This lesson has passed peer-review! See the publication in JOSE.

Other Resources


Teaching: 5 min
Exercises: 10 min
  • Where are other metagenomic resources?

  • Know some places where to find more information.

Other resources

Cuatro Ciénegas

More information about 4 Ciénegas is available in these podcasts Mexican oasis in the desert and Mexican Oasis, in this Cuatro Ciénegas Video, and finally, the manuscript Cuatro Ciénegas.

Other tutorials and books

Now that you finished this metagenomic lesson, you are ready to explore on your own the universe of available tutorials. Phyloseq tutorial contains much more examples of metagenomic data manipulation.
The Computational Genomics tutorial by Schmeier explains each step of the process carefully. There is a beautiful entry called [History of metagenomics] in the Meren Lab blog ( as well as several videos explaining Metapangenomics: A nexus between pangenomes and metagenomes, The power of metagenomic read recruitment, Genome-resolved metagenomics: key concepts in reconstructing genomes from metagenomes. Finally, for Spanish speakers, the ISME course is a detailed tutorial for 16s metabarcoding ISME Análisis de diversidad.

The book Microbiomes shares a contemporary concept of microbiomes. Books Statistical analysis of microbiome data and statistical analysis of microbiome data with r contain a state-of-the-art compendium of the statistical and computational microbiome analysis techniques beyond diversity analysis.

Other studies and databases

Some databases are jgi, The Earth microbiome project, metaSUB, The atlas of soil microbiome, and The Human microbiome project.


A valuable and easy-to-use resource is MG-RAST, which is at the same time a database and an online analysis tool. MG-RAST is an online metagenomic platform where you can upload your raw data with its corresponding metadata and get a complete taxonomic analysis of it. MG-RAST is a great place to get started in this type of analysis, and it is also an extensive repository of available data for future experiments. On the downside, it is not possible to modify significantly the steps and parameters in the MG-RAST workflow, so there is little room when it comes to implementing our preferred analysis tools when using MG-RAST.

The Cuatro Ciénegas data that we used in the workshop is already in MG-RAST! You can check it out here.

We can check the taxonomical distribution of our sample at different taxonomical levels.

The most abundant phylum is Proteobacteria.
Pie chart showing the relative abundance at the phylum level, and the legend with the phylum names, read count, and percentages.

Since we have a shotgun metagenome, we can also investigate the metabolic functions present in our sample. MG-RAST can find genes and annotate their function through the implementation of RAST or Rapid Annotation using Subsystems Technology. By looking at the charts generated by this analysis, we see that most of the genes are dedicated to metabolism.

Pie chart showing the relative abundance of general functional categories, and the legend with the category names, read count, and percentages.

Pie chart showing the relative abundance of specific functional categories, and the legend with the category names, read count, and percentages.

MG-RAST has its own specific pipeline, so it is a handy tool to have a quick look at your data and also to store and share it! However, it does not keep you from making your own personalized analysis like we just learned!

Discussion: Exploring more resources

Explore one of the suggested resources and discuss your findings with a neighbor.

Carpentries Philosophy

A good lesson should be as complete and transparent that becomes easy to teach by any instructor. Carpentries lessons are developed for the community, and now you are part of us. This lesson is being developed, and we are sure that you can collaborate and help us improve it.

Key Points

  • Enjoy metagenomics.