Exploring the Potential of Metatranscriptomics to Describe Microbial Communities and Their Effects in Molluscs
Abstract
:1. Introduction
2. Results
2.1. Comparison between 16S rRNA Sequencing and RNA-Seq Taxonomic Profiling
2.2. Microbiome Comparison between Gills and Haemocytes of Mytilus galloprovincialis
2.3. Effect of a Pathogenic Stimulus on the Microbiome Composition of M. galloprovincialis and Gene Expression
2.4. Haemocyte Microbiome of Molluscs
3. Discussion
4. Materials and Methods
4.1. 16S rRNA Sequencing
4.2. Taxonomic Profiling from RNA-Seq Data
4.3. Differential Abundance Analysis and Alpha Diversity
4.4. Correlation Microbiome/Transcriptome Results
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Project | Species | Tissue | Sample Features | Reference |
---|---|---|---|---|
PRJNA858246 PRJNA858248 | Mytilus galloprovincialis | Whole body | 16S rRNA sequencing Ría de Vigo | Current work |
PRJNA638821 | Mytilus galloprovincialis | Gills | Mussel gills after a V. splendidus infection by bath | [20] |
PRJNA466718 | Mytilus galloprovincialis | Haemocytes | Mussel haemocytes after a V. splendidus injection in the adductor muscle | [21] |
PRJNA222492 | Pecten maximus | Haemocytes | Control from Vigo | [22] |
PRJNA481417 | Haliotis diversicolor | Haemocytes | Control from China | [23] |
PRJNA253995 | Octopus vulgaris | Haemocytes | Control from Vigo | [24] |
Gillbath | |||
ID | Pearson | Uniprot Annotation | Function |
C_8095 | −0.993 | Regulator of MON1-CCZ1 complex | Endosomal/autophagic flux |
C_35153 | −0.991 | Beta-galactosidase-1-like protein | Probable glycosyl hydrolase |
C_53367 | −0.991 | Zinc finger protein 233 | Transcriptional regulation |
C_83652 | −0.990 | tRNA-splicing endonuclease subunit Sen54 | Responsible for identification and cleavage of the splice sites in pre-tRNA |
C_51191 | 0.989 | AP-5 complex subunit mu-1 | May be involved in endosomal transport |
C_36214 | 0.989 | NA- and Cl-dependent neutral and basic amino acid transporter B(0+) | Uptake of a broad range of amino acids in a Na+/Cl--dependent manner |
C_35181 | 0.989 | Pre-mRNA-splicing factor ISY1 homolog | Processing of microRNAs during embryonic stem cell differentiation |
C_55942 | −0.987 | Protein mab-21-like 3 | Neural development |
C_63893 | −0.986 | E3 ubiquitin-protein ligase TRIM56 | Role in innate antiviral immunity |
C_28519 | −0.985 | Metabotropic glutamate receptor 3 | Signalling via G proteins |
C_32331 | −0.985 | 15-hydroxyprostaglandin dehydrogenase | Conversion of hydroxylated arachidonic acid to oxidised metabolites |
C_111951 | 0.985 | Retrovirus-related Pol polyprotein from type-2 | - |
C_94710 | −0.985 | Chromatin assembly factor 1 subunit A | Chromatin assembly in DNA replication and DNA repair |
C_92181 | −0.985 | Embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein | - |
C_17718 | −0.984 | Ankyrin-1 | Attaches integral membrane proteins to cytoskeletal elements |
C_21601 | −0.984 | Sialoadhesin | Acts as an endocytic receptor-mediating clathrin-dependent endocytosis |
C_9272 | −0.983 | Neuronal acetylcholine receptor subunit alpha-10 | Ionotropic receptor with a role in the modulation of auditory stimuli |
C_36504 | −0.983 | Innexin unc-9 | Plays a role in maintaining gap junction activity to promote locomotion |
C_48464 | 0.983 | Neurensin-1 | Neural organelle transport |
