Introducing: Dr Thomas Jeffries

The npj Biofilms and Microbiomes Community team asked me to introduce myself to the community by answering these 5 questions…

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1) If I had to describe what I do in 3 sentences I’d say…

I use cutting-edge molecular tools to understand the diversity, function and distribution of the most important organisms on the planet. I do this in a variety of habitats ranging from the ocean to oil refineries and on scales ranging from the micro-scale to the global.

I am interested in how we can put microbiomes to good use: to clean-up contaminated sites, to improve food security and improve human health.

2) This isn’t where I started out, however. My career path to date has looked like this…

Whilst I have always worked with microbes, I began studying viruses infecting corals on the Great Barrier Reef. Then I switched to hypersaline mud metagenomes for my PhD. before “setting sail” and becoming a marine microbiologist during my first post-doc.

In my most recent position I work on soil microbiomes and have a more applied focus to investigate the degradation of contaminants by microorganisms. I still work collaboratively on projects from a wide variety of habitats however – I think it is beneficial to maintain connections across different areas of your work.

I was fortunate enough to begin my research career when tools such as metagenomics and next-generation DNA sequencing emerged, and these tools have been the focus of my work across my career path.

3) The reason I decided to join the npj Biofilms and Microbiomes Community is…

I think forums such as this are an excellent way to enhance the literature by facilitating the active discussion of research and building networks of people with similar interests.

It is also a good way for students, early career researchers and an interested public to interact with each other and with more senior researchers. Given the multi-disciplinary nature of biofilm and microbiome research, it is good to see a centralized location for this topic that can bring together diverse applications and skills.

4) My key areas of interest, on which I’d especially like to hear from community members, are…

I am a microbial ecologist. I would like to hear from people interested in harnessing microbiomes and biofilms to perform useful environmental functions such as bioremediation. Central to this is discussing how the metabolic function of microbiomes is influenced by changing environmental variables. I am also interested in the biogeographic distribution of microorganisms and how this influences the function of microbiomes.

On a technical level I am interested in using metagenomics, 16S-rDNA sequencing and network analysis to understand microbial ecology.

5) And if I had to choose one topic on which I’m especially able to answer questions it’d be…

As above: microbial biogeography, linking microbiome structure and function to environmental variables and using metagenome and amplicon sequencing and its associated software.

If you are interested in my areas of research, I’d love to hear from you. Please feel free to comment below, send me a message or ask a question via Q&A.

Thomas Jeffries

Research Associate (Environmental Microbiology), University of Western Sydney

@Thomas_Jeffries Dr Thomas Jeffries is a Microbial Ecologist with a wide range of expertise in molecular microbiology, bioinformatics and microbial biogeography. He obtained his PhD. in 2012 from Flinders University (Adelaide Australia). During his doctoral work he used metagenomics to investigate shifts in microbial community gene abundance in response to salinity and nutrient gradients within a hypersaline lagoon (the Coorong, Australia). His work demonstrated the influence of environmental variables on the abundance of salinity tolerance and photosynthesis pathways in bacterial genomes on local scales. On global scales he demonstrated that bacterial genome content is broadly determined by the physical substrate type of the habitat. His postdoctoral research has focused on marine microbial biogeography, the microbiome of Sydney Harbour, The distribution of marine fungal diversity and the role of microscale interactions in structuring microbial communities. Dr. Jeffries is also a contributor to the INDIGOV expedition utilizing citizen oceanography to investigate marine microbiomes on global scales. Dr Jeffries has extensive experience in using bioinformatics and ecogenomic tools to understand the diversity and function of microbiomes. He also is experienced in using multivariate statistics and network analysis to visualise highly complex data sets. He regularly runs tutorial workshops on various software packages. He is a steering committee member and chair of the Joint Academic Microbiology Seminar Series (JAMS) and is on the local organising committee for the Australian Society for Microbiology. Dr. Jeffries joined the Hawkesbury Institute for the Environment in 2014. His current work will focus on a CRC-CARE funded project to apply next-generation 'omics' tools and a systems-biology approach to understand the microbial bioremediation of organophosphorus and aromatic hydrocarbon contaminants, which pose a major global and local threat to human and environmental health. This work will deliver a predictive framework directly applicable to practitioners to aid the decision-making process and increase the efficiency of remediating contaminated sites


Go to the profile of Martin Delahunty
about 7 years ago
Many thanks Thomas for this background and introduction. Welcome and I look forward to your future posts.
Go to the profile of Jen Thoroughgood
about 7 years ago
Welcome to the community Thomas! Great to have you on board.
Go to the profile of Bhabananda Biswas
almost 7 years ago
Good to know the research area you are exploring. It motivates me to be attached in this field as a learner, as a researcher. Thanks Thomas!