
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
2023
Journal Article
Near infrared spectroscopy for prediction of yeast and mould counts in black soldier fly larvae, feed and frass: a proof of concept
Alagappan, Shanmugam, Dong, Anran, Mikkelsen, Deirdre, Hoffman, Louwrens C., Mantilla, Sandra Milena Olarte, James, Peter, Yarger, Olympia and Cozzolino, Daniel (2023). Near infrared spectroscopy for prediction of yeast and mould counts in black soldier fly larvae, feed and frass: a proof of concept. Sensors, 23 (15) 6946, 1-13. doi: 10.3390/s23156946
2023
Journal Article
Composition and functional profiles of human faecal microbiota fermenting plant-based food particles are related to water-holding capacity more than particle size
Yao, Hong, Williams, Barbara A., Mikkelsen, Deirdre, Flanagan, Bernadine M. and Gidley, Michael J. (2023). Composition and functional profiles of human faecal microbiota fermenting plant-based food particles are related to water-holding capacity more than particle size. Food Hydrocolloids, 141 108714, 1-11. doi: 10.1016/j.foodhyd.2023.108714
2023
Journal Article
Bacterial physiology highlighted by the δ13C fractionation of bacteriohopanetetrol isomers
Schwartz-Narbonne, Rachel, Schaeffer, Philippe, Lengger, Sabine K., Blewett, Jerome, Martin Jones, D., Motsch, Estelle, Crombie, Andrew, Jetten, Mike S.-M., Mikkelsen, Deirdre, Normand, Philippe, Nuijten, Guylaine H.L., Pancost, Richard D. and Rush, Darci (2023). Bacterial physiology highlighted by the δ13C fractionation of bacteriohopanetetrol isomers. Organic Geochemistry, 181 104617, 104617. doi: 10.1016/j.orggeochem.2023.104617
2023
Journal Article
Nasal microbiota profiles in shelter dogs with dermatological conditions carrying methicillin-resistant and methicillin-sensitive Staphylococcus species
Horsman, Sara, Meler, Erika, Mikkelsen, Deirdre, Mallyon, John, Yao, Hong, Soares Magalhães, Ricardo J. and Gibson, Justine S. (2023). Nasal microbiota profiles in shelter dogs with dermatological conditions carrying methicillin-resistant and methicillin-sensitive Staphylococcus species. Scientific Reports, 13 (1) 4844, 4844. doi: 10.1038/s41598-023-31385-2
2023
Journal Article
Hemicellulose-bacterial cellulose ribbon interactions affect the anisotropic mechanical behaviour of bacterial cellulose hydrogels
Chen, Si-Qian, Lopez-Sanchez, Patricia, Mikkelsen, Deirdre, Martinez-Sanz, Marta, Li, Zhaofeng, Zhang, Shuyan, Gilbert, Elliot P., Li, Lin and Gidley, Michael J. (2023). Hemicellulose-bacterial cellulose ribbon interactions affect the anisotropic mechanical behaviour of bacterial cellulose hydrogels. Food Hydrocolloids, 136 108283, 1-9. doi: 10.1016/j.foodhyd.2022.108283
2023
Journal Article
Lactate and buyrate proportions, methanogen growth and gas production during in vitro dietary fibre fermentation all depend on fibre concentration
Yao, Hong, Flanagan, Bernadine M., Williams, Barbara A., Mikkelsen, Deirdre and Gidley, Michael J. (2023). Lactate and buyrate proportions, methanogen growth and gas production during in vitro dietary fibre fermentation all depend on fibre concentration. Food Hydrocolloids, 134 108061, 1-11. doi: 10.1016/j.foodhyd.2022.108061
2023
Conference Publication
Identification and antimicrobial resistance of bacterial isolates cultured from clinical canine skin and ear samples in Queensland
Horsman, Sara, Meler, Erika, Mikkelsen, Deirdre, Soares Magalhães, Ricardo J. and Gibson, Justine S. (2023). Identification and antimicrobial resistance of bacterial isolates cultured from clinical canine skin and ear samples in Queensland. Antimicrobials 2023 Annual Scientific Meeting, Brisbane, QLD, Australia, 23-25 February 2023.
2023
Journal Article
Particle size of dietary fibre has diverse effects on in vitro gut fermentation rate and end-products depending on food source
Yao, Hong, Flanagan, Bernadine M., Williams, Barbara A., Mikkelsen, Deirdre and Gidley, Michael J. (2023). Particle size of dietary fibre has diverse effects on in vitro gut fermentation rate and end-products depending on food source. Food Hydrocolloids, 134 108096, 1-9. doi: 10.1016/j.foodhyd.2022.108096
2023
Journal Article
Novel constituents of Salvia hispanica L. (chia) nutlet mucilage and the improved in vitro fermentation of nutlets when ground
Ang, Main Ern, Cowley, James M., Yap, Kuok, Hahn, Michael G., Mikkelsen, Deirdre, Tucker, Matthew R., Williams, Barbara A. and Burton, Rachel A. (2023). Novel constituents of Salvia hispanica L. (chia) nutlet mucilage and the improved in vitro fermentation of nutlets when ground. Food and Function, 14 (3), 1401-1414. doi: 10.1039/d2fo03002k
2022
Journal Article
Soluble fibre concentration effects during in vitro fermentation: Higher concentration leads to increased butyrate proportion
Yao, Hong, Williams, Barbara A., Flanagan, Bernadine M., Lisle, Allan, Mikkelsen, Deirdre and Gidley, Michael J. (2022). Soluble fibre concentration effects during in vitro fermentation: Higher concentration leads to increased butyrate proportion. Food Hydrocolloids, 130 107728, 107728. doi: 10.1016/j.foodhyd.2022.107728
2022
Journal Article
Developing an antiviral surface cleaner utilising unique surface adsorption properties of hydroxyproline-rich-proteins
Shewan, Heather M. , Siauw, Meiliana , Vinden, Naomi , Dong, Anran , Beheshti, Amir , Chew, Keng Yih, Stokes, Jason R. , Short, Kirsty R., Mikkelsen, Deirdre, Koehler, Berthold and Reihmann, Matthias (2022). Developing an antiviral surface cleaner utilising unique surface adsorption properties of hydroxyproline-rich-proteins. Household and Personal Care Today, 17 (5), 57-61.
