Dr Emily Hoedt

Dr Emily Hoedt

Research Interests

  • Studying the gut microbiome and how it can be used to predict disease
  • Isolating novel microbes from the gut
  • Understanding how microbes interact with the human host in relation to our health and disease

Why did you get into research?

I’ve always enjoyed sciencing, and my undergraduate degree solidified my love for microbiology. Microbes are everywhere and make up a huge part of our lives and yet there’s so much we still don’t know about the microbiological world and that means the chances of discovering new microbes (and getting to name them) is high. I started my studies investigating the microbes responsible for methane production in kangaroos and cows, in fact the same bugs also live in the human gut and were suggested to be involved in gastrointestinal disease. The fact that these microbes were not only responsible for greenhouse gas emissions, but also human health was fascinating and drove me to focus my attention on how our microbes can influence our health.

What would be the ultimate goal for your research?

The microbiome is an unseen force that we are beginning to appreciate for the role it can play in our everyday health and disease. Gastrointestinal disease affects a large percentage of the population and is tending dramatically upwards, most likely due to what we are feeding our microbes. The ultimate goal of my research is to understand how we affect our gut microbiome (for better or worse) and how our microbiome then affects us. Can we identify key microbial signatures for gastrointestinal disease that could help us with future diagnosis and treatments?


Dr Emily Hoedt is a microbiologist with expertise in microbiome/metagenome analysis and interpretation. Her research experience includes microbiome studies within gastroenterology, probiotic development and microbial/food bioreactors. She was awarded a BBioTech Hons I and PhD in Microbiology Biotechnology by the University of Queensland, Australia in 2017. Her PhD studies focused on the functional and comparative study of heterotrophic methanogens from different gastrointestinal environments. The project received funding through an Australian Postgraduate Award in addition to an industry top-up scholarship from Meat and Livestock Australia. 

In June 2018 Dr Hoedt relocated to Ireland to pursue an Academic-Industry collaborative project conducted at APC Microbiome Ireland. Her role as the lead Postdoctoral Researcher required her to plan, manage and liaise with the Industry partner for the successful completion of the project. This work encompassed the molecular interrogation (in silico and in vitro) of bifidobacterial strains as well as assessing potential host and microbiota (mouse model) benefits during gastrointestinal distress (antibiotic and/or pathogen) in order to determine the commercial viability of the bifidobacterial strains as a probiotic product. During her career Dr Hoedt developed a refined set of skills for the computational analysis of isolate microbial genomes as well as complex 16S/metagenomic datasets.

Dr Hoedt has published on various microbiological driven studies, examples include the isolation and characterisation of novel microorganisms, pan-genomic analysis of microbial isolate and shotgun recovered genomes, and microbiome shifts in response to different dietary fibre types in bioreactors. She has collaborated on a wide variety of projects outside her appointed roles in order to provide computational support and as such is listed as a contributing author on associated publications in leading microbiological and molecular biology research journals.

Dr Hoedt now works The University of Newcastle, Australia as a member of the Centre of Research (CRE) in Digestive Health team, here she oversees all aspects of microbiome research conducted by the CRE.

Future Focus

Dr Hoedt would like to continue her broadly collaborative research in the gastrointestinal field with clinician and fellow scientist who specialize in other facets of human health in order to better interrogate the interaction between the microbiome and host.

Specialised/Technical Skills

  • Aerobic and anaerobic microbiology
  • Isolation and culturing of fastidious microorganisms
  • Microbial metabolism/substrate studies
  • Comparative pan/genomic analyses
  • 16S amplicon sequencing and shotgun metagenomics analyses


  • NHMRC Centre for Research Excellence in Digestive Health
  • Australian Gastrointestinal Research Alliance
  • NEW1000 E/MCR committee