Beyond Antibiotics: Can Microbiota-Based Therapies Change the Future of Canine CIE?

For years, antibiotics and immunosuppressants have formed the backbone of canine chronic inflammatory enteropathy (CIE) management. While many patients improve initially, long-term treatment often raises familiar concerns for veterinarians, microbial resistance, dysbiosis, medication adverse effects and declining responsiveness over time^1,2,3,4,5,6. 

As understanding of the canine gut microbiome evolves, attention is rapidly shifting toward therapies designed not to suppress the intestine, but to restore it. 

From probiotics and prebiotics to faecal microbiota transplantation (FMT), microbiota-directed therapies are emerging as one of the most intriguing frontiers in companion animal gastroenterology. 

Dysbiosis: More Than a Secondary Finding 

Several studies discussed in the review demonstrate that dogs with CIE consistently exhibit alterations in intestinal microbial composition^1,7. 

One of the recurring patterns observed includes: 

• reduced microbial richness and diversity  

• increased abundance of Proteobacteria and Enterobacteriaceae  

• decreased representation of beneficial Clostridiales populations^1,8 

Importantly, these microbial shifts are not merely academic observations. Gut microbes actively influence: 

• mucosal immunity  

• epithelial barrier integrity  

• inflammatory signalling  

• short-chain fatty acid (SCFA) production¹ 

This creates a compelling therapeutic rationale: if dysbiosis contributes to intestinal inflammation, then correcting dysbiosis may help restore intestinal homeostasis. 

Probiotics: Promising but Inconsistent 

Probiotics are perhaps the most familiar microbiota-modulating tools in clinical practice. Their proposed benefits extend beyond simple “good bacteria” replacement. 

According to the review, probiotic organisms may: 

• competitively inhibit pathogenic microbes  

• strengthen epithelial barrier function  

• modulate cytokine expression  

• stimulate mucosal immunity¹ 

Experimental studies have produced encouraging findings. In ex vivo intestinal biopsy models, Lactobacillus-based probiotic combinations reduced ratios of proinflammatory cytokines such as TNF-α and IFN-γ relative to IL-10¹. 

However, translating these findings into predictable clinical outcomes has proven difficult. 

Several clinical trials in food-responsive enteropathy (FRE) failed to show significant differences in clinical remission, histology scores, or inflammatory gene expression when probiotics or synbiotics were added to elimination diets^1,9,10. 

Yet the picture becomes more interesting in immunosuppressive-responsive enteropathy (IRE). 

A comparative study evaluating a high-concentration multistrain probiotic preparation versus prednisone and metronidazole demonstrated comparable improvement in clinical signs and histological scores in both groups. Notably, probiotic-treated dogs showed increased numbers of FoxP3+ regulatory cells and higher abundance of Faecalibacterium, a bacterial genus associated with anti-inflammatory activity¹. 

Another study found improved expression of tight-junction proteins such as occludin and zonulin following probiotic supplementation, suggesting enhanced epithelial barrier integrity¹¹. 

For clinicians, the takeaway is becoming clearer: probiotics may not replace conventional therapy, but they may influence disease biology in ways that extend beyond symptom control. 

Prebiotics: Feeding the Right Microbes 

Unlike probiotics, prebiotics work indirectly by selectively nourishing beneficial intestinal microorganisms. 

Compounds such as fructooligosaccharides (FOSs), mannan-oligosaccharides (MOSs), resistant starch, and inulin have demonstrated the ability to increase SCFA production and support beneficial bacterial populations¹. 

This matters clinically because SCFAs, particularly butyrate, help: 

• fuel colonocytes  

• strengthen mucosal barrier function  

• reduce inflammation  

• regulate intestinal immunity¹ 

In dogs with CIE, prebiotic supplementation has shown modest but potentially meaningful microbiota changes. One study reported reductions in sulfate-reducing bacteria and increases in Clostridium clusters following supplementation with a fibre-rich blend¹. 

However, clinical improvement remains inconsistent. Another investigation involving Ascophyllum nodosum supplementation improved faecal acetate concentrations and beneficial bacterial populations without significantly improving clinical scores¹². 

This highlights an important clinical reality: microbiota modulation may precede visible symptomatic improvement. 

Faecal Microbiota Transplantation: The Most Radical Reset? 

Among all microbiota-targeted therapies, FMT arguably generates the greatest curiosity. 

By transferring faecal material from healthy donors into diseased recipients, FMT attempts to restore entire microbial ecosystems rather than introducing isolated bacterial strains¹. 

The concept is supported by strong biological plausibility. Donor stool contains: 

• live microbial communities  

• microbial metabolites  

• colonocytes  

• immunologically active compounds¹³ 

Experimental colitis models in mice have demonstrated reduced inflammation and disease activity following FMT administration^1,14. 

Although veterinary evidence remains limited, early canine studies suggest potential benefit in refractory enteropathies¹. However, protocols remain highly variable, and major questions still exist regarding: 

• donor selection  

• screening standards  

• administration routes  

• treatment frequency  

• long-term safety  

For now, FMT remains promising but investigational. 

Where Does This Leave the Clinician? 

The review makes one thing increasingly evident: the microbiome is no longer a passive bystander in canine CIE. 

While probiotics, prebiotics and FMT are not yet universal solutions, they are reshaping how veterinarians think about chronic intestinal disease. Future management may rely less on suppressing inflammation alone and more on restoring ecological balance within the gut itself. 