2022
Journal Article
Near infrared spectroscopy as a traceability tool to monitor black soldier fly larvae (Hermetia illucens) intended as animal feed
Alagappan, Shanmugam, Hoffman, Louwrens C., Olarte Mantilla, Sandra M., Mikkelsen, Deirdre, James, Peter, Yarger, Olympia and Cozzolino, Daniel (2022). Near infrared spectroscopy as a traceability tool to monitor black soldier fly larvae (Hermetia illucens) intended as animal feed. Applied Sciences, 12 (16) 8168, 8168. doi: 10.3390/app12168168
2022
Conference Publication
Uncovering the geographical associations between antimicrobial resistance and antimicrobial usage in dogs treated with anti-pruritic therapies for pruritic skin and ear diseases through data linkage
Horsman, S., Croton, C., Meler, E., Mikkelsen, D., Soares Magalhães, R. and Gibson, J. (2022). Uncovering the geographical associations between antimicrobial resistance and antimicrobial usage in dogs treated with anti-pruritic therapies for pruritic skin and ear diseases through data linkage. Vet Compass Australia Symposium, Online, 16 August 2022.
2022
Conference Publication
Geographical variation in antimicrobial resistance patterns of bacteria isolated from canine skin and ear samples in Queensland
Horsman, Sara, Meler, Erika, Mikkelsen, Deirdre, Gibson, Justine and Soares Magalhaes, Ricardo (2022). Geographical variation in antimicrobial resistance patterns of bacteria isolated from canine skin and ear samples in Queensland. Australian Society for Microbiology, Sydney, NSW, Australia, 11-14 July 2022.
2022
Journal Article
Absolute abundance values reveal microbial shifts and co-occurrence patterns during gut microbiota fermentation of dietary fibres in vitro
Yao, Hong, Lu, Shiyi, Williams, Barbara A., Flanagan, Bernadine M., Gidley, Michael J. and Mikkelsen, Deirdre (2022). Absolute abundance values reveal microbial shifts and co-occurrence patterns during gut microbiota fermentation of dietary fibres in vitro. Food Hydrocolloids, 127 107422, 107422. doi: 10.1016/j.foodhyd.2021.107422
2022
Journal Article
In vitro fermentation profiles of undigested fractions from legume and nut particles are affected by particle cohesion and entrapped macronutrients
Widaningrum, , Flanagan, Bernadine M., Williams, Barbara A., Sonni, Francesca, Chen, Pengfei, Mikkelsen, Deirdre and Gidley, Michael J. (2022). In vitro fermentation profiles of undigested fractions from legume and nut particles are affected by particle cohesion and entrapped macronutrients. Food and Function, 13 (9), 5075-5088. doi: 10.1039/d2fo00250g
2022
Journal Article
In vitro fermentation of onion cell walls and model polysaccharides using human faecal inoculum: effects of molecular interactions and cell wall architecture
Lu, Shiyi, Flanagan, Bernadine M., Mikkelsen, Deirdre, Williams, Barbara A. and Gidley, Michael J. (2022). In vitro fermentation of onion cell walls and model polysaccharides using human faecal inoculum: effects of molecular interactions and cell wall architecture. Food Hydrocolloids, 124 107257, 107257. doi: 10.1016/j.foodhyd.2021.107257
2022
Conference Publication
Is the equine gut colonised in utero?
Mols, Kirsty, Boe-Hansen, Gry B., Mikkelsen, Deirdre, Bryden, Wayne L. and Cawdell-Smith, Judy (2022). Is the equine gut colonised in utero?. Recent Advances in Animal Nutrition, Australia, June 2021. Clayton, VIC, Australia: CSIRO Publishing.
2022
Journal Article
Organic side streams (bioproducts) as substrate for black soldier fly (Hermetia illucens) intended as animal feed: chemical safety issues
Alagappan, Shanmugam, Rowland, Duncan, Barwell, Rob, Cozzolino, Daniel, Mikkelsen, Deirdre, Olarte Mantilla, Sandra M., James, Peter, Yarger, Olympia and Hoffman, Louwrens (2022). Organic side streams (bioproducts) as substrate for black soldier fly (Hermetia illucens) intended as animal feed: chemical safety issues. Animal Production Science, 62 (17), 1639-1651. doi: 10.1071/an22155
2021
Journal Article
Fermentation outcomes of wheat cell wall related polysaccharides are driven by substrate effects as well as initial faecal inoculum
Lu, Shiyi, Williams, Barbara A., Flanagan, Bernadine M., Yao, Hong, Mikkelsen, Deirdre and Gidley, Michael J. (2021). Fermentation outcomes of wheat cell wall related polysaccharides are driven by substrate effects as well as initial faecal inoculum. Food Hydrocolloids, 120 106978, 106978. doi: 10.1016/j.foodhyd.2021.106978
Funding
Current funding
Past funding
Supervision
Availability
- Dr Deirdre Mikkelsen is:
- Available for supervision
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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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