Are Pet Owners’ Microbiome Unique?

A Brief Background: 

Microbes found in our body and gut are responsible for many different functions of everyday life. Specifically, the human microbiome has prominent influences on health and disease (Kates et al., 2020). Have you ever questioned what can contribute to changes in our microbiome? The microbiome is defined as the community of microorganisms such as bacteria or fungi in a specific environment (Ursell et al., 2012). Although microbial changes are being considered in diet trends, probiotics, and environmental factors, pet ownership is often overlooked. Today, approximately 67% of U.S. households own a pet (APPA, 2021). Pet ownership brings us to the question, how may our microbiomes be impacted by pets living in our households? Many cats and dogs have similar microbiota compared to humans (Honneffer et al., 2014). Human-pet relationships can bring to light many pros and cons within our health. Many animals, especially those that roam outside, tend to bring in bacteria from the environment. This bacteria can then be easily transmitted (Resnick, 2012) to those living in the house, whether it’s via furniture, snuggling with your pet, or even something we consider harmless, like kissing your pet. Not only that, but bacteria such as Salmonella, E. coli, Clostridia, and Campylobacter are transmitted via pets and cause severe intestinal diseases for humans. 

However, it has also been shown that living with pets can have significant benefits. According to a study conducted on young children, it was demonstrated that household pets increased diversity in the human gut microbiome (Azad et al., 2013). Diversity is characterized by the variation of life forms that’s present in varying ecosystems. This leads to protection against allergic diseases and influences the early development of gut microbiota (Azad et al., 2013). The human microbiota consists of about 10-100 trillion microbial cells that have a symbiotic relationship (Ursell et al., 2012). Other benefits include a decrease in allergic diseases, a decreased risk of obesity, and the ability to reduce the risk of metabolic diseases (Tun et al., 2017). It’s also been identified that microbial diversity is dictated by age, birth method, diet, and antibiotic treatment. Since microbiota clearly have major impacts on human health, we must consider how pets impact our microbiomes. Therefore we need to continue research and study how household pets can impact our microbiome in all aspects. The paper Household Pet Ownership and the Microbial Diversity of the Human Gut Microbiota looks at the relationship between pets in the house and how this can impact the composition and diversity of the adult gut microbiome (Kates et al., 2020).  

Research Question

What is the difference in the gut microbiota of individuals with and without a pet present in the home? 

Supporting Evidence

To test the hypothesis that adults with a minimum of one pet will have a different gut microbiome than those who don’t, Kates et al. (2020) conducted a case-controlled study where the effects of pet exposure on adult health microbiota were examined. A case-controlled study is observational, which compares two groups and the differences in the outcomes. In this case, they compared participants’ microbiomes who owned a pet to those who didn’t own a pet. Pets considered for the survey included dogs, cats, birds, rodents, and reptiles. A total of 332 participants (18+ years old) completed the Survey of Health of Wisconsin (SHOW) and submitted a stool sample for analysis to the Wisconsin Microbiome Study (WMS). Only 178 of these participants had some sort of pet in their home, with dogs being the most common.  

The microbial differences found between the participants with and without pets yielded minimal differences. There were no differences between the variety of microbes in a single sample or the variation of microbial communities found between samples; however, there were differences presented in operational taxonomic units (OTUs). The operational taxonomic units account for the classification of closely related phylogenetic groups. The bacteria found with higher abundance in participants who had a pet compared to those who didn’t were classified as Lactobacillus gasseri, Clostridium oroticum, Bacteroides cellulosilyticus, and Akkermansia muciniphila. These bacterias are commonly found in probiotics and are responsible for breaking down differing macromolecules. Seven OTUs were significantly more abundant in those with pets when compared to those without pets (Kates et al., 2020). These bacteria are found in stool samples and aid in the recovery from certain infections. Lifestyle choices like antibiotic use, probiotic consumption, and healthcare needs also accounted for the differences in OTU counts between individuals living with pets and those not. The bacteria included were Clostridium XIVa, Anaerotruncus, Bacteroides.  

Figure 1. A chart of the OTU differences between those with and without pets. The positive values are the OTU’s that are more abundant in those with pets while the negative values are the OTU’s more abundant in those without pets (Figure 6 from Kates et al., 2020).

Figure 1. demonstrates the difference between the OTUs in those with and without pets. The microbiota found was dominated by members of the Firmicutes phylum and had a lower relative abundance of Actinobacteria & Bacteroidetes (Kates et al., 2020). This is consistent with pets because cats have a high abundance of bacteria in the Firmicutes and Bacteroidetes class, and dogs’ microbiome is characterized by those as well as Proteobacteria and Fusobacteria. However, these findings are inconsistent with previous studies conducted by The Human Microbiome Project Consortium, 2012. The Human Microbiome Project has shown that Bacteroidetes and Firmicutes are the most prevalent gut phyla. It was ultimately determined that Firmicutes dominated the microbiome of both pet owners and non-pet owners, with Actinobacteria and Bacteridetes being the following most prevalent phyla (Kates et al., 2020). It was also found that as we age, our gut microbiome becomes less diverse. This could be due to the microbiome being changed as we age. Ultimately the results indicate that there is likely minimal impact of owning a pet on the composition of the adult gut microbiota in terms of alpha and beta diversity (Kates et al., 2020). 

Future Studies: 

More studies should be conducted to solidify the effect that pets have on the human microbiome. We should expand our research and look at how long the participant has owned a pet and how that could potentially change the results. I’m curious about the differences we’d find between someone who’s owned a pet for one year versus someone who owned single or multiple pets over ten years. I also wonder if the type of pet could play a role in the microbial diversity found in a human.  Not only that, but the amount of interaction that participant has with their pet can also impact the microbiome. For example, you’ll have minimal interaction with a fish compared to a dog. The best way to go about this study would be to have a longitudinal study of individuals with pets, set standards, and then recruit them based on a survey. To get sufficient data, I feel we’d have to examine the participant’s gut microbiota over a few years.  

