Prebiotics in dogs and cats:
microbiome, butyrate and intestinal barrier
How prebiotic fiber nourishes the gut microbiome, boosts butyrate, and strengthens the gut barrier. The scientific background of a broad prebiotic spectrum in dogs and cats, substantiated by recent literature.
By Stefan Veenstra DVM
Prebiotics vs. Probiotics: A Fundamental Distinction
In microbiome science, the distinction between prebiotics and probiotics is often underestimated. Probiotics add live bacteria from the outside; Prebiotics nourish and stimulate the bacteria already present in the gut microbiome. This distinction is not only relevant in definition but also clinically: probiotic strains do not colonize sustainably in an existing microbiome in most cases, while prebiotics cause direct and measurable changes in the composition and activity of the existing microbiome. [1]
A recent review in Veterinary Record (Wilson et al., 2024) summarizes the state of science for dogs and cats: prebiotic supplementation consistently leads to elevation of Bifidobacterium and Lactobacillus species, increased production of short-chain fatty acids (SCFAs), and improved gut barrier parameters. [2] The specific changes depend strongly on the type of prebiotic fiber, the dose, and the baseline composition of the individual animal’s microbiome.
NGD Care Gut Protocol: Prebiotic Fibers as an essential component
NGD Care Giardiaprotocol: Prebiotics for Microbiome Recovery After Infection
Butyrate: the key molecule of prebiotic action
When prebiotic fibers reach the large intestine, they are fermented by anaerobic gut bacteria into short-chain fatty acids: acetate, propionate, and butyrate. Butyrate is the most clinically relevant of these: it is the primary energy source for colonocytes (intestinal epithelial cells) and a direct modulator of tight junction expression, immune function and epigenetic regulation in the intestine. [3]
Butyrate stimulates the expression of claudine and occludin, the structural proteins that form the tight junctions between enterocytes. Higher butyrate production by the microbiome directly correlates with a stronger gut barrier and less systemic endotoxemia via LPS leakage. [4] Veterinary research confirms this pattern: prebiotic supplementation in dogs and cats increases SCFA-producing bacterial strains and measurable butyrate levels in the feces. [5]
Butyrate also has direct epigenetic effects via histone deacetylase (HDAC) inhibition, which modulates the expression of anti-inflammatory genes in the intestinal epithelium and immune cells. This explains the immunomodulatory effect of a fibrous diet outside the direct prebiotic microbiome effects.
The four ingredients: each with its own fermentation profile
Inulin and FOS from chicory root
Inulin and fructooligosaccharides (FOS) are the best-documented prebiotic fibers in both human and veterinary literature. They are selectively fermented by Bifidobacterium and Lactobacillus species in the proximal colon, leading to rapid and substantial changes in microbiome composition. [6] A veterinary study with FOS and inulin in healthy dogs and cats showed significant increases in Bifidobacterium in fecal samples as early as 16 days of supplementation, measured via 16S rRNA sequencing. [6]
FOS is fermented rapidly in the proximal colon, inulin more slowly and more distally. The combination of both therefore provides a wider distribution zone of prebiotic activity throughout the colon, giving a more complete stimulation of the microbiome than either individually.
Arabinogalactans from acacia fibre
Arabinogalactans are high-molecular, highly branched polysaccharides that occur naturally in acacia trees and are resistant to digestion in the small intestine. They reach the colon intact and are fermented more slowly than FOS, stimulating a different and complementary bacterial spectrum, including Bifidobacterium longum, Faecalibacterium prausnitzii , and Roseburia species associated with butyrate production and anti-inflammatory effects. [7]
The slower fermentation rate of arabinogalactans is a clinical advantage in animals with a sensitive gut: less risk of sudden gas production and fermentation stress compared to fast-fermenting FOS. Acacia arabinogalactans also stimulate the mucus layer of the intestinal epithelium via increased goblet cell activity, which directly contributes to the physical intestinal barrier. [8]
MOS from Saccharomyces boulardii
Mannan oligosaccharides (MOS) are cell wall components of Saccharomyces boulardii with a unique dual mechanism of action. First, they act as a prebiotic substrate for beneficial bacteria. Second, MOS binds to the mannose-specific fimbriae of pathogenic bacteria such as E. coli and Salmonella, preventing these pathogens from attaching to the intestinal wall and excreting them without colonizing. [9] This competitive exclusion mechanism is particularly relevant in animals recovering from intestinal infections or antibiotic courses, where pathogenic recolonization is a real risk.
Saccharomyces boulardii additionally produces proteases that cut Giardia receptors on the intestinal epithelium and stimulate secretory IgA production in the intestinal wall, a local immune mechanism that strengthens intestinal wall integrity. This makes the MOS fraction of Prebiotic Fibers a contributing factor in both the Giardia Protocol and the Gut Protocol.
Beta-glucans from Agaricus blazei
Agaricus blazei is a medicinal mushroom from the Brazilian rainforests with a high concentration of beta-glucans, a specific structure with both prebiotic and pronounced immune-modulating properties. Beta-glucans bind to pattern recognition receptors on immune cells (dectin-1, TLR2) and activate macrophages, natural killer cells, and dendritic cells, which boosts innate immunity. [10]
A recent review in Discover Food (2025) describes how beta-glucans as prebiotic fibers contribute to SCFA production via microbiome fermentation, reducing intestinal permeability, and inhibiting metabolic endotoxemia — the process by which bacterial LPS crosses the intestinal wall and causes systemic inflammation. [11] Agaricus blazei extract has also demonstrated direct anti-tumor activity in human studies via NK cell stimulation and Th1/Th2 balance improvement, a property that overlaps with that of the Myco Immune Complex mushrooms in the NGD Care range.
Each prebiotic fiber molecule has a specific fermentation profile: it feeds certain strains of bacteria, in certain locations in the intestine, at a certain rate. FOS feeds quickly and proximally; arabinogalactans slow and distal; MOS blocks pathogens and stimulates IgA; Beta-glucans modulate the immune system outside of the direct fermentation pathway. Only the combination covers the full spectrum. Prebiotic Fibers is designed on this principle: no overlapping but complementary prebiotic mechanisms in one formula.
Clinical applications in dogs and cats
Recovery after antibiotics or deworming
Antibiotics significantly reduce microbiome diversity and increase the risk of pathogenic overgrowth by Clostridium and other opportunistic species. Prebiotic supplementation after a course of antibiotics accelerates the recovery of microbiome composition and reduces the risk of post-antibiotic dysbiosis and diarrhea. [12] Deworming has a similar, albeit milder effect on the microbiome via disruption of the gut environment.
Chronic bowel complaints and IBD
In dogs and cats with inflammatory bowel disease (IBD), microbiome diversity is consistently reduced and the butyrate-producing fraction of the microbiome is significantly reduced. Prebiotic fibers that stimulate butyrate-producing species, such as Faecalibacterium prausnitzii, are mechanistically relevant as an additional intervention in IBD management in addition to dietary modifications and medication.
Immune support and allergies
A diverse and functional microbiome is the basis for a balanced immune system. Through the gut immune axis, the microbiome regulates Th1/Th2 balance, regulatory T cell activity, and systemic inflammatory tone. Prebiotic fibers that support a diverse microbiome composition thus contribute to reducing the allergic Th2 dominance that plays a central role in atopic skin conditions.
Scope of application Prebiotic Fibers
Daily microbiome support in dogs and cats at all stages of life. Recovery after antibiotics, deworming or diarrhea. Chronic intestinal complaints and dysbiosis. Support of the intestinal barrier in case of increased intestinal permeability. Immune support via the gut-immune axis. Essential part of the NGD Care Bowel Protocol and Giardia Protocol.
Conclusion
Prebiotic Fibers combines four prebiotic fibers, each with its own fermentation profile, bacterial target spectrum and mechanism of action. The combination of FOS and inulin for rapid Bifidobacterium stimulation, arabinogalactans for slower and wider fermentation distaler in the gut, MOS for pathogen exclusion and IgA stimulation, and beta-glucans for immune modulation via dectin-1 activation, makes this one of the most complete prebiotic formulas for veterinary application.
A diverse microbiome is the biological foundation of digestive power, immune balance, and overall resilience. Prebiotic Fibers is intended as a daily food for that microbiome, both standalone and part of an integral gut protocol.
View Prebiotic Fibers in the NGD Care webshop
Literature
- Marteau P, Boutron-Ruault MC. Nutritional advantages of probiotics and prebiotics. Br J Nutr. 2002; 87(Suppl 2):S153–S157.
- Wilson S, Higgins D, Swanson KS, et al. The influence of ‘biotics’ on the gut microbiome of dogs and cats. Fat Rec. 2024; 195(10):e4914. [Recent Veterinary Review 2024]
- Martin-Gallausiaux C, Marinelli L, Blottière HM, et al. SCFA: mechanisms and functional importance in the gut. Proc Nutr Soc. 2021; 80(1):37–49.
- Canani RB, Costanzo MD, Leone L, et al. Potential beneficial effects of butyrate in intestinal and extraintestinal diseases. World J Gastroenterol. 2011; 17(12):1519–1528.
- Pinna C, Stefanelli C, Biagi G. Effect of dietary carbohydrates and fibers on the in vitro production of short-chain fatty acids by dog fecal inocula. J Anim Sci. 2018; 96(1):119–130.
- Garcia-Mazcorro JF, Lanerie DJ, Dowd SE, et al. Effect of a multi-species synbiotic formulation on fecal bacterial microbiota of healthy cats and dogs as evaluated by pyrosequencing. FEMS Microbiol Ecol. 2011; 78(3):542–554. [FOS/Inulin in Dogs and Cats, 16S rRNA Sequencing]
- Rasoulimehrabani H, Khadem S, Hodžić A, et al. Evaluating the prebiotic activity of arabinogalactan on the human gut microbiota using 16S rRNA gene sequencing and Raman-activated cell sorting. Microbiome Res Rep. 2025. doi:10.20517/mrr.2025.29. [Most Recent Arabinogalactan Microbiome Study 2025]
- Calame W, Weseler AR, Viebke C, et al. Gum arabic establishes prebiotic functionality in healthy human volunteers in a dose-dependent manner. Br J Nutr. 2008; 100(6):1269–1275.
- Buts JP, Bernasconi P, Vaerman JP, Dive C. Stimulation of secretory IgA and secretory component of immunoglobulins in small intestine of rats treated with Saccharomyces boulardii. Dig Dis Sci. 1990; 35(2):251–256.
- Hetland G, Johnson E, Lyberg T, Kvalheim G. The mushroom Agaricus blazei Murill elicits medicinal effects on tumor, infection, allergy, and inflammation through its modulation of innate immunity and amelioration of Th1/Th2 imbalance and inflammation. J Immunol Res. 2011;2011:157015.
- Alabboud M, Javadipour M. Mechanistic insights into β-glucans and gut microbiota interactions for enhancing human health. Discov Food. 2025;5:58. [Recent review beta-glucans and gut microbiome 2025]
- Dethlefsen L, Huse S, Sogin ML, Relman DA. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol. 2008; 6(11):e280.
This information is educational in nature and based on available scientific literature. The studies mentioned are not always directly veterinary or specific to the formulation described here. This text does not replace a veterinary consultation and does not contain any therapeutic claims.