Fig. 1.
Analysis of commensal microbial community compositions in five jellyfish species.
A) From (a) to (e): Aurelia coerulea, Rhopilema esculentum, Phacellophora camtschatica, Cassiopea andromeda, and Chrysaora quinquecirrha; B) the microbial community compositions at the taxonomic level of the family for different jellyfish species. C) the shared and unique counts of microbial families among different jellyfish samples at the family level. D) the Circos relationship diagram depicting the top commensal microbial families corresponding to different jellyfish species based on their abundance. We selected the top 30 bacteria with the highest abundance and drew these figures.
Fig. 2.
Microbial community diversity analysis in five jellyfish species.
A) Alpha diversity based on the Chao1 index; B) alpha diversity based on the Shannon index. C) alpha diversity based on the Simpson index; D) within-group PCA analysis among different jellyfish species; E) PCoA analysis among different jellyfish species; F) NMDS analysis among different jellyfish species.
* – p < 0.05, ** – p < 0.01
Fig. 3.
Analysis of microbial community differences in the five jellyfish species.
A) Evolutionary branching of the most abundant commensal microbial species from the order to genera level across the five jellyfish species. B) comparative differences in relative abundance among the top 14 families of commensal microbes at the family level; C) random forest analysis based on the mean decrease accuracy index. D) random forest analysis based on the mean decrease Gini index. We selected the dominant bacteria and drew these figures.
Fig. 4.
The correlation network heatmap of commensal microbiota across the five species of jellyfish. (The red lines indicate positive correlations and blue lines for negative correlations). Solid lines represent significant differences, while dashed lines indicate non-significant differences. The thickness of the lines represents the relative abundance. We selected the top 20 bacteria and drew this figure.
Fig. 5.
Correlation analysis between the five jellyfish and their associated microbial communities.
A-F) Correlation analysis between the associated jellyfish and microbial communities at different levels of taxonomical categories. RDA analysis was conducted using the top 10 abundant associated microbial communities across all samples.
Fig. 6.
Analysis of predicted gene functions and pathogenic phenotype prediction in microbial communities associated with five jellyfish species.
A) Number of annotated genes unique and shared among different jellyfish samples; B) predicted pathogenic phenotype in microbial communities associated with different jellyfish species; C) differential analysis of predicted gene functions and metabolic pathways in microbial communities using STAMP analysis; D) composition of potential pathogenic bacterial communities across different jellyfish samples; E) composition of potential beneficial bacterial communities across different jellyfish samples.
We selected the dominant bacteria and the top 30 genes with total expression levels from shared expression genes to draw these figures.
Table I
Gene annotation and enriched pathways.
| Entry | Symbol | Name | Pathway or Brite |
|---|---|---|---|
| K00059 | FabG, OAR1 | 3-oxoacyl-acyl carrier protein reductase | fatty acid biosynthesis, prodigiosin biosynthesis, biotin metabolism, metabolic pathways, biosynthesis of secondary metabolites, fatty acid metabolism, biosynthesis of cofactors |
| K00257 | mbtN, fadE14 | acyl-acyl carrier protein dehydrogenase | unclassified: metabolism |
| K00626 | ACAT, atoB | acetyl-CoA C-acetyltransferase | fatty acid degradation, valine, leucine and isoleucine degradation, lysine degradation, benzoate degradation, tryptophan metabolism, pyruvate metabolism, glyoxylate and dicarboxylate metabolism, butanoate metabolism, carbon fixation pathways in prokaryotes, terpenoid backbone biosynthesis, metabolic pathways, biosynthesis of secondary metabolites, microbial metabolism in diverse environments, carbon metabolism, fatty acid metabolism, two-component system, fat digestion and absorption |
