Canine And Feline Gut Microbiome Studies Of Interest

The Gut Microbiome plays a vital role in the proper functioning of the immune system. We have previously written about the Gut Microbiome and how it may play a role in both GDV (Bloat), and Congestive Heart Failure.

In humans and rats, there is extensive literature about how early life gut microbiome plays a significant role later in life for a number of health conditions

Studies have shown that children exposed to antibiotics early in life were more likely to develop IBD, Obesity, and Asthma.

The number of studies evaluating the long-term effects on our dogs and cats are few and far between.

One study on cats treated with amoxicillin/clavulanic Acid and Pradofloxacin developed diarrhea; while the non-treated cats did not develop clinical signs when both were exposed to E Coli.

Studies of Interest

The first study we wanted to discuss involves cats and the effects of amoxicillin/clavulanic Acid or Doxycycline on the Microbiome of growing kittens.

The second study looks at the long-term recovery from SRE and prednisone on the Microbiome of dogs.

Antibiotics are commonly prescribed by vets, for a number of health conditions.

Amoxicillin/Clavulanic acid and Doxycycline

23 Cats with upper respiratory tract disease were treated with amoxicillin/clavulanic Acid, and 21 were treated with Doxycycline, and 26 Cats were enrolled as healthy controls. Both Antibiotics are the first-line treatment for URTD when a result of bacterial infection.

Fecal samples were taken at Day 0 Day 20 for the Amoxicillin 28 for Doxycycline, and for all 3 Days 60, 120 and 300.

The study showed that there were substantial changes in the gut microbiome that lasted until the cats were one year old. While the effects of amoxicillin/clavulanic Acid were immediate, the effects of Doxycycline became apparent 1 month after treatment ceased.

Both Antibiotics treatments resulted in a delay in the development of the kitten’s Microbiome when compared to the healthy controls. Furthermore, the results from the healthy controls suggest that the kitten’s Microbiome reaches relative maturity at around 6 months.

“compared to untreated cats of our study, a delay in maturation was observed in both antibiotic-treated groups. This delay was characterized by reduced abundances of taxa belonging to Firmicutes and increased abundances of taxa belonging to Proteobacteria. The most profound delay occurred between 2 to 3 months of age in the amoxicillin/clavulanic acid-treated cats and between 3 to 6 months of age in the doxycycline-treated cats.”

The effects of Amoxicillin led to reduced species richness, while Doxycycline actually resulted in an increase in species richness.

“In addition, in our study, a trend for significant differences in microbial community composition were observed in amoxicillin/clavulanic acid-treated cats 3 and 9 months after antibiotic withdrawal. This effect persisted in the amoxicillin-clavulanic acid group for 9 months. Early colonization with Collinsella spp. within the first 6 months of life is associated with increased adiposity in humans,  and also increased Collinsella spp. abundances have been reported in cats with diarrhea.” (Pilla, et al. 2021)

Based both on sequencing and qPCR analysis, bacterial taxa belonging to Proteobacteria, and Enterobacteriaceae, Escherichia coli) were found at significantly higher abundances on the last day of treatment (20 days) for amoxicillin/ clavulanic Acid and at 3 months after discontinuation of Doxycycline before decreasing to similar abundances to that of control cats. Both Phylums contain well known pathogens which are known to be increased in dogs and cats with GI Disease.

Furthermore, the antibiotic-treated groups had higher fecal scores during treatment than the healthy cats. This could have been a result of the increased abundance of the above phyla.

“Amoxicillin/clavulanic acid and doxycycline treatment early in life significantly affected the developing microbiome richness and composition in cats. The abundance of members of Firmicutes decreased and that of members of Proteobacteria increased after 20 days of amoxicillin/clavulanic acid treatment and 1 month after a 28-day course of Doxycycline. Only minor changes were observed 9 months after amoxicillin/clavulanic acid or doxycycline discontinuation with an increase in the abundance of unclassified Collinsella spp. and unclassified Bulleidia spp., respectively.” (Pilla, et al. 2021)

Amoxicillin/Clavulanic Acid Conclusion

None of this means that these antibiotics shouldn’t be used as they can be necessary. However, it demonstrates the necessity of at the very least attempting to mitigate their long-term effects by providing a wide range of probiotics to help repair the damage done to the Microbiome.

