Microbiome modulation in regeneration in jellyfish

Description

Abstract

The moon jelly Aurelia coerulea does not typically regenerate appendages. A previous study found that increasing nutrient availability promotes the activation of appendage regeneration. In this study, we found that changes in nutrient availability alter microbiome composition. Genome-scale metabolic modeling of the microbial symbionts suggests that the microbiome modulation reduces the abundance of a symbiont that competes with the host for metabolic resources. Antibiotic treatment that recapitulates the microbiome shift significantly promotes regeneration. Transcriptomic analysis of the host shows an upregulation of genes involved in the arginine biosynthetic pathway, including argininosuccinate synthase and carbamoyl phosphate synthase. Exogenous arginine supplementation promotes appendage regeneration. These findings suggest that microbiome composition, influenced by nutrient availability, contributes to the activation of host regeneration, and identify a role for arginine in promoting regeneration.

Technical info

1. Raw images of Aurelia coerulea in the amputation experiments. Animals were treated with control amounts of food, penicillin treatment, or arginine treatment and imaged after 14 days of recovery. Raw images are organized by experiment.
   1. Experiment 1
      1. RawImages_Exp1_Control_Treatment.zip
      2. RawImages_Exp1_ArginineTreatment.zip
      3. RawImages_Exp1_Pen_Treatment.zip
   2. Experiment 2
      1. RawImages_Exp2_ControlTreatment.zip
      2. RawImages_Exp2_ArginineTreatment.zip
      3. RawImages_Exp2_PenTreatmnet.zip
   3. Experiment 3
      1. RawImages_Pen_Exp3.zip
   4. Experiment 4
      1. RawImages_Pen_Exp4.zip
   5. Experiment 5 *Also contains images of Arginine treatment for Arginine supplementation Experiment 3
      1. RawImages_Pen_Exp5.zip
   6. Experiment 6
      1. RawImages_Pen_Exp6.zip
   7. Experiment 7
      1. RawImages_Pen_Exp7.zip
   8. Experiment 8 *Also contains images of Arginine treatment for Arginine supplementation Experiment 4
      1. RawImages_Pen_Exp8.zip
   9. Experiment 9
      1. RawImages_Pen_Exp9.zip
   10. Experiment 10
       1. RawImages_Pen_Exp10.zip
   11. Experiment 11
       1. RawImages_Pen_Exp11.zip
2. Input files for genome scale metabolic modeling analysis. Genome (.fasta) and annotation (.gff) files were used to generate inputs for CarveMe to produce the draft genome scale metabolic model (GEM). The models were manually curated to generate the final model (.sbml).
   1. Metagenome assembled genome of Candidatus Mariplasa lunae, associated annotation file (.gff), and final GEM (.sbml).
      1. Mariplasma_genome.fasta
      2. Mariplasma_codingseqs.gff
      3. iAO314_Mariplasma-GEM.sbml
   2. Metagenome assembled genome of Candidatus Marinirickettsia aquamalans, associated annotation file (.gff), and final GEM (.sbml).
      1. Marinirickettsia_genome.fasta
      2. Marinirickettsia_codingseqs.gff
      3. iAO833_Marinirickettsia-GEM.sbml
3. R script and inputs to generate the Aurelia genome databse for the GO enrichment analysis with ClusterProfiler and to run the DESeq2 analysis. Transcriptome reads can be retrieved from the NCBI Sequence Read Archive (SRA): Project accession - PRJNA1248490.
   1. anno.txt
   2. gene_names_anno.csv
   3. DEseq2_analysis_script.docx