The Magnificent Microbiome and how it can Impact the Health of Your Pets!
Updated: Apr 19
“All disease begins in the gut.” This statement was coined by Hippocrates and has been proven true time and time again, not only for humans but also for our furry companions.
By now I am sure a majority of you have heard about the gut microbiome and its profound influence on your overall health. If not, here is a SparkNotes version so you are caught up and ready to dive into this post! In short, each person has a unique network of microbiota that is originally influenced by your DNA. As we progress through life, diet and environmental exposures alter the microbiome in either a beneficial or detrimental way7. Our gut microbiome is so important to our health that it has even been labeled as a supporting organ and this “organ” is not unique to humans, it is also present in our animal friends. This is a complex topic that has not been fully understood in humans and even less so in animals. The purpose of this post is to provide some background knowledge and discuss some of the things that researchers have been able to learn about the animal gut microbiome. While the research pertaining to humans is more advanced, the importance of learning about this complex system is pushing for research on the veterinary aspect which is exciting!
Before we dive into the thick “sciencey” material I want you to think of the gut microbiome like a little colony of helpers. They are working inside you to help maintain a multitude of homeostatic functions. A few of these functions include gut epithelial health, energy homeostasis, immunologic activity, metabolism, and even neurobehavioral development. When they are balanced and receiving the nutrients they need, all is well, and the body is likely functioning normally. When these little friends become unbalanced, this is known as gut dysbiosis. Gut dysbiosis can lead to a slew of health issues such as asthma, inflammatory bowel disease, cardiovascular disease, obesity, immune-mediated conditions, metabolic syndrome, and even neurodevelopmental conditions. This is not only true in humans but has also been found to be true in animals. Now that we are all on the same page and understand the significance of these little critters, let’s dive in!
Here are some of the things we know at this point in time...
The gut microbiome consists of bacteria, archaea, eukaryotic organisms, and viruses that take up residence in the gastrointestinal tract. These little microbes interact with a host in a way that is beneficial to both parties (symbiotic relationship) and they also aid in a plethora of metabolic and immune functions! One example of this symbiotic relationship is the production of short-chain fatty acids that aid in the health of the intestinal epithelium. Some bacteria that feed off of the epithelium mucous produce these short-chain fatty acids. The bacteria support the host’s intestinal epithelium while also getting a nice snack12.
This excitement around gut health has led researchers to dive into ways of sampling the microbial population with the hopes of expanding their knowledge. This has been done on the human side for a while and while it is still a complex process, understanding an animal’s microbiome is slightly more challenging due to the variation in their gastrointestinal tracts. Within the gastrointestinal tract, the population of microbes vary depending on the intestinal segment8. This can make it difficult to collect a sample from a specific region and analyze that colony, which is why most research data is focused on the fecal microbiota. Luckily for us, fecal samples from our canine friends consistently present most of the relevant taxa. This is slightly different than that of humans since the most important taxa are associated with the mucosa8. These differences are thought to be related to the anatomical differences between humans and canines. A dog’s gastrointestinal tract is shorter than a human’s and they also have a faster transit time.
According to a study that focused on pyrosequencing the canine fecal microbiota and one that looked at phylogenetic characterization of fecal microbial communities in dogs, there are thought to be at least three co-dominant phyla that reside in the fecal microbiome of a healthy dog. These include Fusobacterium, Firmicutes, and Bacteroidetes11. It is interesting to note that while healthy dogs had populations of the same bacteria, the quantity of these bacteria varied. Dogs that were genetically related had more similar proportions of these organisms compared to unrelated dogs, indicating that the gut microbiome may also influenced by genetics6,11.
These studies gave some insight into the complex world of the microbiome, but all resulted in similar conclusions that fell along the lines of some sort of uncertainty. There are ideas of what may be going on and will likely become clearer in the future as the research evolves!
Now we are going to discuss some things that have been found to impact the gut microbiome.
First up, diet!
