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Microbiome for beginners

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Morgan Langille edited this page Sep 11, 2023 · 10 revisions

Microbiome for beginners

This section is currently under construction, and we hope to collect resources (recommended reading, helpful tutorials, etc.) that are useful to those just starting out in microbiome research. This is aimed at new members of the lab group, but we think it may be useful for others, too. If there are resources that you have found helpful and we haven't included here, we'd love to hear about them. It won't be necessary to work through everything that's here in order for you to be able to process your own data, but different parts of it will probably be useful at different stages.

If you are at Dalhousie, we would encourage you to join our Dalhousie Microbiome User Group (DalMUG) - we hold a journal club every two weeks where we discuss a new microbiome paper. You can find summaries of previous papers on the site, and also join the Google group where we send out details of the next meetings and sometimes other useful things like upcoming conferences. These are informal meetings where one person will usually lead the discussion on a paper, but anyone should feel welcome to jump in with questions or comments.

Descriptions of work flows

These are all YouTube videos giving an overview of some aspect of microbiome sequencing or data analysis.

Recommended tutorials to work through

  • Patrick Schloss posts a weekly code club YouTube tutorial. These are aimed at some general topics in using R for data analysis, but are taught by a microbiome researcher and we think many are very useful. There are quite a lot available so we think it would be worth you working through at least some of them that seem like they would be of interest to you. Find a full list of them here
  • Microbiome Helper Amplicon sequencing - this is the standard amplicon sequencing workflow that we use in the lab.
  • QIIME2 tutorials - there are several different tutorials that you can work through on the QIIME2 website, with some toy data to use.
  • Metagenome analysis tutorials/workshops
  • Note that there are some further tutorials in the random section at the bottom of this page.

Recommended reading

Here we have some papers that we think give a great overview of microbiome research and what a typical analysis workflow might look like as well as some papers that give a deeper dive on a particular topic. It is worth noting that as microbiome research is still a relatively new field (as we know it now, at least - leaning heavily on nucleic acid sequencing and bioinformatics for analysis). There are therefore several topics that are a bit contentious and many researchers disagree on the correct, or best, way to deal with them. In several cases, there are multiple methods/tools that are all designed for the same task. Researchers will also often have particular tools that they like using and may feel strongly about the use of different tools - or there may be tools that are possibly able to perform "better" than those, but if development isn't continued then these can often become very difficult to actually use (particularly for someone for which bioinformatics is only a small part of the methods that they use). My personal take on this is that the most important thing is that you should understand the methods you use, know why you are using those methods and also be aware of what the limitations of those methods are.

General overview

Amplicon sequencing methods

Metagenomic methods

Biases

Compositional data analysis

Rarefying

Differential abundance analysis

Additional considerations for metagenomic analyses

Slightly random resources, mainly taken from Twitter

Contact

Useful Links

Main SOPs

Amplicon SOP v2 (qiime2-amplicon-2024.5)

PacBio Amplicon SOP v2 (qiime2-2022.2)

Metagenomics SOP v3

Wet-Lab SOPs on Protocols.io

Old SOPs

Tutorials

Microbiome for beginners

Metagenomics Resources

mSystems paper data

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