We study the common and chronic inflammatory bowel diseases, progression to cancer, and associated autoimmune diseases of the gut-liver-brain axis (e.g., multiple sclerosis, MASLD). Our work spans from pregnancy to childhood development, to adulthood in health and diseases.

The etiology of autoimmune diseases remains poorly understood, and incidence rates are rising. Studies continue to demonstrate the significance of dysbiosis (altered gut microbiome) in disease pathogenesis, suggesting the importance of the microbe community overall. Many factors influence the effects of microbes in IBD for example, but in particular, the role of dietary factors has been gaining greater traction in recent years.

Non-digestible carbohydrates (fibres and starches) support beneficial outcomes in host health and diseases, including IBD. However, fibres are not digested by the host, but rather fermented by gut microbes; fermentation byproducts (mostly short-chain fatty-acids; SCFAs) are thought to mediate the highlighted health benefits. For unknown reasons, fibres have only shown benefit in select IBD patients, and studies demonstrating the possible negative impact of fibres continue to be downplayed. Many patients report sensitivity to high-fibre foods, especially during active disease, yet with limited understanding of the mechanisms behind this sensitivity, clinicians often recommend these patients avoid fibre through carbohydrate exclusion, low-FODMAP, or low-fibre diets. These diets can reduce pain and bloating in select patients but can also impair access to essential nutrients, which are especially important in intestinal diseases. Our pioneering research program has identified how dysbiosis and altered microbe function in IBD and other autoimmune diseases and cancers leads to dysregulated fibre fermentation resulting in worsened inflammation in select patients. Our findings further showed that this particular chronic inflammation in patients is directly associated with pathways known to increase risk of worsening disease severity and progression to cancer and mortality. 

In collaboration with patient and community advocates, our team has expanded our research focus, demonstrating that environmental factors promote changes in the gut microbiome composition and functions which are directly involved in diseases of the gut-brain axis. The gut microbiome in turn mediates whether the host elicits a beneficial or detrimental response to their diet and environment. The goal of the Armstrong lab is to uncover the factors influencing composition and functions of the gut microbiome (e.g., sleep, mental health, geography, ethnicity, genetics), how the gut microbiome mediates host response to diet and environment, and the role that the gut microbiome plays in conditions of the gut-brain axis (intestine, liver, CNS). The team studies how these factors change throughout life from pregnancy and infancy to adulthood. Moving forward, the team has several well-funded projects that seek to use these early findings to develop a better understanding of the mechanisms underlying these environment-microbiome-host interactions, supporting tailored dietary interventions and microbiome-altering therapies. The goal of these interventions is to re-establish a healthier gut microbiome to reduce disease burden and improve quality of life. The ongoing work is well supported through funding and collaborations with government, industry partners and clinical teams capable of developing products (biomarker tests, prebiotics and probiotics) along with delivering guidelines (apps) and whole-food diet advice (dietitians and physicians). 

Science-backed nutrition remains a largely untapped therapy with great potential, in contrast to current immunosuppressive therapies, offering a novel, safe, and easily available therapeutic option; highlighted by the benefits of science-driven exclusion diets in IBD, such as Exclusive Enteral Nutrition and Crohn’s Disease Exclusion Diet which have not focused on fibres, yet have shown clinical benefit with other targeted exclusions. 

SELECT FUNDED ARMSTRONG TEAM RESEARCH & CLINICAL PROJECTS

Selected publications - *Google Scholar

1. Tshikudi DM, Bernstein C, Mishra S, Ghia JE, Armstrong H (2025). Influence of sex in inflammatory bowel diseases. Nature Reviews Gastro Hep 

2. Piper H, Bording-Jorgensen M, Veniamen S, Zhang Z, Suarez R., Armstrong H, Silverman J, Wine E (2024). Intestinal microbial and metabolite profile in infants with small bowel stomas after bowel resection. JPGN 

3. Ariaee A, Wardill H, Prestidge C, Armstrong H.K*, Joyce P* (2024). Prebiotic Adjuvants as Therapeutic Allies in Inflammatory Bowel Diseases: A Review of the Preclinical and Clinical Evidence. eGastroenterology

4. Vu V, Mahmood R, Armstrong HK, Santer D (2024). Crosstalk between microbiota, microbial metabolites and interferons in the inflammatory bowel disease gut. JCAG

5. Armstrong H, Bording-Jorgensen M, Rempel J, Veniamin S, Jovel J, Wine E, El-Matary W (2023). Sleep disturbance in children with inflammatory bowel disease is associated with alterations in intestinal microbiome which is an early sign of mucosal inflammation and disease activity. Journal of Sleep Medicine and Disorders

6. Lawal S, Voisin A, Olof H, Bording-Jorgensen M, Armstrong H (2023). Microbiota communities found in the various organs of the intestinal tract in healthy individuals and inflammatory bowel diseases. Frontiers Microbiology.

7. Armstrong H (2023). Invited editorial: A controversial topic: the double edge sword of dietary β-fructans in IBD. Bioactive Carbohydrates and Dietary Fibre.