Just like how our animals change as they go through life, their gut microbiome also has the ability to adapt and change based upon the food that they eat and the environment that they live in. To test the degree that diet has on modulating the composition of the gut microbiome, a comparative study of BARF-type and commercial diets was performed. BARF stands for “biologically appropriate raw food” and as the name suggests, those dogs were fed a diet of vegetables, raw meat, organs, and meaty bones. In comparison to the dogs that were fed commercial dry kibble diets, those in the BARF category exhibited a greater richness in diversity of their fecal microbiota3. Additional studies have been done that have led to similar results indicating diet directly relates to microbiota composition regardless of outside factors such as sex and breed13.
While it was hinted earlier that the microbiome may be partially influenced by genetics, additional research and literature review posted in the Journal of Veterinary Internal Medicine mentioned, “studies implicate diet and environment as the primary influences on the structural and functional characteristics of the fecal microbiome”2. This is great news considering owners have control over these two factors!
In an owner-reported longitudinal and cross-sectional study it was found that diet choices during puppyhood and adolescence had the ability to lessen or increase the risk of chronic enteropathy. The term “enteropathy” is referring to a group of complex, nonspecific GI disorders with chronic clinical signs. It was found that feeding a non-processed or minimally processed meat-based diet to puppies and adolescent dogs ranging from 2 to 18 months was significantly associated with a decreased incidence of chronic enteropathy in adulthood (p=0.008)15. On the other hand, feeding an ultra-processed dry dog food based diet was significantly associated with an increased incidence of chronic enteropathy in adulthood15. A few other interesting notes from that study include the idea that organ meats were also found to have a positive impact on gut health, while rawhides negatively impacted gut health. *While this study demonstrates results that are similar to that of other studies indicating the importance of diet on the microbiome, it is important to keep in mind that since this was owner-reported and not an experimental cause-effect design, it is susceptible to recall bias and misclassification of food items.
Even though we do not have a comprehensive understanding of the gut microbiome in animals (or people), it is safe to assume that diet plays a significant role and feeding a larger proportion of fresh foods is more beneficial to the microorganisms than the processed food. It is also important to ensure that the diet you are feeding is completely balanced so that the animal does not develop any nutritional deficiencies while trying to improve their gut microbiome.
Disease!
It is easy to think that the gut microbiome only affects things related to the gastrointestinal tract and thus dysbiosis would only lead to annoying GI symptoms. Through research, this has been proven to be an incorrect assumption and it is actually pretty incredible to see how much of an impact the microbiome has on an animal’s overall health! A review of recent canine microbiome research mentioned that pets with autoimmune disorders/diseases have alterations in their gut microbiome compared to that of a normal dog. These alterations are thought to include a loss of beneficial microbes and an increase in pro-inflammatory bacteria leading to a vicious cycle that facilitates the development of autoimmune conditions9.
While examining the gut microbiome of dogs with irritable bowel disease it was noted that they had less diverse microbiome populations than canines without the disease2. It is also interesting to note that gut dysbiosis is linked to obesity and metabolic syndrome. Obesity is an issue that affects countless animals, so understanding the influence of the host’s microbial population and identifying how we can impact it can provide additional therapeutic options!
One other surprising effect of dysbiosis that is not characterized by GI symptoms is the effect that the gut microbiome may have on joint degeneration. In a study done on traumatic joint injury in mice it was shown that overweight mice with systemic inflammation (due to a dysbiosis induced by diet) had profound joint degeneration compared to the mice that did not have the dysbiosis9,16. It was initially uncertain if this model would be applicable to canines but an additional study comparing dogs with chronic arthritis to healthy dogs found that the gut microbial community in arthritic dogs was significantly different than that of the healthy dogs. This suggests that this difference in microbial population and diversity may induce systemic inflammation that influences the degeneration of joints and bones4. Since age, breed, and weight may influence the gut microbiome, this study used a variety of breeds around the same age and same weight to validate their findings.
How to help improve your pet’s microbiome...
By this point you have probably learned way more about the gut microbiome than you ever wanted or needed to know. I hope you have found it interesting and are itching to see how you can help improve your pet’s complex microbe community! Here are some ways you can help improve your pet’s microbiome!
A common theme in this research has emphasized the importance of diet and its influence on the microbiome. Feeding your pet a balanced diet that incorporates a variety of different foods will help keep this microbial population thriving. *Before changing your pet’s diet or turning to home-cooked pet food please talk to your veterinarian and make sure that you understand how to do this in a beneficial way. More information can be found in this blog post.
A way that veterinarians can help the gut microbiome flourish is through antibiotic stewardship. Many veterinarians have been trained to throw antibiotics such as metronidazole at dogs that come in with diarrhea. Metronidazole is a common therapeutic agent for anaerobic, bacterial, and protozoal infections and has also been reported to have some anti-inflammatory properties5. This drug has been so impactful that it is even on the World Small Animal Veterinary Association’s list of essential medications14! Unfortunately, new research suggests that this drug is not kind to the microbe community that resides inside your beloved pet. A study analyzing metronidazole’s effect on the microbiome of healthy dogs found that after 14 days of administering metronidazole, the composition of the microbiome was significantly altered. This alteration lasted a minimum of 4 weeks meaning that by the time the study was over, these dogs still had gut dysbiosis indicating a long-term disruption of the microenvironment5. This does not mean that antibiotics should never be used to treat diarrhea, it just means that careful consideration should be taken before they are prescribed, and the potential benefits and costs should be discussed.
An additional interesting therapy in veterinary medicine is the use of fecal microbiome transplantation. This involves taking feces from a healthy donor and transferring them into the intestinal tract of a diseased recipient. Fecal microbiome transplantation started in China during the 4th century and has now been seen to be effective in animals17! While this is still considerably new to veterinary medicine, a few case studies have been published. One study looked at a dog with eosinophilic irritable bowel disease and found that two days after the fecal microbiome transplantation, the diseased dog’s microbiome was more similar to that of the donor than its own pretreatment sample2. This demonstrates just how powerful these microbial communities are and their influence on overall health! While it is exciting to see successful human treatments become available to animals and have similarly beneficial results, it is important to realize that fecal microbiome transplantation alone, without a significant diet and lifestyle change, is not the most complete way of improving gut health. This “quick fix” mentality is comparable to expecting life-changing results after buying a gym membership and going once without changing anything about your diet or lifestyle. Introducing beneficial microbes and then supercharging them with a diverse and balanced diet is key!
Due to recent advances in testing pet owners and veterinarians now have the ability to test the gut health of their animal/patient. Churro and I were recently gifted a test kit from AnimalBiome, a company that is focused on revolutionizing animal health by utilizing microbiome science to create products that help improve the lives of our pets1! They have at-home tests that allow owners or veterinarians to send in fecal samples and get a snapshot of what is happening within the animal’s microbial community. They have a variety of supplements tailored to help correct gut dysbiosis and are currently the leader in microbiome science for companion animals. To find out more about AnimalBiome click HERE!
Churro’s Results!
Churro’s test results came back, and his gut microbiome is fairly balanced. I had the opportunity to discuss his results with one of the company’s specialists and found he did have slightly elevated levels of Prevotella which I learned has a strong association to the carbohydrate levels in the diet10. This may be due to the fact that while he does get some fresh food with his kibble, he is eating a fairly carbohydrate high diet. He did not have any harmful bacteria detected and all his other ranges were fairly unremarkable. While I did not suspect that Churro had any significant dysbiosis this test was a fun way to see how his microbial community is doing.
*Background on Churro: 3-year-old, male neutered Australian Shepherd, diet: Merrick Chicken and rice healthy grain dog food with supplemental fresh food mixed in. His BCS is 5/9 and he gets significant daily activity and is not on any current medication.
Tying this all together...
While there are still a lot of things that we do not know about the gut microbiome in animals, it is safe to say that it plays a significant role in their health. Diet, along with the environment that an animals is raised in, has repeatedly been seen to impact this microbial community and is something that can be changed to positively influence their health. As the research continues to progress, it will be exciting to see how it impacts the health of our furry companions!
Acknowledgement: I would like to thank Alex from AnimalBiome for sending Churro and I a kit to try as well as Beth Marty for her phone consultation regarding Churro's results! I would also like to thank the people that helped proof this post and Dr. Natasha Lilly for entertaining my ongoing dialogue on the microbiome.
References:
1. Animalbiome. “Our Science.” AnimalBiome.Com, 7 June 2023, animalbiome.com/our science.
2. Barko, P C et al. “The Gastrointestinal Microbiome: A Review.”Journal of veterinary internal medicine vol. 32,1 (2018): 9-25. doi:10.1111/jvim.14875
3. Castañeda, Sergio et al. “Diet-induced changes in fecal microbiota composition and diversity in dogs (Canis lupus familiaris): A comparative study of BARF-type and commercial diets.” Comparative immunology, microbiology and infectious diseases vol. 98 (2023): 102007. doi:10.1016/j.cimid.2023.102007
4. Cintio, Michela et al. “Gut Microbiome of Healthy and Arthritic Dogs.” Veterinary sciences vol. 7,3 92. 14 Jul. 2020, doi:10.3390/vetsci7030092
5. Connor Ellis, Adesola Odunayo, M Katherine Tolbert. “The use of metronidazole in acute diarrhea in dogs: a narrative review.” Topics in Companion Animal Medicine, Volumes 56–57, 2023, 100824
6. Hand, Daniel, et al. “Pyrosequencing the Canine Faecal Microbiota: Breadth and Depth of Biodiversity.” PLOS ONE, Public Library of Science, journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0053115#s2. Accessed 4, Feb. 2024.
7. “The Microbiome.” The Nutrition Source, 25 July 2022 www.hsph.harvard.edu/nutritionsource/microbiome/.
8. Honneffer, J.B., Steiner, J.M., Lidbury, J.A. et al. Variation of the microbiota and metabolome along the canine gastrointestinal tract. Metabolomics 13, 26 (2017). https://doi.org/10.1007/s11306-017-1165-3
9. Ji, Yun et al. “Programming of metabolic and autoimmune diseases in canine and feline: linkage to the gut microbiome.” Microbial pathogenesis vol. 185 (2023):106436. doi:10.1016/j.micpath.2023.106436
10. Li L. Effects of the dietary protein and carbohydrate ratio on gut microbiomes in dogs of different body conditions. mBio. 2017;8(1):e01703-16-. doi:10.1128/mBio.01703-16 \
11. Middelbos, Ingmar S., et al. “Phylogenetic Characterization of Fecal Microbial Communities of Dogs Fed Diets with or without Supplemental Dietary Fiber Using 454 Pyrosequencing.” PLOS ONE, Public Library of Science, journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0009768. Accessed 4 Feb. 2024.
12. Pilla, Rachel, and Jan S. Suchodolski. “The Role of the Canine Gut Microbiome and Metabolome in Health and Gastrointestinal Disease.” Frontiers, Frontiers, 17 Dec. 2019, www.frontiersin.org/articles/10.3389/fvets.2019.00498/full#B9.
13. Rachel Pilla, Jan S. Suchodolski. “The Gut Microbiome of Dogs and Cats, and the Influence of Diet.” Veterinary Clinics of North America: Small Animal Practice, Volume 51, Issue 3, 2021, Pages 605-621
14. Steagall PV, Pelligand L, Page SW, et al. The world small animal veterinary association (WSAVA): list of essential medicines for cats and dogs. J Small Anim Pract. 2020;61(9):E162–E176.
15. Vuori, Kristiina A et al. “The effect of puppyhood and adolescent diet on the incidence of chronic enteropathy in dogs later in life.” Scientific reports vol. 13,1 1830. 9 Feb. 2023, doi:10.1038/s41598-023-27866-z
16. V. Ulici, K.L. Kelley, M.A. Azcarate-Peril, R.J. Cleveland, R.B. Sartor, T. A. Schwartz, et al., Osteoarthritis induced by destabilization of the medial meniscus is reduced in germ-free mice, Osteoarthritis Cartilage 26 (2018) 1098–1109.
17. Zhang F, Luo W, Shi Y, Fan Z, Ji G. Should we standardize the 1,700-year-old fecal microbiota transplantation? Am J Gastroenterol [Internet] 2012. [cited 2015February13]; 107:1755; author reply p.1755-p.6. Available from: http://dx.doi.org/ 10.1038/ajg.2012.251; PMID:23160295; http://dx.doi.org/ 10.1038/ajg.2012.251
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