Overview
Background
United Nations (UN) member states in 2015 agreed to 17 global Sustainable Development Goals (SDGs) to end poverty, protect the planet and ensure prosperity for all. Dr Deirdre Mikkelsen is a microbiologist and Senior Lecturer in Food Science at the School of Agriculture and Food Sustainability, where her teaching and research contribute to several UN SDGs, including:
- Goal 2 – Zero Hunger
- Goal 3 – Good Health and Well-being
- Goal 4 – Quality Education
- Goal 12 – Responsible Consumption and Production
- Goal 13 – Climate Action
- Goal 15 – Life on Land
Deirdre holds a B.Sc. (First Class Honours, 1999) and a PhD in Microbiology (2005), both from UQ. She has expertise in molecular microbial ecology, bioinformatics and fermentation microbiology. Her academic journey includes research roles at the Advanced Wastewater Management Centre (2005) and from 2006 at the Centre for Nutrition and Food Sciences (CNAFS), Queensland Alliance for Agriculture and Food Innovation (QAAFI), where she held Postdoctoral and Research Fellow positions. She joined her current School in 2019.
Program Coordination and Teaching
Dr Deirdre Mikkelsen is the Program Coordinator for the following postgraduate programs:
- Master of Food Science and Technology
- Master of Food Science and Technology (Research Extensive)
- Graduate Certificate in Food Science and Technology
She also coordinates and teaches:
- FOOD2000 – Food Science
- FOOD3017 – Food Safety & Quality Management
- FOOD7021 – Professional Experience (Work Integrated Learning)
Professional Memberships and Engagement
- Member, Australian Institute of Food Science and Technology (AIFST) – Queensland Branch Committee
- Member, International Union of Food Science and Technology (IUFoST) Education Oversight Group – Australasia representative
- Member, IUFoST – Food Safety Working Committee 2.2 (Education focus)
- Academic Advisory Group Member, Ag Connections Agriskills Accelerator Program
- Member, Australian Society for Microbiology (ASM)
Availability
- Dr Deirdre Mikkelsen is:
- Available for supervision
Fields of research
Qualifications
- Bachelor (Honours) of Microbiology, The University of Queensland
- Doctor of Philosophy, The University of Queensland
Research impacts
Research Interests
Deirdre’s research focuses on understanding how foods, diets, and nutrients influence the gut microbiota in humans and monogastric animal models. Her work integrates molecular microbial ecology and biopolymer science to explore:
- The structure and function of plant cell walls in cereals and grasses
- The fermentability of dietary fibres as potential prebiotics
- Microbial interactions with dietary fibres using molecular techniques
- The impact of dietary fibres on gut microbiota diversity and abundance
Research Impact
Deirdre’s research supports sustainable food systems and improved health outcomes by advancing knowledge of gut microbiota–diet interactions. Her work informs the development of functional foods and dietary strategies to promote gut health.
She has published 88 peer-reviewed articles, with an h-index of 30 and 3916 citations. Over 80% of her publications appear in Q1 journals. A highlight of her career is a 2020 publication in Nature Communications, co-authored with colleagues from CNAFS and KTH Sweden.
Works
Search Professor Deirdre Mikkelsen’s works on UQ eSpace
2025
Journal Article
The fungus among us: innovations and applications of mycelium-based composites
Parhizi, Zahra, Dearnaley, John, Kauter, Kate, Mikkelsen, Deirdre, Pal, Priya, Shelley, Tristan and Burey, Paulomi (Polly) (2025). The fungus among us: innovations and applications of mycelium-based composites. Journal of Fungi, 11 (8) 549, 549. doi: 10.3390/jof11080549
2025
Journal Article
Investigating the effect of larval instar, post-harvest treatments, and substrate on the nutritional profile of black soldier fly larvae (Hermetia illucens)
Alagappan, Shanmugam, Hong, Hung, Mikkelsen, Deirdre, Olarte Mantilla, Sandra, James, Peter, Yarger, Olympia, Hoffman, Louwrens and Cozzolino, Daniel (2025). Investigating the effect of larval instar, post-harvest treatments, and substrate on the nutritional profile of black soldier fly larvae (Hermetia illucens). Animal Production Science, 65 (8) AN24108. doi: 10.1071/an24108
2025
Journal Article
Correction: Rame Hau et al. The Prevalence and Risk Factors Associated with the Presence of Antibiotic Residues in Milk from Peri-Urban Dairy Cattle Farms in Kathmandu, Nepal. Antibiotics 2025, 14, 98
Rame Hau, Erda E., Sharma, Minu, Khanal, Bal K. Sharma, Sly, Peter D., Mikkelsen, Deirdre, Clark, Nicholas and Soares Magalhães, Ricardo J. (2025). Correction: Rame Hau et al. The Prevalence and Risk Factors Associated with the Presence of Antibiotic Residues in Milk from Peri-Urban Dairy Cattle Farms in Kathmandu, Nepal. Antibiotics 2025, 14, 98. Antibiotics, 14 (5) 473, 473. doi: 10.3390/antibiotics14050473