For veterinarians managing difficult enteropathy cases, that shift could eventually change not only treatment outcomes but the entire therapeutic philosophy behind CIE care. 

References 

1. Isidori M, Corbee RJ, Trabalza-Marinucci M. Nonpharmacological treatment strategies for the management of canine chronic inflammatory enteropathy—A narrative review. Veterinary Sciences. 2022 Jan 20;9(2):37. https://www.mdpi.com/2306-7381/9/2/37 

2. Francino M. Antibiotics and the human gut microbiome: dysbioses and accumulation of resistances. Frontiers in microbiology. 2016 Jan 12;6:164577. https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2015.01543/full?source=post_page 

3. Manchester AC, Webb CB, Blake AB, Sarwar F, Lidbury JA, Steiner JM, Suchodolski JS. Long-term impact of tylosin on fecal microbiota and fecal bile acids of healthy dogs. Journal of veterinary internal medicine. 2019 Nov;33(6):2605-17. https://academic.oup.com/jvim/article-pdf/33/6/2605/66656857/jvim15635.pdf 

4. Schmidt VM, Pinchbeck G, McIntyre KM, Nuttall T, McEwan N, Dawson S, Williams NJ. Routine antibiotic therapy in dogs increases the detection of antimicrobial-resistant faecal Escherichia coli. Journal of Antimicrobial Chemotherapy. 2018 Dec 1;73(12):3305-16. https://academic.oup.com/jac/article-pdf/73/12/3305/26651077/dky352.pdf 

5. Dickson A, Smith M, Smith F, Park J, King C, Currie K, Langdridge D, Davis M, Flowers P. Understanding the relationship between pet owners and their companion animals as a key context for antimicrobial resistance-related behaviours: an interpretative phenomenological analysis. Health psychology and behavioral medicine. 2019 Jan 1;7(1):45-61. https://www.tandfonline.com/doi/pdf/10.1080/21642850.2019.1577738 

6. Axelrad JE, Lichtiger S, Yajnik V. Inflammatory bowel disease and cancer: The role of inflammation, immunosuppression, and cancer treatment. World journal of gastroenterology. 2016 May 28;22(20):4794. https://pmc.ncbi.nlm.nih.gov/articles/PMC4873872/pdf/WJG-22-4794.pdf 

7. Brüssow H. Problems with the concept of gut microbiota dysbiosis. Microbial biotechnology. 2020 Mar;13(2):423-34. https://enviromicro-journals.onlinelibrary.wiley.com/doi/pdfdirect/10.1111/1751-7915.13479 

8. Cassmann E, White R, Atherly T, Wang C, Sun Y, Khoda S, Mosher C, Ackermann M, Jergens A. Alterations of the ileal and colonic mucosal microbiota in canine chronic enteropathies. PloS one. 2016 Feb 3;11(2):e0147321. https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0147321&type=printable 

9. Schmitz S, Glanemann B, Garden OA, Brooks H, Chang YM, Werling D, Allenspach K. A prospective, randomized, blinded, placebo-controlled pilot study on the effect of Enterococcus faecium on clinical activity and intestinal gene expression in canine food-responsive chronic enteropathy. Journal of Veterinary Internal Medicine. 2015 Mar;29(2):533-43. https://academic.oup.com/jvim/article-pdf/29/2/533/66689467/jvim12563.pdf 

10. Pilla R, Guard BC, Steiner JM, Gaschen FP, Olson E, Werling D, Allenspach K, Salavati Schmitz S, Suchodolski JS. Administration of a synbiotic containing Enterococcus faecium does not significantly alter fecal microbiota richness or diversity in dogs with and without food-responsive chronic enteropathy. Frontiers in veterinary science. 2019 Aug 30;6:277. https://www.frontiersin.org/journals/veterinary-science/articles/10.3389/fvets.2019.00277/pdf 

11. White R, Atherly T, Guard B, Rossi G, Wang C, Mosher C, Webb C, Hill S, Ackermann M, Sciabarra P, Allenspach K. Randomized, controlled trial evaluating the effect of multi-strain probiotic on the mucosal microbiota in canine idiopathic inflammatory bowel disease. Gut microbes. 2017 Sep 3;8(5):451-66. https://www.tandfonline.com/doi/pdf/10.1080/19490976.2017.1334754 

12. Isidori M, Rueca F, Massacci FR, Diaferia M, Giontella A, Caldin M, Furlanello T, Corbee RJ, Mannucci G, Pezzotti G, Trabalza-Marinucci M. The use of Ascophyllum nodosum and Bacillus subtilis C-3102 in the management of canine chronic inflammatory enteropathy: A pilot study. Animals. 2021 Nov 30;11(12):3417. https://www.mdpi.com/2076-2615/11/12/3417 

13. Bojanova DP, Bordenstein SR. Fecal transplants: what is being transferred?. PLoS biology. 2016 Jul 12;14(7):e1002503.  https://journals.plos.org/plosbiology/article/file?id=10.1371/journal.pbio.1002503&type=printable 
14. Zhou J, Zhou Z, Ji P, Ma M, Guo J, Jiang S. Effect of fecal microbiota transplantation on experimental colitis in mice. Experimental and Therapeutic Medicine. 2019 Apr 1;17(4):2581-6. https://www.spandidos-publications.com/etm/17/4/2581/download