Future research could look at how human microbial diversity is impacted over a longitudinal period. Not only that but taking into account the length of the relationship with the pet and the individual’s age. The study should start when the participant is young and carry out through adulthood. It could also be impacted if they have multiple pets or if a pet dies and is replaced. I think we’d also have to consider if this subject lives alone and how many pets they have or if they interact with pets daily. We could do this by setting a minimum standard of what counts as pet contact. Understanding the metabolic relationship between pets and our microbiomes will allow us to better understand how our health can beneficially be impacted. 


One limitation mentioned in the study is that the significant impacts of pets on microbial communities in humans may not have been recognized due to the possibility of pet exposure having a more substantial effect in earlier life. As an infant and child, we are more susceptible to change, and environmental factors play a prominent role in genotypic and phenotypic expression. An earlier study showed that by the time age 3 or 4 arrives (Yatsunenko et al., 2021), this begins reflecting the microbiome seen in adulthood; therefore, there is a short period for extensive changes to occur in the guts microbial diversity. By excluding anyone under the age of 18, could have limited the study results by excluding another possible set of data and differences. 

Another limitation is that the microbiome of the pet living in the household could not be assessed. This leads to constraints because there is no baseline of microbial diversity to compare to the owner’s microbial diversity. Humans can come into contact with the pet’s gut microbiome in several different ways, including cleaning up the pets’ waste and the animals directly transferring it to them via their tongues after grooming themselves. The study itself was a cross-sectional study; therefore, the analysis from SHOW and the Wisconsin Microbiome were only looking at one period of time. This limits data analysis due to the inability to determine changes in pet exposure and how other factors can relate to the gut microbiota over a long period in the same individual.  

Further Information: 

For more information regarding the gut microbiome and how pets interact with your microbiome, click below:

Your Gut Microbiome: The Most Important Organ You’ve Never Heard Of – Erika Ebbel Angle- TEDxFargo 

This TedX by Dr. Erika Ebbel Angle describes why the microbiome is the most crucial organ in our body and explains how our gut health affects our health overall. It goes into depth on how lifestyle choices can lead to different medical diseases. To watch this TEDx: CLICK HERE

Exposure to household furry pets influences the gut microbiota of infants at 3–4 months following various birth scenarios

This paper discusses how the exposure of household pets can reduce the risks of certain metabolic diseases and reduce certain health risks. It specifically looks at infants and how their microbiomes are being affected beneficially by living with pets. To read more about this article: CLICK HERE 

Infant gut microbiota and the hygiene hypothesis of allergic disease: Impact of household pets and siblings on microbiota composition and diversity

This paper focuses on the “hygiene hypothesis” and discusses how low diversity in infant gut microbiota has been linked to health problems and allergic diseases. It explains how exposure to pets and siblings can influence gut microbiota in early development. To read more about this article: CLICK HERE


Azad, M. B., Konya, T., Maughan, H., Guttman, D. S., Field, C. J., Sears, M. R., . . . Kozyrskyj, A. L. (2013). Infant gut microbiota and the hygiene hypothesis of allergic disease: Impact of household pets and siblings on microbiota composition and diversity. Allergy, Asthma & Clinical Immunology, 9(1). doi:10.1186/1710-1492-9-15

Caugant, D. A., Levin, B. R., & Selander, R. K. (1984). Distribution of multilocus genotypes of escherichia coli within and between host families. Journal of Hygiene, 92(3), 377-384. doi:10.1017/s0022172400064597

Facts + statistics: Pet ownership and insurance. (n.d.). Retrieved September 24, 2021, from 

Honneffer, J. B. (2014). Microbiota alterations in acute and chronic gastrointestinal inflammation of cats and dogs. World Journal of Gastroenterology, 20(44), 16489. doi:10.3748/wjg.v20.i44.16489

Kates, A. E., Jarrett, O., Skarlupka, J. H., Sethi, A., Duster, M., Watson, L., . . . Safdar, N. (2020). Household pet ownership and the microbial diversity of the human gut microbiota. Frontiers in Cellular and Infection Microbiology, 10. doi:10.3389/fcimb.2020.00073

Resnick, L. (2012, April 06). Simple steps for avoiding infections from dogs and cats. Retrieved October 11, 2021, from 

The Human Microbiome Project Consortium. Structure, function, and diversity of the healthy human microbiome. (2012). Nature, 486(7402), 207-214. doi:10.1038/nature11234

TEDxTalks. (2019, December 12). Your gut microbiome: The most important organ you’ve never heard of | Erika Ebbel Angle | tedxfargo. Retrieved October 11, 2021, from 

Tun, H. M., Konya, T., Takaro, T. K., Brook, J. R., Chari, R., Field, C. J., . . . Kozyrskyj, A. L. (2017). Exposure to household furry pets influences the gut microbiota of infants at 3–4 months following various birth scenarios. Microbiome, 5(1). doi:10.1186/s40168-017-0254-x

Ursell, L. K., Metcalf, J. L., Parfrey, L. W., & Knight, R. (2012). Defining the human microbiome. Nutrition Reviews, 70. doi:10.1111/j.1753-4887.2012.00493.x

Yatsunenko, T., Rey, F. E., Manary, M. J., Trehan, I., Dominguez-Bello, M. G., Contreras, M., . . . Gordon, J. I. (2012). Human gut microbiome viewed across age and geography. Nature, 486(7402), 222-227. doi:10.1038/nature11053