Study Title: Cultivation of Bacteria from Aplysina aerophoba: Effects of Oxygen and Nutrient Gradients

Authors: Johanna Gutleben¹, Catarina Loureiro¹, Laura Adriana Ramírez Romero¹, Sudarshan Shetty¹, René H. Wijffels^2,3, Hauke Smidt¹, Detmer Sipkema¹

Correspondence: Dr. Johanna Gutleben and/or Dr. Detmer Sipkema
For queries: johanna.gutleben[@]gmx.at and/or detmer.sipkema[@]wur.nl

This repository contains the codes and files necessary for the analyses of results from cultivation experiments on bacteria derived from the sponge A. aerophoba.
Sipkema, Detmer, Johanna Gutleben, Catarina Loureiro, Laura Ramirez, Sudarshan Anand Shetty, Rene H. Wijffels, and Hauke Smidt. "Cultivation of Bacteria from Aplysina aerophoba: Effects of Oxygen and Nutrient Gradients." Frontiers in Microbiology 11 (2020): 175. link to article

Complete Project Structure:

AplysinaCultivation6_Final_Analysis_1.Rmd     # the R Markdown file containing all scripts used for this analysis

Data: 

all_otus.tre                      # Phylogenetic tree, derived from NG-Tax 

Aplysina_cultivation.biom         # OTU count table with taxonomic assignments, derived from NG-Tax 

Map_file_Aplysina_cultivation.txt # Metadata on all samples included in this analysis

all_otus.fasta                    # OTU sequences, 100bp length. 

Clone or download the repository as zipped file, unzip and open the .Rmd file in R to re-run the analysis.

Author Affiliations:

1. Laboratory of Microbiology, Wageningen UR, Stippeneng 4, 6708 WE, Wageningen, The Netherlands, johanna.gutleben@wur.nl, detmer.sipkema@wur.nl
2. Bioprocess Engineering, AlgaePARC, Wageningen University, 6700 AA, Wageningen, The Netherlands
3. Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway