Roger Huerlimann is a post-doctoral researcher at the Okinawa Institute of Science and Technology, Japan. There, he is researching how tropical reef fish can accimlate to raising sea temperatures and heat waves. He still has strong ties to James Cook Unviersity, being involved in multiple ongoing projects.

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.

  • BC3203: Bioinformatics (Level 3; TSV)
  • BC5203: Advanced Bioinformatics (Level 5; TSV)
  • 2020 to present - Post-doctoral researcher, Okinawa Institute of Science and Technology (Okinawa, Japan)
  • 2015 to 2020 - 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
  • 2008 - MAppSc: University Medal for Excellence
  • 2002 - BSc: Award for outstanding performance by the Swiss Union of Applied Chemistry (SVC)

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

ResearchOnline@JCU stores 48+ 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.

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

Exploring the Long-Term Effects of Probiotic Supplementation in Premature Infants

Indicative Funding
$12,700 over 5 years (administered by Townsville Hospital and Health Service)
Probiotic supplementation is now standard care for pre-term infants in the neonatal intensive care unit (NICU); significantly reducing the risk of Necrotising Enterocolitis (NEC) and mortality. What is not known is the long-term impact of this probiotic treatment on the developing infant gut microbiome. Evidence from a previous study shows positive effects, however, two important questions remain. 1. Microbes from probiotic supplementation appear to colonize the infant gut, cause positive modulation and reduce the incidence of disease, does this effect persist over the first year of life? 2. Should the criteria for probiotic supplementation be expanded to include all infants?
Yoga Kandasamy, Donna Rudd, Roger Huerlimann and Jacob Westaway (Townsville Hospital and Health Service, College of Public Health, Medical & Vet Sciences and College of Science & Engineering)
Microbiome; Neonatal; NICU; Gut microbiome

Townsville City Council - Contract Research

Ecological Impact of Antibiotic Resistance Released from the Cleveland Bay Purification Plant using Marine Turtle Species

Indicative Funding
$260,139 over 3 years
Cleveland Bay is a grazing ground for turtle species. Cleveland Bay Purification plant (CBPP) treats waste that may contain a variety of antibiotics. This study aims to determine the prevalence and distribution patterns of antibiotic resistant genes in the CBPP effluent and in the immediate receiving environment. Marine turtles in Cleveland Bay will be used to determine the localized impacts of both antibiotics and antibiotic resistant genes as compared to resident turtles from a pristine environment. This study will provide valuable insight into the direct effect that antibiotics and ARG?s in WWTP effluent have on ecological health and ecological risk.
Madoc Sheehan, Robert Kinobe, Ellen Ariel, Roger Huerlimann, Kezia Drane, Anna Whelan and Ian Bell (College of Science & Engineering, College of Public Health, Medical & Vet Sciences, Townsville City Council and QLD Department of Environment and Science)
Anitbiotics; Turtle; Risk Assessment; Antibiotic Resistant Genes; Wastewater Treatment; Microbiota

CRC for Developing Northern Australia Scheme - Projects

Biosecurity in northern Australian prawn aquaculture

Indicative Funding
$441,819 over 2 years
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.
Dean Jerry, Ellen Ariel, Kelly Condon and Roger Huerlimann (College of Science & Engineering, College of Public Health and Medical & Vet Sciences)
Penaeus monodon (Penaidae); Disease; Prawn; Aquaculture

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
$273,586 over 3 years (administered by University of Guam)
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.
Tom Schils, Jan Strugnell, Agnes Le Port and Roger Huerlimann in collaboration with Madalyn Cooper (University of Guam and College of Science & Engineering)
eDNA; Guam; Sphyrna lewini (Sphyrnidae); scalloped hammerhead shark

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.

  • Monitoring tropical freshwater biodiversity using environmental DNA (eDNA) (PhD , Secondary Advisor)
  • Intestinal and environmental microbiome community analysis in farmed black tiger and banana shrimps as a tool for prawn health and production biomonitoring (PhD , Secondary Advisor)
  • Assessment of the ecological risk of emerging Antibiotic Resistance released from the Cleveland Bay Purification Plant on marine Testudine species. (PhD , Secondary Advisor)

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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