DOI: 10.5281/zenodo.5608678
title: Input data and Supplementary Results for "Turnover in life-strategies recapitulates marine microbial succession colonizing model particles"

description: <strong>README</strong> This page contains processed input data used for downstream analysis and some Supplementary Results for the paper: Pascual-García, A., Schwartzman, J., Enke, T.N., Iffland-Stettner, A., Cordero, O.X., Bonhoeffer, S., Turnover in life-strategies recapitulates marine microbial succession colonizing model particles (2022). <strong>Input data</strong> File <em>“count_table.ESV.biom”</em>: Table containing the abundance of each Exact Sequence Variant (ESV) in the different samples (biom format). File <em>“count-table_</em><em>metagenomes</em><em>_KEGGs.L3.spf”</em>. Table containing the abundances of genes found in the shotgun metagenomics experiments annotated in KEGG and then aggregated into classes according to the finest classification in KEGG's hierarchy (level 3). This is a tsv-formatted file that can be directly used in STAMP to perform statistical analysis (spf format). File <em>“count-table_</em><em>PICRUST2</em><em>_KEGGs.L3.spf</em>”. Table containing the abundances of genes predicted with PICRUSt v2. These genes were annotated in KEGG and aggregated into classes according to the finest hierarchy in KEGG (level 3). This is a tsv-formatted file that can be directly used in STAMP to perform statistical analysis (spf format). File <em>“count-table_Isolates_KEGGs.L3.spf</em>”. Table containing the abundances of genes found in the isolates genomes that were annotated in KEGG and aggregated into classes according to the finest classification in KEGG's hierarchy (level 3). This is a tsv-formatted file that can be directly used in STAMP to perform statistical analysis (spf format). File <em>“samples_metadata.tsv”</em>. Metadata table describing the samples. File <em>“isolates_metadata.tsv”.</em> Metadata table describing the isolates, it includes shallow phylogenetic levels and a categorical identifier describing the environmental preference estimated for the ESV having a 100% sequence identity with a ZINB-GLM. File <em>“sequences.ESV.</em><em>fasta</em><em>”.</em> File containing the Exact Sequence Variants fasta. <strong>Supplementary Materials</strong> File <em>“qiime2_visualizations.zip”</em>. A file containing visualizations compatible with the qiime2 viewer (simply drag and drop the file in https://view.qiime2.org/) for each sample or combination of samples, labelled as `$substrate.$medium.$replicate`, where `$medium = {Beads, Seawater}` and `$replicate = {A,B,C}`. If the label is not present for one field, it means that all samples are aggregated for that field e.g.: “<em>count_table.ESV.Chitosan.Beads.A.bar-plots.</em><em>qzv”</em> Contains the replicate experiment A for communities on the synthetic beads in chitosan. “<em>count_table.ESV.Chitosan.bar-plots.</em><em>qzv”</em> Contains all samples in chitosan (both seawater communities and the three replicates of communities on the beads). File <em>“README.odt”</em>. This readme in libreoffice format. File <em>“</em><em>Genome_deposition_information.xlsx”. </em> NCBI identifiers for the isolates’ genomes. File "barcodes_to_samples_MGRAST.xlsx". Contains the barcodes of each sample and its metadata as it was deposited in MG-RAST. In a second tab, there is a subset of samples with a low number of reads that MG-RAST analyzed together, generating a single entry (termed "mixed"). Access to raw an processed metagenomes and analysis are provided through MG-RAST following [this link](https://www.mg-rast.org/mgmain.html?mgpage=project&project=mgp85635). As of May 30th, 2022, there are two issues with the dataset in MG-RAST which are out of our scope to solve. We will report any update here. The first problem is related to the entry TCCTGAGC-GTAAGGAG-s_2_, which does not load in MG-RAST. These are very low samples and were discarded in most analyses. In addition, you will find in the metadata 17 metagenomes that do not belong to our project.
description: This work was supported by the Simons Collaboration PRiME, award number 542381 (to S.B) and 542395 (to O.X.C.).