Data anlalysis for the project hambiLOOPairwiseNMR


Shane Hogle


May 16, 2024

1 Manuscript:


Preprint available from bioRxiv

2 Introduction

This is project contains data from the hambiLOOPairwiseNMR project.

3 Experiment overview

In this project, clonal/ancestral forms of 16 HAMBI species (the top 16 abundant species from YSK) were grown alone, together in pairs, leave-one-out (LOO) communities of 15 species, and all 16 species together. The growth media used was R2A and cultures were grown under the same conditions as the “bacteria only” treatment from YSK. Species were inoculated in equal proportions, and after one growth cycle (48 hours in batch growth) cultures were destructively harvested to determine community composition from amplicon sequencing of the harvested DNA. Assuming a weekly dilution factor of 1/10 in the serial transfer, then \(\mathrm{log_2(10)} \approx 3.3\) generations will have elapsed over the 48 hour period. Additionally filtrates were collected from all of these experimental conditions, which will be analyzed using nuclear magnetic resonance spectroscopy (NMR) to determine structural signals for different carbon moieties present in the complex medium and after each species had used the medium.

4 Measurements and data types

  • Community DNA was sampled after 48 hours growtth.
  • 16S rRNA amplicon sequencing was performed on samples with multiple species
  • filtrates collected for NMR analysis

5 Code

DOI Data and code here is provided under GPL3. Feel free to use or remix as you see fit.

5.1 Project structure

  1. /R contains R scripts
  2. /data contains data that has been processed in some way for later use
  3. /_data_raw contains unprocessed data scraped from compute cluster
  4. /figs contains figures generated from R scripts

6 Availability

The rendered project site is available at The website has been produced using Quarto notebooks.

This GitLab repository ( hosts the code and data for this project. The rendered webpage can be fully recreated using the code at

7 Reproducibility

The project uses renv to create reproducible environment to execute the code in this project. See here for a brief overview on collaboration and reproduction of the entire project. To get up and running you can do: