About

Roger Huerlimann is a post-doctoral researcher using 16S diversity profiling, metagenomic, transcriptomic, and genomic tools to help improve tropical aquaculture industries.

Roger has a PhD in the genetics and biochemistry of microalgae, an MSc in marine biology, and a BSc in biochemical engineering. Since completing my PhD in 2014, Roger has been working first as a research assistant (1 year) and then as a post-doctoral research (4 years), primarily in the fields of aquaculture genomics and molecular biology, with a strong applied industrial focus. In his career, Roger has worked on several commercial important aquaculture (barramundi, black tiger prawn, and silver lipped pearl oyster) and fisheries species (coral trouts), as well as other marine species (green sea turtles, hammerhead sharks and sawfish). In this work, Roger has strong collaborations with scientists from James Cook University’s College of Marine and Environmental Sciences and especially the Centre for Sustainable Tropical Fisheries and Aquaculture, the Agriculture and Food Sector of CSIRO, and the Australian Genome Research Facility.

Roger has extensive experience in carrying out and supervising molecular biology and genomics related research from the laboratory through to completing all required bioinformatic analyses. This includes sequencing, assembly and annotation of genomes, transcriptomes, metabarcoding (bacterial 16S, fungal ITS, eukaryotic 12S or COI, and bisulfide treated genes for epigenetic analyses) and viral/bacterial metagenomics.

As part of the ARC ITRH for Advanced Prawn Genomics executive team, Roger is leading the work package tasked with the assembly and annotation of the complex Penaeus monodon genome, including optimizing DNA extraction methods, guiding the sequencing based on long and short read data, and developing a genome assembly strategy, in close collaboration with the Australian Genome Research Facility. This work also included the assembly, annotation and analysis of the transcriptomes of P. monodon and other penaeid species, which lead to several publications (e.g., Huerlimann et al, 2019, published in Scientific Reports, and Berry et al, 2019, published in Fish & Shellfish Immunology).

Since 2014, Roger has been overseeing the use of JCU’s Illumina MiSeq desktop sequencer. In this time, he has carried out close to 30 sequencing runs, facilitating the research of several JCU research groups. His work was especially focussed on enabling PhD students to carry out their own sequencing runs locally at JCU, providing them with hands-on sequencing experience. Roger has developed the amplicon sequencing (i.e., metabarcoding) library preparation, sequencing and bioinformatics protocols used by JCU’s aquaculture genetics group. Examples of the research he has been involved with include the microbiomes of faeces of mice fed with a high-fat diet (Villamil et al., 2017), turtle intestines (Ahasan et al., 2017; Ahasan et al., 2019ab), methanotrophic bacterial consortia (Chidambarampadmavathy et al., 2017ab), barramundi infected with parasites (Gomes et al., 2019), and prawn intestines (Villamil et al., 2019).

More recently, Roger has especially been focussing on the correlation between shifts in microbial communities and disease in prawn and pearl oyster aquaculture. As part of this, Roger is supervising a student investigating the bacterial microbiomes in P. monodon and Fenneropenaeus merguiensis through all stages from brood stock and larvae in the hatchery to grow out ponds. In terms of his own research, Roger is investigating the correlation between microbiome of oysters and Juvenile Pearl Oyster Mortality Syndrome as part of a larger project.

Roger is also familiar with non-bacterial metabarcoding work, for example dietary metabarcoding of coral trout stomach content (Delvoo-Delva et al., 2019, Matley et al., 2019).

In terms of metagenomic analysis, one of Roger’s more recent projects involved investigating unsolved mortalities in of P. monodon post-larvae (PLs) in a hatchery in collaboration with Dr. Kelly Condon, manager of JCU’s AquaPath laboratory. To solve this problem, Roger used high-throughput sequencing on a mixed bacterial community grown on am agar plate which led to the discovery of multiple toxin genes which are potentially associated with the disease.

Roger is also part of several environmental DNA (eDNA) projects in collaboration with other researchers. This includes a project to use eDNA to investigate the presence of scalloped hammerhead sharks in Guam for the United States Navy.

Teaching
  • BC3101: Genes, Genomes and Development (Level 3; TSV)
  • BC3203: Bioinformatics (Level 3; TSV)
  • BC5101: Advanced Genes, Genomes and Development (Level 5; TSV)
  • BC5203: Advanced Bioinformatics (Level 5; TSV)
Experience
  • 2015 to present - Post-doctoral researcher, James Cook University (Townsville, Australia)
  • 2014 to 2015 - Research Assistant, James Cook University (Townsville, Australia)
  • 2009 to 2014 - Doctor of Philosophy. Thesis title: Microalgal lipid biosynthesis - Phylogeny of Acetyl-CoA carboxylase and gene expression patterns of key enzymes, James Cook University (Townsville, Australia)
  • 2007 to 2008 - Master of Applied Science. Major: Marine Biology, James Cook University (Townsville, Australia)
  • 2003 to 2006 - Senior Analyst, Study Director and Deputy Team Leader, MDS Pharma Services Switzerland AG (Fehraltorf, Switzerland)
  • 1999 to 2002 - Bachelor of Chemistry (Biotechnological Engineer). Major: Biological Chemistry, Focus: Biochemistry, Zurich University of Applied Science Winterthur (ZHAW) (Winterthur, Switzerland)
  • 1995 to 1998 - Apprenticeship as Chemical Laboratory Assistant, Swiss Federal Institute of Aquatic Science and Technology (EAWAG) (Duebendorf, Switzerland)
Research Disciplines
Honours
Awards
  • 2008 - MAppSc: University Medal for Excellence
  • 2002 - BSc: Award for outstanding performance by the Swiss Union of Applied Chemistry (SVC)
Publications

These are the most recent publications associated with this author. To see a detailed profile of all publications stored at JCU, visit ResearchOnline@JCU. Hover over Altmetrics badges to see social impact.

Journal Articles
Book Chapters
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ResearchOnline@JCU stores 20+ research outputs authored by Dr Roger Huerlimann from 2010 onwards.

Current Funding

Current and recent Research Funding to JCU is shown by funding source and project.

CRC for Developing Northern Australia Scheme - Projects

Biosecurity in northern Australian prawn aquaculture

Indicative Funding
$441,819 over 3 years
Summary
This project addresses biosecurity risk through conducting the first comprehensive and widespread biosecurity audit of Australian prawn farms. This project has two components. The first is to conduct a biosecurity metanalysis using traditional and molecular diagnostic tools to establish what pathogens currently occur on prawn farms and how they relate to productivity. Secondly, once the pathobiome is established the project will formulate a risk management strategy for industry and provide on-farm biosecurity training. Understanding the risk of disease, and increased capacity to detect and monitor on-farm, will lead to more effective management practices for northern Australian prawn aquaculture.
Investigators
Dean Jerry, Ellen Ariel, Kelly Condon and Roger Huerlimann (College of Science & Engineering, College of Public Health and Medical & Vet Sciences)
Keywords
Penaeus monodon (Penaidae); Disease; Prawn; Aquaculture

Department of the Environment and Energy - National Environmental Science Programme (NESP) - Northern Australia Environmental Resources Hub

The Northern Australia eDNA Program - Revolutionising Aquatic Monitoring and Field Surveys in Tropical Waters

Indicative Funding
$570,000 over 3 years
Summary
All organisms shed DNA into their environment. This is termed environment DNA (eDNA). Capture and analysis of eDNA (in soil or water samples) is a highly efficient and sensitive method to detect the presence of a wide range of species without actually requiring physical capture, or sighting of the organisms themselves. eDNA field sampling can involve as little as collecting water samples and
Investigators
Damien Burrows, Jan Strugnell, Roger Huerlimann, Richard C Edmunds and Dean Jerry (TropWATER and College of Science & Engineering)
Keywords
eDNA; Threatened Species; Northern Australia; exotic pest species; aquatic monitoring; Genetics

Townsville Hospital and Health Service - Study Education Research Trust Account (SERTA)

