Data for the publication: 'Host and microbiome proteins in eco-coronas: abundance, physicochemical properties and binding partners'

This submission presents metagenomic sequencing identifications and mass-spectrometry datasets for the following publication:

Brinkmann, B.W.; Zhiling, G.; Vijver, M.G..; Peijnenburg, W.J.G.M.; Chetwynd, A.J. Host and microbiome proteins in eco-coronas: abundance, physicochemical properties and binding partners. Environ. Sci.: Nano. 2025, DOI: 10.1039/d5en00493d.

1. Metagenomic sequencing identifications

Tab-delimited text files with genus-level read abundances identified in whole-body metagenomes of:

• Daphnia magna neonates (5-6 days old): Metagenomics_Genus_Read_Abundance_Dmagna.tsv
• Danio rerio (5 days post-fertilization): Metagenomics_Genus_Read_Abundance_Drerio.tsv

The data of both files were generated using the Pavian webtool (https://fbreitwieser.shinyapps.io/pavian/) accessed on 25 October 2024. Columns with read abudances present results for 3 biological replicates and an extraction kit metagenome (blank). The TaxId column presents the Taxonomy Identifier of NCBI Taxonomy Browser. The associated metagenomic data are deposited in the NCBI Sequence Read Archive under BioProject ID: PRJNA1336773 (http://www.ncbi.nlm.nih.gov/bioproject/1336773).

2. Proteomic datasets

Tab-delimited mass-spectrometry datasets and metadata obtained for experiments with:

• Daphnia magna neonates (3-6 days old):
  • Raw mass spectrometry report: MS_report_Dmagna_20241016.tsv
  • Relative protein abundances (processed dataset): MS_relative-abundances_Dmagna.txt
  • List with excluded accessions: MS_excluded_accessions_Dmagna.txt
  • Acquired metadata: MS_metadata_Dmagna.txt
• Danio rerio (3-5 days post-fertilization): 
  • Raw mass spectrometry report: MS_report_Drerio_20241016.tsv
  • Relative protein abundances (processed dataset): MS_relative-abundances_Drerio.txt
  • List with excluded accessions: MS_excluded_accessions_Drerio.txt
  • Acquired metadata: MS_metadata_Drerio.txt

Sample names in the mass spectrometry datasets consist of the following three elements: {sample type}_{microbiome condition}_{replicate}

where: 

1. sample type: 'medium', 'TiO2' (eco-corona), 'CNT' (eco-corona), or 'blank'.
2. microbiome condition: 'col' for microbially colonized samples, 'GF' for germ-free samples
3. replicate: the number of the replicate (1, 2 or 3)

Accession numbers were obtained from the UniProt KB protein knowledgebase.

Column names for metadata present:

• 'Accession', 'Genes', and 'Description' from Spectronaut mass spectrometry reports
• 'MultipleAcessions' indicating if there were multiple identifications (matching proteins) from the reference database
• Organism, protein name, taxonomy, function, gene ontologies ('GO') of three types ('GO_BP': Biological Process; 'GO_CC': Cellular Component; 'GO_MF': Molecular Function), GO IDs, keywords and keyword IDs obtained from the UniProt KB protein knowledgebase on 18 November 2024.
• 'Species' indicating if the protein has a 'microbial' or host ('daphnid' or 'zebrafish') origin.
• Predictions of total, polar and apolar solvent accessible surface area ('totalSASA', 'PolarSASA' and 'ApolarSASA', respectively)
• Predicted iso-electric point ('pI') and molecular weight ('MW')