
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
2021
Journal Article
Legislative landscape of black soldier fly (Hermetia illucens) as feed
Alagappan, S., Rowland, D., Barwell, R., Mantilla, S. M. O., Mikkelsen, D., James, P., Yarger, O. and Hoffman, L.C. (2021). Legislative landscape of black soldier fly (Hermetia illucens) as feed. Journal of Insects as Food and Feed, 8 (4), 343-355. doi: 10.3920/jiff2021.0111
2021
Conference Publication
Nasal microbiota diversity and abundance in shelter dogs carrying methicillin-resistant and -sensitive Staphylococcus species
Horsman, S., Mikkelsen, D., Mallyon, J., Soares Magalhães, R.J. , Meler, E. and Gibson, J.S. (2021). Nasal microbiota diversity and abundance in shelter dogs carrying methicillin-resistant and -sensitive Staphylococcus species. Australian Society for Microbiology, Melbourne, VIC, Australia, 31 May-3 June 2021.
2021
Conference Publication
Is the equine gut colonised in utero by amniotic bacteria?
Mols, K.L., Boe-Hansen, G.B., Mikkelsen, D., Bryden, W.L. and Cawdell-Smith, A.J. (2021). Is the equine gut colonised in utero by amniotic bacteria?. Virtual Equine Science Symposium, Online, 1 – 4 June 2021. Amsterdam, Netherlands: Elsevier. doi: 10.1016/j.jevs.2021.103572
2021
Journal Article
Wheat-based food form has a greater effect than amylose content on fermentation outcomes and microbial community shifts in an in vitro fermentation model
Bui, Alexander T., Williams, Barbara A., Murtaza, Nida, Lisle, Allan, Mikkelsen, Deirdre, Morrison, Mark and Gidley, Michael J. (2021). Wheat-based food form has a greater effect than amylose content on fermentation outcomes and microbial community shifts in an in vitro fermentation model. Food Hydrocolloids, 114 106560, 1-9. doi: 10.1016/j.foodhyd.2020.106560
2021
Journal Article
In vitro fermentation of legume cells and components: Effects of cell encapsulation and starch/protein interactions
Bhattarai, Rewati R., Dhital, Sushil, Williams, Barbara A., Yang, Hong Jian, Mikkelsen, Deirdre, Flanagan, Bernadine M. and Gidley, Michael J. (2021). In vitro fermentation of legume cells and components: Effects of cell encapsulation and starch/protein interactions. Food Hydrocolloids, 113 106538, 106538. doi: 10.1016/j.foodhyd.2020.106538
2021
Journal Article
Interaction of cellulose and xyloglucan influences in vitro fermentation outcomes
Lu, Shiyi, Mikkelsen, Deirdre, Flanagan, Bernadine M., Williams, Barbara A. and Gidley, Michael J. (2021). Interaction of cellulose and xyloglucan influences in vitro fermentation outcomes. Carbohydrate Polymers, 258 117698, 1-9. doi: 10.1016/j.carbpol.2021.117698
2021
Journal Article
Wheat cell walls and constituent polysaccharides induce similar microbiota profiles upon in vitro fermentation despite different short chain fatty acid end-product levels
Lu, Shiyi, Mikkelsen, Deirdre, Yao, Hong, Williams, Barbara A., Flanagan, Bernadine M. and Gidley, Michael J. (2021). Wheat cell walls and constituent polysaccharides induce similar microbiota profiles upon in vitro fermentation despite different short chain fatty acid end-product levels. Food and Function, 12 (3), 1135-1146. doi: 10.1039/d0fo02509g
2020
Journal Article
Multienzyme super-dosing in broiler chicken diets: the implications for gut morphology, microbial profile, nutrient digestibility, and bone mineralization
Madigan-Stretton, Jacoba, Mikkelsen, Deirdre and Soumeh, Elham Assadi (2020). Multienzyme super-dosing in broiler chicken diets: the implications for gut morphology, microbial profile, nutrient digestibility, and bone mineralization. Animals, 11 (1) 1, 1-17. doi: 10.3390/ani11010001
2020
Journal Article
Metabolism of Black Carrot Polyphenols during In Vitro Fermentation is Not Affected by Cellulose or Cell Wall Association
Netzel, Gabriele, Mikkelsen, Deirdre, Flanagan, Bernadine M., Netzel, Michael E., Gidley, Michael J. and Williams, Barbara A. (2020). Metabolism of Black Carrot Polyphenols during In Vitro Fermentation is Not Affected by Cellulose or Cell Wall Association. Foods, 9 (12) 1911, 1911. doi: 10.3390/foods9121911
2020
Journal Article
Prenatal establishment of the foal gut microbiota: a critique of the in utero colonisation hypothesis
Mols, Kirsty L., Boe-Hansen, Gry B., Mikkelsen, Deirdre, Bryden, Wayne L. and Cawdell-Smith, A. Judy (2020). Prenatal establishment of the foal gut microbiota: a critique of the in utero colonisation hypothesis. Animal Production Science, 60 (18), 2080-2092. doi: 10.1071/AN20010
2020
Journal Article
Cell wall architecture as well as chemical composition determines fermentation of wheat cell walls by a faecal inoculum
Lu, Shiyi, Flanagan, Bernadine M., Williams, Barbara A., Mikkelsen, Deirdre and Gidley, Michael J. (2020). Cell wall architecture as well as chemical composition determines fermentation of wheat cell walls by a faecal inoculum. Food Hydrocolloids, 107 105858, 105858. doi: 10.1016/j.foodhyd.2020.105858