Hopefully, the researchers will continue to follow up with these cats in the future to see whether there are any increased rates of various health conditions which are theorized or demonstrated in both human and rat studies.

Steroid Responsive Enteropathy

The study involved dogs that were previously involved in a clinical trial. The dogs were diagnosed with IBD by a board-certified veterinary internist.

The dogs that were used from the clinical trial received the standard therapy, which was an elimination diet which was either Purina HA or Royal Canin hydrolyzed protein HP wet and/or dry, fed exclusively for the duration of trial and prednisone at a dosage of 0.5–1 mg/kg 12h for 3 weeks then 0.5 mg/kg  12h for 3 weeks then maintained or tapered over the 8 week duration of the study).

The dogs with SRE had a mean severity of 8.7 out of 18 and after 3 and 8 weeks of treatment, it had decreased to 2.2 and .7. At the year follow up none of the dogs were receiving prednisone, and their diets were adjusted at the discretion of the attending clinician.

Beta Diversity

The Beta diversity of the dogs with SRE before treatment was significantly different than that of the healthy controls. After both 3 and 8 weeks, the Microbiome remained significantly different than the healthy controls. After 1 year, there was no statistical difference.

Individual Bacterial

All dogs with SRE had significant differences in comparison to the healthy controls. The SRE dogs had an increased abundance of both Actinobacteria and Firmicutes, while Bacteroidetes, Fusobacteria, and Proteobacteria were lower. 

Despite the improvement of clinical signs, there were still significant differences between the SRE and healthy controls at 8 weeks. At the 1-year mark, there was no longer a significant difference. So, at some point between 8 weeks and 1 year, the Gut Microbiome returned to at least a relatively healthy state.

In the study, the researchers found that Firmicutes were driven mostly by unidentified species within the order Lactobacillales. The level of Lactobacillales decreased with treatment. While it was not significant after 1 year, it was still higher than that of the healthy dogs. 

Furthermore, Bacteroidetes such as Bacteroides spp. and Prevotella spp were decreased at both 3 and 8 weeks. These are of particular interest as they are important for Short-chain fatty acid (SCFA) production


This study also took the important next step in actually analyzing the Metabolome.

A total of 75 compounds were found to be significantly different from the healthy dogs.

Thirteen metabolites were still significantly different from controls after 1 year. 3 of these only became altered during treatment. A majority of them normalized at some point between the 8 weeks and the follow-up at 1 year.

These results suggest that dogs with SRE have compromised absorption in both the short and long term.

Amino Acids

A total of 16 Amino acids were altered; some of the Amino Acids such as Tryptophan, Methionine Threonine, and Proline are essential for the proper maintenance as well as the recovery of the GI system. Both Tryptophan, Methionine remained altered at 1 year. At the same time, many of them returned to normal levels at some point after 8 weeks.

Tryptophan is an essential amino acid that plays a vital role in the health of the GI system as well as general health.

“Increased tryptophan catabolism also limits the production of serotonin, a neurotransmitter that is essential for GI secretion, motility, and pain perception , which may be another mechanism through which tryptophan affects GI health. In dogs with protein-losing enteropathy, a severe enteropathy leading to hypoproteinemia, tryptophan was the only serum amino acid found to be decreased, and correlated with serum albumin concentrations. Tryptophan and its bacteria-produced indole metabolites have anti-inflammatory properties, and in animal models, supplementation with tryptophan ameliorates DSS-induced colitis].” (Stavroulaki, et al. 2021)

Threonine is essential for the synthesis of mucin, which aids in the maintenance of the intestinal barrier. 

