Our understanding of the Aotearoa New Zealand environment increasingly depends on bioinformatic tools and skills.
Bioinformatics is a rapidly expanding field for developing methods and software for understanding the biological data derived from genomics. Genomics is a comprehensive tool to study and analyse environmental ecosystems, though inevitably produces enormous quantities of data. As such, bioinformatics is a vital aspect of any genomics project, and is why Genomics Aotearoa is creating a national collaborative platform to help scientists manage and analyse genomic data.
Postdoctoral Fellow Annie West is part of the Genomics Aotearoa team helping develop novel bioinformatic pipelines, working with the Environmental Metagenomics project based at the University of Auckland.
Annie developed an interest in learning and applying bioinformatic techniques during her PhD research on the microbiomes of endangered birds of Aotearoa New Zealand.
She is now working with the Environmental Metagenomics group reconstructing the genomes of abundant archaea and bacteria in the Waiwera estuary systems. The aim is to adapt and develop genomic based methods that improve our understanding of how strain heterogeneity affects genome reconstruction and the overall diversity and function of our estuary ecosystems.
“It’s basically about problem solving – using bioinformatics knowledge to expand the capability of our laboratories to find out how we’re underutilising and underestimating our sequencing data simply due to a lack of standard methodology in this area, particularly for the reconstruction of genomes from microorganisms with considerable strain heterogeneity.”
“This research also helps us better understand what’s in our water, how it interacts with other species and what it needs – all things we need to know for long-term sustainability of our environment.”
“We’re developing new bioinformatic techniques that can be used in all sorts of ways. But while I’m upskilling myself, I’m also helping build our bioinformatics capability by improving pipelines and systems that others can use – interaction and collaboration is the driving force behind these projects.”
“While that’s a big challenge, it’s also a really exciting field to be part of.”
About Annie
Annie completed a BSc and MSc at Te Whare Wānanga o Waikato University of Waikato, studying ecology, genetics, conservation, and physiology. She then undertook a PhD in microbial ecology with Professor Mike Taylor at Waipapa Taumata Rau University of Auckland in Tāmaki Makaurau.
Here she explored the role and potential applications of microbiome research in threatened species conservation, specifically kākāpō and takahē. This was a highly collaborative, multidisciplinary project using a combination of next generation sequencing technologies complemented by genome-wide association and ecological analyses.
Part of her research also focused on a chronic inflammatory disease called exudative cloacitis which significantly impacts kākāpō health and wellbeing. The aim was to investigate the microbial signature of kākāpō individuals infected with cloacitis using a combination of DNA metagenomic and RNA metatranscriptomic techniques.
“I’ve loved working in conservation; I've always been fascinated by the natural world, and I apply this enthusiasm to my work to better understand how microbial ecosystems shape the world around us. I have a passion for learning, and am always happy to collaborate on new, exciting projects,” she said.
“Studying endangered species has been a real driver, but equally, I enjoy sharing the bioinformatics skills I’ve developed with others. I’m looking forward to contributing to our understanding of microbial ecosystems not only on a local scale, but globally so we can start to address the big issues like global warming and climate change.”
Annie’s areas of expertise:
• Microbial ecology
• Gene targeted amplicon, meta(genomic) and (meta)transcriptomic analyses
• Host-symbiont ecosystems
Read more about Environmental Metagenomics here