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Asthma and the Microbiome

Asthma, the microbiome, inflammatory airway disease, heaves, recurrent airway obstruction, and Aspergillus fungi overgrowth.

EquiBiome Facebook Post from 2021 about asthma and the microbiome

 Respiratory Health from the Inside Out

5 facts about equine respiratory health you might not be aware of

1. The lining of the lungs and the lining of the gut share an immune response.

2. Horses with asthma/COPD are likely to have an inflammatory gut problem such as colitis, inflammation or dysbiosis.

3. The gut bacteria can modulate (effect/ change/control) an allergic response.

4. The use of antibiotics early in life alters the microbial community increasing the risk of developing allergic airway diseases such as asthma and COPD

5. Some species/families/genus of gut bacteria produce inflammatory cytokines increasing the risk of developing airway disease, whilst other types of bacteria ‘damp down’ or reduce the effect of the pathogens.

A 2024 update on the progress to date about the role the microbiome plays in asthma and what to do about it.

Aspergillus-associated asthma is on the increase and may be underdiagnosed especially common in horses with PPID.

Aspergillus (fungi) produces a range of different metabolites, some species are pathogenic ie linked to diseases in humans, animals, and plants. The soil is the primary habitat for Aspergillus though the fungi has been detected in all major biomes including the gut and lung.

Filamentous fungi of the Aspergillus genus are opportunistic phytopathogens, there are between 300 and 400 different species. Five are reported to cause disease Aspergillus (Fumigati, Flavi, Nigri, Terrei, and Nid ulante) within the family Aspergillaceae, producing mycotoxins that contaminate agricultural products and cause illness in humans, horses and other animals.

Aspergillus are thought to synthesize metabolites other than mycotoxins that contribute to toxicity in humans and animals, according to recent research their effect is likely to be underestimated.

Aspergillus in the Microbiome and its Role in Health

Immune system homeostasis helps the host remove invasive and opportunistic fungi such as Aspergillus. Fungal infections colonize the lining of the ileum of the gut inducing an intestinal immune response at the same time causing lung autoimmunity through the gut- lung axis therefore a healthy gut response equals a healthy gut lung response.

Once a fungal infection takes hold in the lung or gut there is a reduction in the alpha diversity score, this causes a change in the intestine's immune tolerance predisposing both to inflammation.  


Probiotics are promising new targets for antifungal treatments as they alter the members of the gut microbiome by directly stimulating immune cells and releasing health-promoting metabolites, which, in turn, improves systemic immunity.

Lactobacillus and bifidobacteria both reduce allergic airway response by increasing the number of Tregs in the lungs. Regulatory T cells (Tregs) are a specialized subpopulation of T cells that act to suppress the immune response, thereby maintaining homeostasis and self-tolerance. It has been shown that Tregs can inhibit T cell proliferation and cytokine production and play a critical role in preventing autoimmunity.  (there are links between high levels of lactobacillus and laminitis so it’s important to check the results from the EquiBiome test) email us if you need help with it.

What are Tregs?

Regulatory T cells (Tregs) are T cells that suppress the immune response, helping to maintain homeostasis. It has been shown that Tregs can inhibit T cell proliferation and cytokine production and play an important role in preventing autoimmunity.

Cross-protection immunity (lung and gut) against Aspergillus infection comes from the microbial bacteria population. Antibiotic treatment and chronic disease alters the composition of the gut microbiome, causing overgrowth of certain intestinal bacteria and Calbicans (thrush) which creates an opportunity for opportunistic aspergillus.

An overgrowth of bacteria and a rise in fungi increases plasma concentrations of E2 (PGE2) and induces inflammation in the lungs promoting pathogenic airway inflammation.

 Interestingly most allergic reactions in the airways only occur if the gut microbiome is damaged by antibiotics as C. albicans fungi play a role in maintaining host immunity and resistance to the pathogenic species of Aspergillus.

Aspergillus in soil

Aspergillus is common in soils around the globe, it produces spores that can be breathed in but that can also be ingested from the soil or plants on contaminated land.

The overuse of agrichemicals in the form of fungicides has created resistant species of Aspergillus, a recent study found 4.7% are resistant to the agricultural fungicide tebuconazole, and with a high resistance to azoles used for treating clinical infections, including itraconazole (86%), voriconazole (64%), and isavuconazole (83%). In addition, 51% of the A fumigatus isolates were resistant to three medical azoles, and 14% were resistant to all tested medical azoles.

Aspergillus in food

Another area under observation is the mycotoxin content of distillers or brewers grains which has quickly become a global commodity and although nutritional it varies hugely in quality and content and unless constantly tested can contain an unacceptable level of mycotoxins.

The fermentation process triples the content of mycotoxins already naturally present in the grain. It has been estimated that over 25% of the world's grain is contaminated (7th Symposium of Veterinary Immunology). Mycotoxins interfere with and alter the gut microbiota and reduce the absorption of zinc. Mycotoxins also affect the intestinal epithelial cells changing the integrity of the gut wall, lowering protection (mucosal coating), and altering the immune response, causing a low-grade inflammation to persist along the G.I. tract.

Symptoms of Aspergillus



 poor performance.

Loss of appetite.

Diarrhea or FFWS.

Frequent illness (always sick and sorry).

Altered cycles in mares.

Joint swelling.

Dietary Interventions (Antifungal foods)

Apple Cider Vinegar. The acid and enzymes in apple cider vinegar have been shown to help to kill and get rid of excess yeast in the body.

Dr. Green (pasture turn out)

Coconut Oil.



Ground Flaxseeds and Chia Seeds


How the EquiBiome Test can help

  1. The gut and lung share a mucus membrane identifying a fungal infection in the gut is easier and less invasive. Using population data from affected horses it has been possible to identify a benchmark for horses with aspergillus-associated asthma and percentages within the gut mycobiome/microbiome.

  2. The EquiBiome test accurately identifies the five different species of pathogens, this may help the horse owner to identify the source of contamination ie bedding, food, soil, or pasture.

  3. Resolution of the infection is possible through restoration of the balance within the microbiome, this improves the immune system response whilst reducing the aspergillus overgrowth.


Cai L, Gao P, Wang Z, Dai C, Ning Y, Ilkit M, Xue X, Xiao J, Chen C. Lung and gut microbiomes in pulmonary aspergillosis: Exploring adjunctive therapies to combat the disease. Front Immunol. 2022 Aug 12;13:988708. doi: 10.3389/fimmu.2022.988708. PMID: 36032147; PMCID: PMC9411651.

Cheng C, Sun J, Zheng F, Wu K, Rui Y. Molecular identification of clinical "difficult-to-identify" microbes from sequencing 16S ribosomal DNA and internal transcribed spacer 2. Ann Clin Microbiol Antimicrob. 2014 Jan 3;13:1. doi: 10.1186/1476-0711-13-1. PMID: 24383440; PMCID: PMC3905965.

Dall, C. 2023 Exposure to resistant Aspergillus is widespread across UK, study finds.News brief July 21, 2023

Dobiáš R, Jahn P, Tóthová K, Dobešová O, Višňovská D, Patil R, Škríba A, Jaworská P, Škorič M, Podojil L, Kantorová M, Mrázek J, Krejčí E, Stevens DA, Havlíček V. Diagnosis of Aspergillosis in Horses. J Fungi (Basel). 2023 Jan 25;9(2):161. doi: 10.3390/jof9020161. PMID: 36836276; PMCID: PMC9966232.

Nji QN, Babalola OO, Mwanza M. Soil Aspergillus Species, Pathogenicity and Control Perspectives. J Fungi (Basel). 2023 Jul 20;9(7):766. doi: 10.3390/jof9070766. PMID: 37504754; PMCID: PMC10381279.

Sang Kyu Lee, Hyun-Gu Kang, Ki-Jeong Na, Jae-Ik Han, Fungal Dermatitis Caused by Aspergillus sydowii in a Thoroughbred Horse, Journal of Equine Veterinary Science, Volume 32, Issue 12, 2012, Pages 835-839, ISSN 0737-0806,

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