2025
Journal Article
Impact of pectin and alginate gel particle size and concentration on in vitro gut fermentation
Li, Anqi, Shewan, Heather M., Flanagan, Bernadine M., Williams, Barbara A., Mikkelsen, Deirdre and Gidley, Michael J. (2025). Impact of pectin and alginate gel particle size and concentration on in vitro gut fermentation. Food Hydrocolloids, 160 110808. doi: 10.1016/j.foodhyd.2024.110808
2025
Journal Article
Microbial safety of black soldier fly larvae (Hermetia illucens) reared on food waste streams
Alagappan, Shanmugam, Dong, Anran, Hoffman, Louwrens, Cozzolino, Daniel, Mantilla, Sandra Olarte, James, Peter, Yarger, Olympia and Mikkelsen, Deirdre (2025). Microbial safety of black soldier fly larvae (Hermetia illucens) reared on food waste streams. Waste Management, 194, 221-227. doi: 10.1016/j.wasman.2025.01.019
2025
Journal Article
The prevalence and risk factors associated with the presence of antibiotic residues in milk from peri-urban dairy cattle farms in Kathmandu, Nepal
Rame Hau, Erda E. Rame, Sharma, Minu, Khanal, Bal K. Sharma, Sly, Peter D., Mikkelsen, Deirdre, Clark, Nicholas and Soares Magalhães, Ricardo J. Soares (2025). The prevalence and risk factors associated with the presence of antibiotic residues in milk from peri-urban dairy cattle farms in Kathmandu, Nepal. Antibiotics, 14 (1) 98, 1-18. doi: 10.3390/antibiotics14010098
2025
Journal Article
Molecular epidemiological characteristics of Staphylococcus pseudintermedius, Staphylococcus coagulans, and coagulase-negative staphylococci cultured from clinical canine skin and ear samples in Queensland
Horsman, Sara, Zaugg, Julian, Meler, Erika, Mikkelsen, Deirdre, Soares Magalhães, Ricardo J. and Gibson, Justine S. (2025). Molecular epidemiological characteristics of Staphylococcus pseudintermedius, Staphylococcus coagulans, and coagulase-negative staphylococci cultured from clinical canine skin and ear samples in Queensland. Antibiotics, 14 (1) 80, 1-25. doi: 10.3390/antibiotics14010080
2025
Journal Article
Factors affecting plant food particle behaviour during in vitro colonic microbial fermentation
Yao, Hong, Flanagan, Bernadine M., Williams, Barbara A., Mikkelsen, Deirdre and Gidley, Michael J. (2025). Factors affecting plant food particle behaviour during in vitro colonic microbial fermentation. Trends in Food Science and Technology, 155 104802, 1-9. doi: 10.1016/j.tifs.2024.104802
2025
Journal Article
Characterization and comparison of fecal microbiota in horses with pituitary pars intermedia dysfunction and age-matched controls
Wang, Wenqing, Gibson, Justine, Horsman, Sara, Mikkelsen, Deirdre and Bertin, François-René (2025). Characterization and comparison of fecal microbiota in horses with pituitary pars intermedia dysfunction and age-matched controls. Journal of Veterinary Internal Medicine, 39 (1) e17288, 1-11. doi: 10.1111/jvim.17288
2024
Journal Article
Design characteristics of integrated surveillance of antimicrobial resistance at the human, animal, and environment interfaces
Hau, Erda Eni Rame, Sly, Peter D., Mikkelsen, Deirdre, Taneja, Neelam, Penjor, Kinley, Ryu, Sukhyun, Donner, Erica, Mollinger, Joanne, Ferreira, Jorge Pinto, Schipp, Mark and Soares Magalhaes, Ricardo J. (2024). Design characteristics of integrated surveillance of antimicrobial resistance at the human, animal, and environment interfaces. CABI Reviews, 19 (1), 1-12. doi: 10.1079/cabireviews.2024.0047
2024
Journal Article
Effect of larval instar and post‐harvest treatments on heavy metals in BSFL and frass reared on commercial food waste streams
Alagappan, Shanmugam, Mallard, Sam, Cozzolino, Daniel, Mikkelsen, Deirdre, James, Peter, Mantilla, Sandra Olarte, Yarger, Olympia and Hoffman, Louwrens (2024). Effect of larval instar and post‐harvest treatments on heavy metals in BSFL and frass reared on commercial food waste streams. International Journal of Food Science and Technology, 59 (11), 8214-8223. doi: 10.1111/ijfs.17511
2024
Conference Publication
Geographical variation and co-distribution of antimicrobial resistance and usage for canine skin and ear infections in Queensland: the need for continued integrated surveillance
Horsman, Sara, Gibson, Justine, Meler, Erika, Mikkelsen, Deirdre and Soares Magalhaes, Ricardo (2024). Geographical variation and co-distribution of antimicrobial resistance and usage for canine skin and ear infections in Queensland: the need for continued integrated surveillance. SAAFE CRC 2024 AMR Solutions Summit From AMR Sources to Solutions, Adelaide, SA Australia, 17-18 September 2024.
2024
Journal Article
Differential effects of pectin-based dietary fibre type and gut microbiota composition on in vitro fermentation outcomes
Yao, Hong, Flanagan, Bernadine M., Williams, Barbara A., Wu, Xiyang, Mikkelsen, Deirdre and Gidley, Michael J. (2024). Differential effects of pectin-based dietary fibre type and gut microbiota composition on in vitro fermentation outcomes. Carbohydrate Polymers, 339 122284, 122284. doi: 10.1016/j.carbpol.2024.122284
2024
Journal Article
Faecal bacterial communities differ amongst discrete foraging populations of dugongs along the east Australian coast
Mikkelsen, Deirdre, McGowan, Alexandra M, Gibson, Justine S, Lanyon, Janet M, Horsman, Sara and Seddon, Jennifer M (2024). Faecal bacterial communities differ amongst discrete foraging populations of dugongs along the east Australian coast. FEMS Microbiology Ecology, 100 (6) fiae051. doi: 10.1093/femsec/fiae051
2024
Journal Article
Monitoring compositional changes in black soldier fly larvae after processing (drying and blanching) using near infrared spectroscopy
Cozzolino, D., Alagappan, S., Ochoa, M., Zhang, S., Yarger, O., Hoffman, L.C. and Mikkelsen, D. (2024). Monitoring compositional changes in black soldier fly larvae after processing (drying and blanching) using near infrared spectroscopy. Infrared Physics & Technology, 138 105212, 1-7. doi: 10.1016/j.infrared.2024.105212
2024
Journal Article
Near-infrared spectroscopy (NIRS) for monitoring the nutritional composition of black soldier fly larvae (BSFL) and frass
Alagappan, Shanmugam, Hoffman, Louwrens, Mikkelsen, Deirdre, Olarte Mantilla, Sandra, James, Peter, Yarger, Olympia and Cozzolino, Daniel (2024). Near-infrared spectroscopy (NIRS) for monitoring the nutritional composition of black soldier fly larvae (BSFL) and frass. Journal of the Science of Food and Agriculture, 104 (3), 1487-1496. doi: 10.1002/jsfa.13044
2024
Journal Article
Biomass attachment and microbiota shifts during porcine faecal in vitro fermentation of almond and macadamia nuts differing in particle sizes
Bermudez, Cindy, Yao, Hong, Widaningrum, Williams, Barbara A., Flanagan, Bernadine M., Gidley, Michael J. and Mikkelsen, Deirdre (2024). Biomass attachment and microbiota shifts during porcine faecal in vitro fermentation of almond and macadamia nuts differing in particle sizes. Food and Function, 15 (5), 2406-2421. doi: 10.1039/d3fo03612j
2024
Journal Article
In vitro fermentation characteristics of fruit and vegetable juicing wastes using human fecal inoculum are determined by cell wall architecture
Widaningrum, Flanagan, Bernadine M., Williams, Barbara A., Sonni, Francesca, Mikkelsen, Deirdre and Gidley, Michael J. (2024). In vitro fermentation characteristics of fruit and vegetable juicing wastes using human fecal inoculum are determined by cell wall architecture. Food Hydrocolloids, 146 (Part A) 109205, 109205. doi: 10.1016/j.foodhyd.2023.109205
2024
Conference Publication
Molecular epidemiological characteristics of Staphylococcus species cultured from clinical canine skin and ear samples in Queensland
Horsman, Sara, Zaugg, Julian, Mikkelsen, Deirdre, Soares Magalhaes, Ricardo J., Meler, Erika and Gibson, Justine S. (2024). Molecular epidemiological characteristics of Staphylococcus species cultured from clinical canine skin and ear samples in Queensland. Antimicrobials 2024 Annual Scientific Meeting, Sydney, NSW Australia, 15-17 February 2024.
2023
Journal Article
Enzymatic arabinose depletion of wheat arabinoxylan regulates in vitro fermentation profiles and potential microbial degraders
Yao, Hong, Flanagan, Bernadine M., Williams, Barbara A., Ismail, Munirah, Ersya, Astrada Dyna, Gidley, Michael J. and Mikkelsen, Deirdre (2023). Enzymatic arabinose depletion of wheat arabinoxylan regulates in vitro fermentation profiles and potential microbial degraders. Food Hydrocolloids, 142 108743, 1-10. doi: 10.1016/j.foodhyd.2023.108743
Funding
Current funding
Past funding
Supervision
Availability
- Dr Deirdre Mikkelsen is:
- Available for supervision
Looking for a supervisor? Read our advice on how to choose a supervisor.
Supervision history
Current supervision
-
Doctor Philosophy
The Role of Hypothalamic Dopaminergic Degeneration in Intestinal Health in Horses with Pituitary Pars Intermedia Dysfunction
Associate Advisor
Other advisors: Dr Justine Gibson, Dr Viviana Gonzalez Astudillo, Dr Allison Stewart, Associate Professor Francois-Rene Bertin
-
Doctor Philosophy
Epidemiology and control of canine skin and ear conditions in Australia
Associate Advisor
Other advisors: Professor Ricardo Soares Magalhaes, Dr Erika Meler, Dr Justine Gibson
-
Doctor Philosophy
Understanding the relationship between the shape, size and local density of food gels and their functionality in vitro
Associate Advisor
Other advisors: Dr Bernadine Flanagan, Dr Heather Shewan, Professor Mike Gidley
-
Doctor Philosophy
Investigations into the importance of antimicrobial residues in the surveillance of antimicrobial resistance in peri-urban dairy farms of Nepal
Associate Advisor
Other advisors: Professor Peter Sly, Dr Nicholas Clark, Professor Ricardo Soares Magalhaes
-
Doctor Philosophy
Comprehensive use of whole body computed tomography,microbiome and metabolomics analysis to measure the effects ofdietary and exercise interventions on body fat content in dogs a stepforward in the understanding of obesity and overweight in dogs
Associate Advisor
Other advisors: Dr Rebekah Scotney, Professor Joerg Henning, Dr Erika Meler, Dr Justine Gibson
Completed supervision
-
2024
Doctor Philosophy
Microbiota interactions and functionality in response to nut consumption and in vitro fermentation
Principal Advisor
Other advisors: Dr Bernadine Flanagan, Professor Mike Gidley
-
2017
Doctor Philosophy
Changes to gut bacteria composition and diversity by the addition of soluble dietary fibres to porcine diets: human health implications.
Principal Advisor
Other advisors: Professor Mike Gidley
-
2025
Doctor Philosophy
Pathogenicity, Genomic Characterisation, and Management of Fusarium proliferatum and F. oxysporum in Allium spp. with focus on Garlic (Allium sativum)
Associate Advisor
Other advisors: Dr Alwyn Williams, Professor Victor Galea
-
2024
Doctor Philosophy
Optimising and industrialising black soldier fly (BSF) production -redirecting food waste to livestock feed production using insects
Associate Advisor
Other advisors: Associate Professor Daniel Cozzolino, Professor Louw Hoffman
-
2023
Doctor Philosophy
Dietary fibre concentration and particle size drive in vitro gut microbial fermentation behaviours
Associate Advisor
Other advisors: Dr Bernadine Flanagan, Professor Mike Gidley
-
2022
Master Philosophy
Characterisation of a synbiotic product and its impact on human gastrointestinal microbiota
Associate Advisor
Other advisors: Professor Mark Turner, Professor Nidhi Bansal
-
2022
Doctor Philosophy
Mechanisms of Resistant Starch Breakdown by Gut Microbiota Using High Amylose Wheat
Associate Advisor
Other advisors: Professor Mark Morrison, Professor Mike Gidley
-
2021
Doctor Philosophy
In Vitro Fermentation of Insoluble Dietary Fibers and Undigested Fractions from Plant Food Sources
Associate Advisor
Other advisors: Dr Bernadine Flanagan, Professor Mike Gidley
-
2021
Doctor Philosophy
In vitro gut microbial fermentation of models for plant dietary fibre
Associate Advisor
Other advisors: Dr Bernadine Flanagan, Professor Mike Gidley
-
2019
Doctor Philosophy
BACTERIAL MEDIATED ENZYMATIC METABOLISM OF ARABINOXYLAN AND GALACTOXYLOGLUCAN UNDER IN VITRO FERMENTATION CONDITIONS
Associate Advisor
Other advisors: Dr Bernadine Flanagan, Professor Mike Gidley
-
2018
Doctor Philosophy
Characterisation of cellulose produced by different Komagataeibacter strains: Towards an improved plant cell wall model
Associate Advisor
Other advisors: Professor Mike Gidley
-
2017
Doctor Philosophy
Fruit components and their effects on the gastrointestinal bacterial community
Associate Advisor
Other advisors: Professor Mike Gidley
-
2012
Doctor Philosophy
The role of the plant cell wall on the bioaccessibility of anthocyanins and phenolic acids released from fruits and vegetables.
Associate Advisor
Other advisors: Professor Mike Gidley
Media
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