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Microbial Diversity and Screening for Potential Pathogens and Beneficial Bacteria of Five Jellyfish Species-Associated Microorganisms Based on 16S rRNA Sequencing

Polish Journal of Microbiology
Volume 73 (2024): Issue 3 (September 2024)
By:
Open Access
|Aug 2024

Figures & Tables

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.
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
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.
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.
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.
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.
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.

Gene annotation and enriched pathways_

EntrySymbolNamePathway or Brite
K00059FabG, OAR13-oxoacyl-acyl carrier protein reductasefatty acid biosynthesis, prodigiosin biosynthesis, biotin metabolism, metabolic pathways, biosynthesis of secondary metabolites, fatty acid metabolism, biosynthesis of cofactors
K00257mbtN, fadE14acyl-acyl carrier protein dehydrogenaseunclassified: metabolism
K00626ACAT, atoBacetyl-CoA C-acetyltransferasefatty 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
K00799GST, gstglutathione S-transferaseglutathione 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
K01091gphphosphoglycolate phosphataseglyoxylate and dicarboxylate metabolism, metabolic pathways, biosynthesis of secondary metabolites
K01652ilvB, ilvG, ilvIacetolactatesynthase I/II/III large subunitvaline, 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
K01784galE, GALEUDP-glucose4-epimerasegalactose metabolism, amino sugar and nucleotide sugar metabolism, O-antigen nucleotide sugar biosynthesis, metabolic pathways, biosynthesis of nucleotide sugars
K01897ACSL, fadDlong-chain acyl-CoA synthetasefatty acid biosynthesis, fatty acid degradation, metabolic pathways, fatty acid metabolism, quorum sensing, PPAR signaling pathway, peroxisome, ferroptosis, thermogenesis, adipocytokine signaling pathway
K01915glnA, GLULglutamine synthetasearginine 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
K01990ABC-2.AABC-2 type transport system ATP-binding proteinABC transporters
K01992ABC-2.PABC-2 type transport system permease proteinABC transporters
K01995livGbranched-chain amino acid transport system ATP-bindin proteinABC transporters, quorum sensing
K01996livFbranched-chain amino acid transport system ATP-binding proteinABC transporters, quorum sensing
K01997livHbranched-chain amino acid transport system permease proteinABC transporters, quorum sensing
K01998livMbranched-chain amino acid transport system permease proteinABC transporters, quorum sensing
K01999livKbranched-chain amino acid transport system substrate-binding proteinABC transporters, quorum sensing
K02003ABC.CD.Aputative ABC transport system ATP-binding proteinABC transporters
K02004ABC.CD.Pputative ABC transport system permease proteinABC transporters
K02014TC.FEV.OMiron complex outermembrane recepter proteinother transporters
K02015ABC.FEV.Piron complex transport system permease proteinABC transporters
K02016ABC.FEV.Siron complex transport system substrate-binding proteinABC transporters
K02030ABC.PA.Spolar amino acid transport system substrate-binding proteinABC transporters
K02032ABC.PE.A1peptide/nickel transport system ATP-binding proteinABC transporters
K02035ABC.PE.Speptide/nickel transport system substrate-binding proteinABC transporters
K03088rpoERNA polymerase sigma-70 factor, ECF subfamilytranscription machinery (bacterial type)
K03406mcpmethyl-accepting chemotaxis proteintwo-component system, bacterial chemotaxis
K03704cspAcold shock protein (beta-ribbon, CspA family)unclassified
K06147ABCB-BACATP-binding cassette, subfamily B, bacterialABC transporters
K07090uncharacterized proteinuncharacterized proteinunclassified
K07107ybgCacyl-CoA thioester hydrolaseunclassified: metabolism
DOI: https://doi.org/10.33073/pjm-2024-026 | Journal eISSN: 2544-4646 | Journal ISSN: 1733-1331
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Language: English
Page range: 297 - 314
Submitted on: Mar 5, 2024
Accepted on: May 25, 2024
Published on: Aug 26, 2024
Published by: Polish Society of Microbiologists
In partnership with: Paradigm Publishing Services
Publication frequency: 4 times per year
Keywords:
jellyfish,
microorganisms diversity,
pathogenic bacteria,
beneficial bacteria
Related subjects:
Life sciences,
Microbiology and virology

© 2024 Liangzhi Li, Yina Zhu, Feng Wu, Yuxin Shen, Yi Wang, Juan Höfer, Marina Pozzolini, Mingke Wang, Liang Xiao, Xiaojie Dai, published by Polish Society of Microbiologists
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.

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