| K00799 | GST, gst | glutathione S-transferase | glutathione metabolism, metabolism of xenobiotics by cytochrome P450, drug metabolism-cytochrome P450, drug metabolism-other enzymes, metabolic pathways, platinum drug resistance, longevity regulating pathway-worm, pathways in cancer, chemical carcinogenesis-DNA adducts, chemical carcinogenesis-receptor activation, chemical carcinogenesis-reactive oxygen species, hepatocellular carcinoma, fluid shear stress and atherosclerosis |
| K01091 | gph | phosphoglycolate phosphatase | glyoxylate and dicarboxylate metabolism, metabolic pathways, biosynthesis of secondary metabolites |
| K01652 | ilvB, ilvG, ilvI | acetolactatesynthase I/II/III large subunit | valine, leucine and isoleucine biosynthesis, Butanoate metabolism, C5-branched dibasic acid metabolism, pantothenate and CoA biosynthesis, metabolic pathways, biosynthesis of secondary metabolites, 2-oxocarboxylic acid metabolism, biosynthesis of amino acids |
| K01784 | galE, GALE | UDP-glucose4-epimerase | galactose metabolism, amino sugar and nucleotide sugar metabolism, O-antigen nucleotide sugar biosynthesis, metabolic pathways, biosynthesis of nucleotide sugars |
| K01897 | ACSL, fadD | long-chain acyl-CoA synthetase | fatty acid biosynthesis, fatty acid degradation, metabolic pathways, fatty acid metabolism, quorum sensing, PPAR signaling pathway, peroxisome, ferroptosis, thermogenesis, adipocytokine signaling pathway |
| K01915 | glnA, GLUL | glutamine synthetase | arginine biosynthesis, alanine, aspartate and glutamate metabolism, glyoxylate and dicarboxylate metabolism, nitrogen metabolism, metabolic pathways, microbial metabolism in diverse environments, biosynthesis of amino acids, two-component system, necroptosis, glutamatergic synapse, GABAergic synapse |
| K01990 | ABC-2.A | ABC-2 type transport system ATP-binding protein | ABC transporters |
| K01992 | ABC-2.P | ABC-2 type transport system permease protein | ABC transporters |
| K01995 | livG | branched-chain amino acid transport system ATP-bindin protein | ABC transporters, quorum sensing |
| K01996 | livF | branched-chain amino acid transport system ATP-binding protein | ABC transporters, quorum sensing |
| K01997 | livH | branched-chain amino acid transport system permease protein | ABC transporters, quorum sensing |
| K01998 | livM | branched-chain amino acid transport system permease protein | ABC transporters, quorum sensing |
| K01999 | livK | branched-chain amino acid transport system substrate-binding protein | ABC transporters, quorum sensing |
| K02003 | ABC.CD.A | putative ABC transport system ATP-binding protein | ABC transporters |
| K02004 | ABC.CD.P | putative ABC transport system permease protein | ABC transporters |
| K02014 | TC.FEV.OM | iron complex outermembrane recepter protein | other transporters |
| K02015 | ABC.FEV.P | iron complex transport system permease protein | ABC transporters |
| K02016 | ABC.FEV.S | iron complex transport system substrate-binding protein | ABC transporters |
| K02030 | ABC.PA.S | polar amino acid transport system substrate-binding protein | ABC transporters |
| K02032 | ABC.PE.A1 | peptide/nickel transport system ATP-binding protein | ABC transporters |
| K02035 | ABC.PE.S | peptide/nickel transport system substrate-binding protein | ABC transporters |
| K03088 | rpoE | RNA polymerase sigma-70 factor, ECF subfamily | transcription machinery (bacterial type) |
| K03406 | mcp | methyl-accepting chemotaxis protein | two-component system, bacterial chemotaxis |
| K03704 | cspA | cold shock protein (beta-ribbon, CspA family) | unclassified |
| K06147 | ABCB-BAC | ATP-binding cassette, subfamily B, bacterial | ABC transporters |
| K07090 | uncharacterized protein | uncharacterized protein | unclassified |
| K07107 | ybgC | acyl-CoA thioester hydrolase | unclassified: metabolism |
1 Table information reference from https://www.genome.jp/kegg/