Microbial insights into respiratory disease enabled by national training
Considerable microbial diversity was seen on this MacConkey agar plate collected from a study patient.
Image credit: Olusola S Olagoke
Many research programs are driven by the goal of improving the lives of people impacted by chronic diseases. Genetic insights are key and researchers need to apply an arsenal of new and sophisticated tools to progress our understanding of human health. Participants in the recent workshop on the next-generation microbiome bioinformatics platform, QIIME 2, included a microbiologist working on infectious respiratory diseases, and the resulting analysis has just been published.
Researchers from 22 different Australian institutes and organisations gathered online for the Introduction to Metabarcoding using QIIME 2 workshop hosted by BioCommons. A/Prof Erin Price, from the University of the Sunshine Coast, joined the workshop wanting to learn how to use QIIME 2 to investigate pleural infections. The recent publication, Performance of next-generation molecular methods in the diagnosis of pleural infections and their aetiology, acknowledged the workshop, and Erin is positive about the uplift the training provided.
The workshop provided a fantastic, well-paced, clear, thorough, hands-on introduction to QIIME 2. I was impressed with how much ground they covered, and I left feeling very confident that I could use QIIME 2 for my own work.
Erin’s ultimate research goal is to improve outcomes for people impacted by respiratory diseases such as chronic obstructive pulmonary disease, bronchiectasis, cystic fibrosis, lung cancer, and pleural infections. Her team applies omics methods to better understand microbial prevalence, origin, transmission, evolution, ecology, diversity, and antimicrobial resistance. To date, only a handful of studies have examined the pleural infection microbiome, and none have been in Australian cohorts. But as Erin explains, her team has changed that:
We used QIIME 2 bacterial (16S rRNA) metataxonomics to compare microbiome profiles with shotgun metagenomics, which allowed us to compare our Australian pleural infection cohort with international studies that predominantly used 16S rRNA metataxonomics.
QIIME 2 enables researchers to start an analysis with raw DNA sequence data and finish with visualised data and statistical outputs. Expert user, Dr Ashley Dungan, generously offered to lead the online workshop to share her skills nationally with peers. As a Research Fellow at The University of Melbourne, Ashley knew others could benefit from using this free, open source, community-developed and extensible tool:
QIIME 2 helps to quantify the changes in microbial communities when an experimental system is exposed to a stressor like disease. Hundreds of samples are sequenced at a time and each is given a unique barcode. This barcode allows the sequencing reads to be binned by sample and go through data quality control and taxonomic assignment in QIIME2. QIIME2 can also then provide immediate visualisations and output files that can be directly used for further statistical analyses.
Read our related story where trainer Ashley explains what motivated her to run this training for a national audience, and what the experience was like.
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