2020
Journal Article
Wood hemicelluloses exert distinct biomechanical contributions to cellulose fibrillar networks
Berglund, Jennie, Mikkelsen, Deirdre, Flanagan, Bernadine M., Dhital, Sushil, Gaunitz, Stefan, Henriksson, Gunnar, Lindström, Mikael E., Yakubov, Gleb E., Gidley, Michael J. and Vilaplana, Francisco (2020). Wood hemicelluloses exert distinct biomechanical contributions to cellulose fibrillar networks. Nature Communications, 11 (1) 4692, 4692. doi: 10.1038/s41467-020-18390-z
2020
Journal Article
In vitro fermentation outcomes of arabinoxylan and galactoxyloglucan depend on fecal inoculum more than substrate chemistry
Feng, Guangli, Mikkelsen, Deirdre, Hoedt, Emily C., Williams, Barbara A., Flanagan, Bernadine M., Morrison, Mark and Gidley, Michael J. (2020). In vitro fermentation outcomes of arabinoxylan and galactoxyloglucan depend on fecal inoculum more than substrate chemistry. Food and Function, 11 (9), 7892-7904. doi: 10.1039/d0fo01103g
2020
Journal Article
Fruit and vegetable insoluble dietary fibre in vitro fermentation characteristics depend on cell wall type
Widaningrum, Flanagan, Bernadine M., Williams, Barbara A., Sonni, Francesca, Mikkelsen, Deirdre and Gidley, Michael J. (2020). Fruit and vegetable insoluble dietary fibre in vitro fermentation characteristics depend on cell wall type. Bioactive Carbohydrates and Dietary Fibre, 23 100223, 100223. doi: 10.1016/j.bcdf.2020.100223
2020
Journal Article
Independent fermentation and metabolism of dietary polyphenols associated with a plant cell wall model
Phan, A. D. T., Williams, B. A., Netzel, G., Mikkelsen, D., D'Arcy, B. R. and Gidley, M. J. (2020). Independent fermentation and metabolism of dietary polyphenols associated with a plant cell wall model. Food and Function, 11 (3), 2218-2230. doi: 10.1039/c9fo02987g
2020
Journal Article
Purified plant cell walls with adsorbed polyphenols alter porcine faecal bacterial communities during in vitro fermentation
Grant, Lucas J., Mikkelsen, Deirdre, Phan, Anh Dao T., Kang, Seungha, Ouwerkerk, Diane, Klieve, Athol V., Gidley, Mike J. and Williams, Barbara (2020). Purified plant cell walls with adsorbed polyphenols alter porcine faecal bacterial communities during in vitro fermentation. Food and Function, 11 (1), 834-845. doi: 10.1039/c9fo02428j
2020
Book Chapter
Formation of cellulose-based composites with hemicelluloses and pectins using Komagataeibacter fermentation
Mikkelsen, Deirdre, Lopez-Sanchez, Patricia, Wang, Dongjie and Gidley, Michael J. (2020). Formation of cellulose-based composites with hemicelluloses and pectins using Komagataeibacter fermentation. The plant cell wall: methods and protocols. (pp. 73-87) New York, NY, United States: Humana Press. doi: 10.1007/978-1-0716-0621-6_5
2020
Journal Article
High amylose wheat starch structures display unique fermentability characteristics, microbial community shifts and enzyme degradation profiles
Bui, Alexander T., Williams, Barbara A., Hoedt, Emily C., Morrison, Mark, Mikkelsen, Deirdre and Gidley, Michael J. (2020). High amylose wheat starch structures display unique fermentability characteristics, microbial community shifts and enzyme degradation profiles. Food and Function, 11 (6), 5635-5646. doi: 10.1039/d0fo00198h
2019
Journal Article
Whole fruit pulp (mango) and a soluble fibre (pectin) impact bacterial diversity and abundance differently within the porcine large intestine
Grant, Lucas J., Mikkelsen, Deirdre, Ouwerkerk, Diane, Klieve, Athol V., Gidley, Michael J. and Williams, Barbara A. (2019). Whole fruit pulp (mango) and a soluble fibre (pectin) impact bacterial diversity and abundance differently within the porcine large intestine. Bioactive Carbohydrates and Dietary Fibre, 19 100192, 100192. doi: 10.1016/j.bcdf.2019.100192
2019
Journal Article
“Dietary fibre”: moving beyond the “soluble/insoluble” classification for monogastric nutrition, with an emphasis on humans and pigs
Williams, Barbara A., Mikkelsen, Deirdre, Flanagan, Bernadine M. and Gidley, Michael J. (2019). “Dietary fibre”: moving beyond the “soluble/insoluble” classification for monogastric nutrition, with an emphasis on humans and pigs. Journal of Animal Science and Biotechnology, 10 (1) 45, 45. doi: 10.1186/s40104-019-0350-9
Funding
Current funding
Past funding
Supervision
Availability
- Dr Deirdre Mikkelsen is:
- Available for supervision
Before you email them, read our advice on how to contact a supervisor.
Supervision history
Current supervision
-
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
-
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
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
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
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
Enquiries
For media enquiries about Dr Deirdre Mikkelsen's areas of expertise, story ideas and help finding experts, contact our Media team: