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Upskilling in metagenomics: why it's so important

Metagenomics, the study of genetic material recovered directly from environmental samples, is giving microbial ecologists a much more detailed look at the previously hidden diversity of microscopic life, significantly adding to our understanding of the living world.

The problem

The fast-moving area of microbiology requires considerable computational resources and skills. Producing datasets from DNA sequences taken from an environment is one thing; being able to analyse and work out how to use the information is another. New Zealand needs more bioinformatics skills for data analysis to derive maximum meaning from environmental samples and metagenomics information now coming through. 

Genomics Aotearoa, in partnership with NeSI, has upped its training on analysis methods to build national capabilities, linking researchers working in the field to create much-needed networks.

What we did

For the first time in New Zealand, researchers and students across a diverse range of disciplines and institutes came together at a Genomics Aotearoa Summer School at the University of Auckland in December 2019 to upskill in fundamental metagenomics approaches, building on basic data carpentry skills taught by Genomics Aotearoa and NeSI. Such was its success, further such specialised genomics training is planned.

Metagenomics Summer School

Metagenomics Summer School participants

While all of the summer school participants had some experience in data analysis, they had many different reasons for being there. Some were planning a sequencing project, several needed more analytical skills to make the most of existing plant or animal datasets, while others were getting into metagenomics research. Most wanted more in-depth evaluation processes they could learn themselves and pass on in their own organisations.

Feedback

Feedback from participants demonstrated the need:

"Our team has a lot of interest in whole genome sequencing (WGS) and metagenomics. As a group, we are largely interested in human health and environmental issues, mainly with a focus on zoonoses (other animal to human) transmission. This means we have interest in identifying (sometimes unknown) pathogens, markers for contamination (e.g. water with antimicrobial resistance genes, etc.). This is why metagenomics is useful. As a group, we are multidisciplinary, which means we are thin across a lot of areas; while we have someone responsible for our team’s bioinformatics, he’s only part-time in our team and super busy. The biggest bottleneck broadly for us is bioinformatics, but metagenomics more specifically, because our bioinformatics person is busy with WGS, and while he has done a lot of 16S, he’s done less shotgun sequencing, so we need more in the team to get started and upskill."
David Hayman, Group Leader - Academic, School of Veterinary Science, Massey University

"The Metagenomics Summer School was a great opportunity for faculty and students from a range of institutions to upskill in metagenomics, an area of microbiology that is moving quickly and requires access to a set of computational resources that many of us have shied away from. Genomics Aotearoa has assembled a crack team of instructors who were able to patiently walk us through the use of the NeSI servers and data analysis pipelines for analysing complex populations in our DNA sequencing projects. In addition, we learned how to identify our bacteria, where our viruses might be hiding and how to present these data using a combination of accessible tools. This was an incredibly useful workshop and I would happily recommend it to colleagues and students who are keen to delve into the fascinating world of microbial metagenomics!"
Heather Hendrickson, Massey University Senior Lecturer in Molecular Biosciences, Vice President, New Zealand Microbiological Society, Major Leader Biological Science and Integrative Biology

Implications

Demystifying data analysis methods provides new pathways and processes for researchers and practitioners. It is a practical kickstart for new research projects and it fosters collaborations across diverse workplaces. Such processes expand the potential uses of valuable environmental or host associated data, unlocking potential new ways to explore and maintain microbial diversity, identify microbial contributions to environment and animal health, and manage precious water resources in an era of climate change.

To know more, read about our Environmental Metagenomics project