C_22050 | −0.983 | Cytochrome P450 10 | Functions as monooxygenases |
Haemocytes injection | |||
ID | Pearson | Uniprot Annotation | Function |
C_7894 | 0.997 | GTPase IMAP family member 4 | Regulation of apoptosis |
C_15253 | −0.997 | Nuclear pore complex protein Nup54 | Required for the trafficking across the nuclear membrane |
C_13141 | −0.997 | Bardet–Biedl syndrome 7 protein homolog | Brain development and ciliary trafficking |
C_58173 | −0.996 | Long-chain fatty acid transport protein 3 | Long-chain fatty acids translocation at the plasma membrane |
C_15154 | −0.996 | tRNA (uracil-5-)-methyltransferase homolog A | May be involved in nucleic acid metabolism and/or modifications |
C_49199 | −0.995 | Choline dehydrogenase, mitochondrial | Dehydrogenation of choline to betaine aldehyde in mitochondria |
C_76285 | −0.995 | Kelch-like protein 25 | Homeostatic mechanism, translational regulation |
C_30541 | −0.994 | 4-aminobutyrate aminotransferase, mitochondrial | Catalyses neurotransmitter conversions |
C_6950 | −0.994 | C-Myc-binding protein | Control transcriptional activity of MYC, involved in cell cycle and apoptosis |
C_98220 | −0.994 | UNC93-like protein | Involved in innate and adaptive immune response by regulating TLR signalling |
C_52106 | −0.991 | Programmed cell death protein 2 | May play an important role in cell death and/or in regulation of cell proliferation |
C_7630 | −0.990 | GPI inositol-deacylase | Important for efficient transport of GPI-anchored proteins from the ER to the Golgi |
C_37669 | 0.990 | Torsin-1A-interacting protein 2 | Required for endoplasmic reticulum integrity |
C_79722 | 0.990 | Collagen alpha-4(VI) chain | Cell-binding protein |
C_18830 | −0.990 | Copper chaperone for superoxide dismutase | Metalloprotein responsible for the delivery of Cu to SOD1. Antioxidant |
C_120023 | −0.990 | Zinc finger protein 45 | May be involved in transcriptional regulation |
C_67714 | −0.990 | Leucine-rich repeat-containing protein 63 | Associated with innate immunity. Specially pathogen recognition |
C_5776 | 0.990 | Rab9 effector protein with Kelch motifs | Rab9 effector required for endosome to trans-Golgi network (TGN) transport |
C_69835 | −0.989 | TATA box-binding protein-associated factor RNA polymerase I subunit C | Involved in the transcription initiation |
C_482 | −0.989 | Ribonuclease Oy | Releases mononucleotides from RNA in the order of 3’-GMP, 3’-AMP and 3’-UMP |
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Rey-Campos, M.; Ríos-Castro, R.; Gallardo-Escárate, C.; Novoa, B.; Figueras, A. Exploring the Potential of Metatranscriptomics to Describe Microbial Communities and Their Effects in Molluscs. Int. J. Mol. Sci. 2022, 23, 16029. https://doi.org/10.3390/ijms232416029
Rey-Campos M, Ríos-Castro R, Gallardo-Escárate C, Novoa B, Figueras A. Exploring the Potential of Metatranscriptomics to Describe Microbial Communities and Their Effects in Molluscs. International Journal of Molecular Sciences. 2022; 23(24):16029. https://doi.org/10.3390/ijms232416029
Chicago/Turabian StyleRey-Campos, Magalí, Raquel Ríos-Castro, Cristian Gallardo-Escárate, Beatriz Novoa, and Antonio Figueras. 2022. "Exploring the Potential of Metatranscriptomics to Describe Microbial Communities and Their Effects in Molluscs" International Journal of Molecular Sciences 23, no. 24: 16029. https://doi.org/10.3390/ijms232416029