Interpreting Your Results

Background on the microbiome

The number one question we get asked is whether the microbiome assessment indicates if your pet is healthy or not. This is a very difficult question to answer, largely because there is lots of information about the microbiome that we have yet to uncover. What we do know is that there are LOTS of different ways that a healthy microbiome can look. At the same time, even small positive changes to the microbiome can result in significant improvements in your pet’s overall health. We are studying the data from your pet and hundreds of others around the world to bring you the best recommendations for how to help you improve your pet’s health.

Biologists organize life into different levels as a way of categorizing and identifying things. For example, humans are categorized as Homo sapiens, where “Homo” is a genus name and "sapiens" is a species name. Species is the most specific level of classification. In order from most broad to most specific, the classifications are: Kingdoms, Phyla, Classes, Orders, Families, Genera, and Species. The method that we use to characterize your pet’s sample identifies bacteria down to the genus (plural “genera”) level. This means that you will never see things like Clostridium difficile or Clostridium perfringens listed in your pet’s sample, because these are both species. Instead, these two would be grouped together and listed under their collective genus name, Clostridium.

There could be as many as 1 trillion species of bacteria on earth, and they haven’t all been identified yet. We do not have a predetermined list of bacteria that we search for: our analysis detects every kind of bacteria present, and some of them haven’t even been described or classified yet by anyone in the world. In these cases, you will see labels such as “g1” or “f2.” These correspond to undescribed genus (1), and undescribed family (2), respectively. There is nothing to worry about if your pet has many undescribed bacteria; it just emphasizes that this is still a very active area of research.


In the context of your pet’s gut microbiome results, “diversity” refers to how much variation exists among all the different live organisms. There are a few different ways that we characterize the diversity of your pet’s sample. You can find these diversity measures for your own pet’s sample by logging into and selecting “View and Compare.”

Richness: Richness describes the number of different types of bacteria present in the population. We measure the richness at the genus level, so if your pet’s richness was listed as 33, that would mean that there were bacteria from 33 different genera present in the sample.

Evenness: This describes how evenly all the different types of bacteria are distributed. It ranges from 0 to 1, where 1 would be a population where all kinds of organisms are present in equal numbers. For example, a population that included 3 cats, 3 dogs, and 3 ferrets would have an evenness value of 1.0, because each kind of animal is represented equally. In very dysbiotic, or unbalanced, gut microbiomes, we might see that one type of bacteria has taken over the vast majority of the microbiome, making it difficult for anything else to exist. These populations would have very low evenness values.

Shannon Diversity Index (SDI): This number takes into account both the richness and the evenness of a population to characterize the diversity of the sample overall. The majority of cat and dog gut microbiomes have SDI values somewhere between 1.0 and 3.0. Having a single number to describe the overall diversity makes it easier to compare your pet’s microbe at different time points, or even to compare your pet’s gut microbiome to your own gut microbiome!

To give you an idea of how these measures come into play, take a look at the graph below. Each bar represents one pet’s gut microbiome; each color represents one kind of bacteria. The microbiome on the left has lots of different colors, meaning it has lots of different kinds of bacteria. This means it has a high richness value. The bar on the right has very few kinds of bacteria, so it has a low richness value. In addition, the microbiome on the left has the different kinds of bacteria distributed much more evenly than the microbiome on the right, which has the bacteria in green taking up the majority of the microbiome, at nearly 80%. This means that the microbiome on the left has a much higher “evenness” value than the one on the right. Since the microbiome on the left has higher values for both richness and evenness, its overall level of diversity, the Shannon diversity index (SDI), is higher, coming to 2.83, compared to just 0.83 for the microbiome on the right.

Microbial Diversity


Is high diversity better than low diversity? In general, yes. The ideal gut microbiome has many different kinds of bacteria, all performing slightly different jobs, keeping things balanced and contributing to the overall health of your pet. However, there are exceptions: sometimes pets with high-diversity microbiomes are sick, while others with low-diversity microbiomes appear healthy. The concern with the latter scenario is that this microbiome may be less resilient when faced with a health challenge, like exposure to a pathogen or development of a chronic illness. If a pet has a high-diversity microbiome but still has symptoms of gastrointestinal distress, some of the specific kinds of microbes currently present might need to be reduced or eliminated.


Like we mentioned above, a phylum (plural “phyla”) is one classification used to help us describe and establish relationships between different organisms. Phylum is one of the broader classifications: to give you an idea, we belong to the phylum Chordata, along with cats, dogs, and sea squirts. You can find your pet’s breakdown of phyla by logging into and selecting “View and Compare.” The phyla are listed to the left of the circular starburst chart, as shown below:

Location of Phyla


Most of the time, all of the bacteria that we find inside the digestive tracts of dogs and cats will fall within the five phyla listed below:

Actinobacteria typically make up a very small proportion of a healthy pet’s gut microbiome. These organisms tend to increase when a pet is consuming lots of fat in the diet. Unsurprisingly, higher levels of Actinobacteria have been linked to weight gain and obesity.

Bacteroidetes often makes up a large part of the microbiome of healthy pets. Bacteroidetes levels tend to be lower if a pet is overweight and/or is consuming lots of fat, and they tend to be higher when they are consuming lots of plant matter, such as from prebiotic supplements or vegetables. Many kinds of Bacteroidetes bacteria have strong anti-inflammatory properties, suggesting that higher levels of Bacteroidetes may make your pet more resilient against a range of chronic illnesses.

Firmicutes often make up a large part of the microbiome of healthy pets. They are very efficient metabolizers, meaning that if undigested food particles reach the large intestine, Firmicutes bacteria can break them down and extract more calories from them. Thus, if we give identical bowls of food to two dogs, where one has very little Firmicutes and the other has many Firmicutes, the latter pup will gain more calories from that same bowl of food, and is therefore at a greater risk for becoming overweight.

Fusobacteria often make up a large part of the microbiome of healthy cats and dogs. They are very efficient protein digesters, so pets that consume lots of easily digestible protein tend to have higher levels of Fusobacteria. Animal protein is considerably easier for cats and dogs to digest compared to plant protein, so pets on plant-based diets often have Fusobacteria deficiencies.

Proteobacteria typically make up a very small proportion of a healthy pet’s gut microbiome, and higher levels have been linked with all kinds of health conditions, including cardiovascular diseases, digestive disorders, and metabolic disorders like diabetes. A growing body of research suggests that the level of Proteobacteria in the gut could potentially act as a “warning sign” indicating that some kind of inflammatory disease is present.


To read about some of the other common bacteria we encounter in samples from cats and dogs, click here. Please also take a look at our blog, which has more posts about the gut microbiome and pet health.

Questions? Please email us at