSecTree2-rooted.tree
- aSecTree2.fasta
- SpeciesTree2-rooted.tree
- SpeciesTree2.fasta
- aSecTree3-rooted.tree
- aSecTree3.fasta
- SpeciesTree3-rooted.tree
- SpeciesTree3.fasta
- aSecTree4-rooted.tree
- aSecTree4.fasta
- SpeciesTree4-rooted.tree
- SpeciesTree4.fasta