8. Armstrong H, Sigall-Boneh R, Wine E. (2023). LTE: Microbial Riboflavin Biosynthesis Associates with Response to Dietary Fiber Consumption: Time to Personalize Adjunct Therapy in Patients with Inflammatory Bowel Disease? Gastroenterology.

9. Guo J, Joshi H, Gordon M, Dooky H, Lai J, Capicio S, Armstrong H, Valcheva R, Dyck J, Thiesen A, Wine E, Dieleman L, Baksh S. (2023) Novel Biomarkers for Inflammatory Bowel Disease and Colorectal Cancer: An interplay Between Metabolic Dysregulation and Excessive Inflammation. International Journal of Molecular Sciences

10. Amstrong H, Rahbari M, Sharon D, Thaker H, Hotte N, Madsen K, Wine E, Reuter B, Mason A. (2023). Mouse mammary tumor virus (MMTV) is implicated in severity of colitis and associated pro-inflammatory response in IL-10-/- mice. Microbiome

11. Mahmood R, Voisin A, Olof H, Lawal S, Khorasaniha R, Armstrong H. (2023). Host microbiomes influence the effects of diet on inflammation and cancer (review). Cancers

12. Khorasaniha R, Olof H, Voisin A, Armstrong K, Wine E, Vasanthan T, Armstrong H (2023). Diversity of fibers in common foods: key to advancing dietary research. Food Hydrocolloids

13. Armstrong H, Bording-Jorgensen M, Santer D, Zhang Z, Valcheva R, Rieger A, Kim JS, Dijk S, Mahmood R, Ogungbola O, Jovel J, Moreau F, Gorman H, Dickner R, Jerasi J, Mander IK, Lafleur D, Petrova A, Jeanson T, Mason A, Sergi C, Rauscher S, Chadee K, Armstrong D, Bernstein C, Carroll MW, Huynh HQ, Walter J, Madsen K, Levine A, Dieleman LA, Wine E (2022). Unfermented β-fructan fibers fuel inflammation in select inflammatory bowel disease patients. Gastroenterology 

14. Valcheva R, Armstrong H, Kovic O, Bording-Jorgensen M, Veniamin S, Pérez-Muñoz ME, Haskey N, Silva M, Peerani F, Wong K, Kao D, Van Zanten S, Kroeker K, Gibson D, Wine E, Gänzle M, Walter J, Dieleman L. (2022). Double blind placebo-controlled trial for the prevention of ulcerative colitis relapses by β-fructan prebiotics: efficacy and metabolomic analysis. medRxIV https://doi.org/10.1101/2022.01.16.22269376     

15. Armstrong H, Bording-Jorgensen M, Wine E. (2021). The Multifaceted Roles of Diet, Microbes, and Metabolites in Cancer. Cancers. 13(4): 767.

16. Armstrong H, Mander I, Zhang Z, Armstrong D, Wine E. (2020). Not all fibres are born equal; variable response to dietary fibre subtypes in IBD. Frontiers Pediatrics. 8:620189.

17. Armstrong H, Bording-Jorgensen M, Chan R, Wine E. (2019). Nigericin Promotes NLRP3-Independent Bacterial Killing in Macrophages. Frontiers Immunology. 10: 2296.

18. Armstrong H, Alipour M, Valcheva R, Bording-Jorgensen M, Jovel J, Zaidi D, Shah P, Lou Y, Mason A, Wong G, Madsen K, Carroll M, Huynh H, Dieleman L, Wine E. (2018). Host immunoglobulin G selectively identifies pathobionts in pediatric inflammatory bowel diseases. Microbiome. 7(1):1.

19. Armstrong H, Bording-Jorgensen M, Dijk S, Wine E. (2018). The complex interplay between chronic inflammation, the microbiome, and cancer: understanding disease progression and what we can do to prevent it. Cancers. 10(3):83.

20. Armstrong H, Gillis J, Johnson I, Nassar Z, Moldovan M, Levrier C, Sadowski M, Chin M, Guns E, Tarulli G, Lynn D, Brooks D, Selth L, Centenera M, Butler L. (2017). Hsp90 inhibition suppresses fibronectin secretion from prostate cancer cells, identifying a novel mechanism to restrict tumour cell invasion. Scientific Reports. 8(1):2090.

21. Armstrong H, Koay Y, Irani S, Das R, Nassar Z, Australian Prostate Cancer BioResource, Selth L, Centenera M, McAlpine S, Butler L. (2016). A novel class of Hsp90 C-terminal modulators have preclinical efficacy in prostate tumor cells without induction of a heat shock response. The Prostate. 76(16):1546-1559.

22. Butler L, Ferraldeschi R, Armstrong H, Centenera M, Workman P. (2015). Maximizing Therapeutic Potential of HSP90 Inhibitors. Molecular Cancer Research . 13(11): 1445-1451.

ARMSTRONG TEAM FUNDING (>$20M in current funding supporting the team until 2030)