Methionine is crucial for the maintenance of intestinal integrity. Methionine remained increased at the long-term follow-up, suggesting that its absorption may have remained impaired despite improvement in clinical parameters and gut microbiome composition.

Proline is an amino acid that is vital to the repair of tissue. That being the case, if synthesis is insufficient or there is impaired absorption, it could result in a slowed recovery period.


The dogs with SRE also had altered vitamin pathways. Nicotinic Acid (vitamin B3) was increased, as was Vitamin E at both weeks 3 and 8; one form of Vitamin E (Gamma) was still higher in feces after 1 year.

Threonic Acid was also found to be increased. While it decreased with treatment at the 1-year follow-up, it was found to be increased again. Theronic Acid is a metabolite from the breakdown of vitamin C; this could be an indicator of increased oxidative stress long term.

SRE Conclusion

The study did have limitations, and that was mainly the small sample size. This is a widespread occurrence in the pet space, as funding is limited.

What the study does demonstrate is that the recovery of the Gut Microbiome is possible, but it is a long-term goal. It also means the prevention of further occurrences is vital to the health and well-being of our dogs; as the affected nutrients also play many other roles. 

The study also provides a plan of action on how we might supplement our dog’s diet to aid in their recovery. Whether it is providing Pre and Probiotics to repopulate and help repair the Gut Microbiome, Bone broth or other rich sources of Proline, Fruits and or Vegetables as a source of Vitamin C and other antioxidants. Foods or treats that are are high in Methionine, Threonine, Vitamin B3, and Vitamin E.

Overall Conclusion

Both studies demonstrate that even though clinical symptoms may subside, the recovery of the Gut Microbiome is a long-drawn-out process, it does not occur overnight. They also demonstrate that if antibiotics or steroids are necessary it’s important to take steps to help repair the gut microbiome.   Some consider the Gut microbiome to be its own super organ as it plays a role in many different biological processes.

The second study, in particular, is concerning as it shows that there may be malabsorption of not only several essential amino acids both in the short and long term but possibly increased levels of oxidative stress in the long term as well.

These effects don’t just impact the gut microbiome but also many other organ systems that rely on those same vitamins and amino acids. It can also impact other nutrients such as Taurine and Choline as methionine is involved in the synthesis of Taurine, as well as being a sparing nutrient for Choline.

Hopefully, the researchers will follow up in the years ahead to see if there are any notable health outcomes like those that have been found in both humans and Rat studies. While the study does involve cats, it is very well possible that if there are long-term effects on our feline companions, those same effects may occur in our canine companions.

These studies show how little we actually know. They demonstrate the need for more studies so that we can improve the health and well-being of our dogs and cats.

One study to look out for in the future will be the curtent study being conducted by Animal Biome and the Golden Retriever Lifetime Study; where Animal Biome will be analyzing fecal samples over several years. The great thing about the study besides the size is the extensive amount of information they have about each individual dogs history.

This also means advocating for the government to fund more research, as research for our pets is far too reliant on large corporations to fund research.  Our Pets shouldn’t be relying in large part on large corporations to fund research, as they can pick and choose what to investigate.  

To read our previous post which detailed a study on the Gut Microbiome and Congestive Heart Failure and a second study on the Gut Microbiome and Gastric Dilation Volvulus (Bloat) Click here.

Works Cited

Pilla, R.; Guard, B.C.; Blake, A.B.; Ackermann, M.; Webb, C.; Hill, S.; Lidbury, J.A.; Steiner, J.M.; Jergens, A.E.; Suchodolski, J.S. Long-Term Recovery of the Fecal Microbiome and Metabolome of Dogs with Steroid-Responsive Enteropathy. Animals 2021, 11, 2498.

Stavroulaki EM, Suchodolski JS, Pilla R, Fosgate GT, Sung C-H, Lidbury JA, et al. (2021) Short- and long-term effects of amoxicillin/clavulanic Acid or Doxycycline on the gastrointestinal Microbiome of growing cats. PLoS ONE 16(12): e0253031.