A World Leading SFI Research Centre - Science Foundation Ireland - For What's Next

APC News

APC scientist publishes first bioinformatics guidebook for clinicians and researchers interested in gut microbiome and brain health.

6 Dec 2023

“An international team of scientists led by Dr. Thomaz Bastiaanssen, a researcher in APC Microbiome Ireland (APC), a world-leading SFI Research Centre based at University College Cork has published a two-part methodological guidebook to the analysis of the microbiome-gut-brain axis in the leading international scientific journal Nature Mental Health.  


APC research has led the charge in unravelling the complex interplay between the microbial communities residing in the gut and their impact on mental health; the microbiome has been shown to be altered in many mental disorders including depression, anxiety, Parkinson’s and Alzheimer’s.

In previous work, the microbiome-gut-brain axis, the two-way connection between the gut microbiome and the brain, has presented itself as a promising clinical target to improve and treat mental health.


However, the computational and biostatistical analysis of microbiome data is all but straightforward; it demands a highly specialized set of skills. There are many quirks and pitfalls that are specific to microbiome data and mistakes are easy to make.  The newly published papers break down these intricacies and provide the background and tools necessary to perform a robust and effective analysis.


The first paper, entitled ‘Bugs as features (part 1): concepts and foundations for the compositional data analysis of the microbiome–gut–brain axis’, focuses on the biological and computational background necessary to understand and effectively analyse the microbiome-gut-brain axis. The second paper, entitled ‘Bugs as features (part 2): a perspective on enriching microbiome–gut–brain axis analyses’, goes a step further and covers more advanced computational methods to get the most out of a microbiome-gut-brain axis study.


Dr. Thomaz Bastiaanssen, the lead researcher on these guidebooks, is particularly excited about the educational value of the papers:


‘We really wrote these guides for our former selves, containing everything we wished we knew before we started our journey into microbiome analysis. The papers come with around thirty pages of annotated R code each, for a fully reproducible analysis to demonstrate and discuss the techniques we cover in the main texts.’


It’s been truly humbling to see the overwhelmingly positive reception of the guidebooks by the international scientific community. Researchers from universities all across the world have reached out to tell us they’ve started using the methods in their own workflows and even in lectures!’


Prof. John Cryan, PI at APC and Vice President of Research and Innovation at UCC welcomes the papers:


“Microbiome Gut–Brain research is a nascent area and so follows that the bioinformatics aspect is really pioneering work. These Nature Mental Health papers will benefit generation of scientists and help form a very robust best practice standard for clinical practice.”


The papers can be found online at the following URLs:

‘Bugs as features (part 1): concepts and foundations for the compositional data analysis of the microbiome–gut–brain axis’

‘Bugs as features (part 2): a perspective on enriching microbiome–gut–brain axis analyses’ 


For more on this story contact:



Media Contacts

Tina Darb             APC Microbiome Ireland    087 7826500        tdarb@ucc.ie


Host Institution

Host Logos - UCC and Teagasc

Partner Institutions

APC Microbiome Ireland

Biosciences Building, University College Cork, Ireland,