Discovering the Faecal Microbiome Associated with Pre-Term Birth

Indicative Funding
$9,494 (administered by Townsville Hospital and Health Service)
Summary
Development of the pre-term gut microbiome is important for immediate and longer term health outcomes. Much of what is known about the infant and neonatal microbiome has been derived from healthy full term infants. Collecting and understanding the microbiome of the TTH NICU cohort would provide a unique insight into the microbial development and in pre-term babies admitted to the NICU. This information will provide further evidence for interventions currently undertaken in the NICU such as administration of probiotics to infants <32 weeks. This project supports evidence-based multidisciplinary research in a novel way to assess the neonatal microbiome development.
Investigators
Yoga Kandasamy, Donna Rudd, Robert Norton and Roger Huerlimann (Townsville Hospital and Health Service, College of Public Health, Medical & Vet Sciences, Townsville Health Service District and College of Science & Engineering)
Keywords
Human; Neonatal; Term or Pre-Term; Microbiome; Probiotics

Department of Agriculture and Water Resources - Research Grant

The validation of molecular diagnostic assays of marine pests of high priority to Australia

Indicative Funding
$45,000 (administered by Department of Fisheries (WA))
Summary
Detection of marine pests using traditional methods is notoriously difficult, lacks accuracy and is costly. Molecular methods for detection of marine pests using environmental DNA offers promise of relatively inexpensive, efficient and sensitive sampling to detect the possible presence of marine pests. However, many of these tests have not been validated to give a level of sensitivity and specificity to inform determination of whether an exotic marine species is present. The validation of molecular techniques for marine pests will determine fitness for purpose and performance for that purpose which can then be factored into design of surveillance.
Investigators
Roger Huerlimann and Dean Jerry (College of Science & Engineering)
Keywords
Marine Pests; eDNA; Early detection; Northern Australia

United States Navy - Detection of scalloped hammerhead sharks in Apra Harbor and adjacent nearshore waters, Guam using environmental DNA

Detection of scalloped hammerhead sharks in Apra Harbor and adjacent waters, Guam using Environmental DNA

Indicative Funding
$154,074 over 3 years (administered by University of Guam)
Summary
Scalloped hammerhead sharks (Sphyrna lewini) are anecdotally reported in Apra Harbor, Guam, but their spatial and temporal patterns of occurrence are not well understood. Lack of knowledge of population abundance, distribution, and habitat use also extends across the geographic range of the Indo-West Pacific subpopulation. All S. lewini are nationally protected under the Endangered Species Act, and their occurrence within Apra Harbor is of concern to management and conservation strategies and mission-essential operations of the U.S. Department of Navy. This project will determine the temporal and spatial distribution and habitat use of the scalloped hammerhead shark within Apra Harbor and Orote Peninsula nearshore waters.
Investigators
Tom Schils, Jan Strugnell, Agnes Le Port and Roger Huerlimann in collaboration with Madalyn Cooper (University of Guam and College of Science & Engineering)
Keywords
eDNA; Guam; Sphyrna lewini (Sphyrnidae); scalloped hammerhead shark
Supervision

Advisory Accreditation: I can be on your Advisory Panel as a Primary or Secondary Advisor.

These Higher Degree Research projects are either current or by students who have completed their studies within the past 5 years at JCU. Linked titles show theses available within ResearchOnline@JCU.

Current
  • Monitoring tropical freshwater biodiversity using environmental DNA (eDNA) (PhD , Secondary Advisor)
  • Genome surveillance of bacterial pathogens (PhD , Secondary Advisor)
  • Discovering Faecal Microbiome Associated with Pre-Term Birth (PhD , Secondary Advisor)
  • Resolving the global occurrence and distribution of sawfishes using genetic techniques (PhD , Secondary Advisor)
  • Intestinal and environmental microbiome community analysis in formed block tiger and banana shrimps as a tool for prawn health and production biomonitoring (PhD , Secondary Advisor)
Collaboration

The map shows research collaborations by institution from the past 7 years.
Note: Map points are indicative of the countries or states that institutions are associated with.

  • 5+ collaborations
  • 4 collaborations
  • 3 collaborations
  • 2 collaborations
  • 1 collaboration
  • Indicates the Tropics (Torrid Zone)

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