Transisthmian Water Microbiomes

Assembly-based metagenomics of coral reef & mangrove water samples from both sides of the Isthmus of Panama.

Welcome. This site provides the reproducible bioinformatics workflow for our study on the Transisthmian water column microbiome project. Here you will find details on how we setup our computational environment, program names and exact parameters we used throughout every step of the analysis, and how to access raw data. In addition we provide field/lab methods, summary data products, and other (potentially) useful information.

To access the complete bioinformatic workflow & raw data use the buttons at the top of the page or visit



In this study, we
  • Investigate the evolution of free-living marine microbes of both sides of the Isthmus of Panama; the Eastern Pacific (EP) & Western Atlantic (WA).
  • Collected a total of 57 water column samples collected from mangroves and coral reefs, dominant benthic habitats.
  • Each sample (4L) was filtered through a 0.22 micron filter. DNA was extracted from the filters and used for metagenomic sequencing.
  • Performed separate co-assemblies for EP samples and for WA samples.
  • Used automatic and manual binning to generate metagenome assembled genomes (MAGs) from each assembly.

Use the buttons at the top of the page or this link to access the molecular data and complete bioinformatic workflow.

Use the Cite button above to access a BibTeX formatted bibliography for the references we used in this study.

Banner photo credits, Sean Mattson.

Jarrod J Scott
Jarrod J Scott
Postdoctoral Fellow

I am interested in complexity, genomics, & natural history.

Matthieu Leray
Matthieu Leray
Postdoctoral Fellow

Drivers, functions, and evolution of marine biodiversity.