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Descriptions of Common Bacteria

How do specific bacteria influence your pet's health?

This is a very active area of research, and we are learning more every day. Below we have provided short summaries of what is currently known about common bacteria we encounter in pet samples, and we will continue to update this as we learn more.

First, we need to describe a little bit about biological classification. You can skip this section if you remember it from Biology class. 

About biological classification of the bacteria in your pet's sample

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" and  "sapiens" is a species name. Species is the smallest 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 used to characterize the diversity in your pet’s sample identifies bacteria all the way to the “genera” level. It’s estimated that there are as many as one trillion different species of bacteria on earth, and the vast majority of bacteria have not yet been identified. When bacteria in your pet’s sample belong to an unidentified category, you will see labels such as “g1”, “g2” or “f1” on the labels. This corresponds to undescribed genera (1 and 2), and undescribed family (1) in the sample. There is nothing to worry about if your pet has many undescribed genera; it just emphasizes that this is still a very active area of research.



Bacterial Descriptions


Bacteroides is a genus of bacteria found in the gut of healthy mammals. One important role they play is preventing potentially harmful pathogens from growing in the gut: they do this by taking up resources that, if left unutilized, would provide a breeding ground for pathogens. This group of bacteria is also responsible for converting complex carbohydrates into compounds more easily utilized by the host organism. Bacteroides has been shown to be more abundant in pets fed a kibble diet.


Blautia is a family of bacteria that is commonly found in the mammalian gut. One of its primary functions is producing butyric acid, a strong-smelling acid that is used for cell processes throughout the body. Importantly for digestive health, recent studies have indicated that butyric acid can be used as a therapy for Inflammatory Bowel Disease (IBD). This is because butyric acid has anti-inflammatory properties and also makes the gut environment less tolerable to pathogenic bacteria.


Catenibacteria is a genus of bacteria that aids the host organism in fermenting a wide variety of carbohydrates. As Catenibacteria carries out its fermentation process, it produces a number of short-chain fatty acids. It has been suggested that higher levels of short-chain fatty acids may reduce the risk of developing gastrointestinal disorders. For example, one of these short-chain fatty acids, butyric acid, has anti-inflammatory properties and also makes the gastrointestinal environment less tolerable to harmful species of bacteria.


Clostridiaceae is an incredibly diverse family of bacteria that is typically found in a healthy mammalian gut. Clostridiaceae appears to play an important role in the breakdown of proteins within the gastrointestinal tract. Though some individual species, such as the infamous C. dificile in humans, have been linked with diarrhea, the family as a whole is not pathogenic.  One group of researchers was able to wipe out colon cancer cells simply by exposing them to strains of dead bacteria belonging to the Clostridiaceae family; the researchers believe that proteins on the surface of the bacteria are responsible for their anti-cancer effects.


Clostridiales is an order of bacteria whose presence is key to maintaining a healthy gut microbiome. The group plays a crucial role in preventing a condition commonly called “leaky gut syndrome,” which occurs when the cells lining the intestinal tract too readily allow pathogens to enter the bloodstream, prompting excessive inflammation. The presence of Clostridiales within the intestinal tract makes the host organism less vulnerable to developing food sensitivities and allergies. Some evidence even suggests that if an allergic individual who is lacking in Clostridiales receives adequate supplementation, the allergic reaction will cease to occur.


Collinsella is a genus within the Actinobacteria phylum. Bacteria belonging to this phylum play crucial roles in detoxifying poisons, protecting against pathogens, and converting food into products that can be more easily utilized by the host organism. However, an overgrowth of the Collinsella genus can be problematic: elevated levels of Collinsella have been linked to diarrhea. In addition,studies have indicated that IBD-affected individuals typically have elevated levels of Collinsella when compared to their unaffected relatives.


Dialister is a genus of bacteria normally found in the mammalian gastrointestinal tract. Two of its main metabolic products are propionate and lactate, both of which have been shown to possess potent anti-inflammatory properties. Individuals with IBD have been shown to have lower levels of Dialister than their healthy counterparts.


Erysipelotrichia is a class of bacteria commonly found in the mammalian gut. It tends to be found in much greater abundance in obese individuals compared to healthy ones.


Fusobacteria are normally found in the mammalian gastrointestinal tract, though they are highly likely to cause disease if they gain access to the bloodstream. Elevated levels of this genus are increasingly being associated with a number of chronic diseases, including Inflammatory Bowel Disease. Some studies have even identified individual species of Fusobacteria that have the potential to serve as biomarkers for the disease, meaning that their mere presence could identify IBD-affected individuals.


Lachnospiraceae is a family of bacteria normally found in a healthy mammalian gut. One of its primary functions is to produce butyric acid, which has anti-inflammatory properties and also makes the gut environment less tolerable to pathogen species of bacteria. Higher levels of Lachnospiraceae have been associated with decreased risk of some types of cancer. This group of bacteria is especially vulnerable to antibiotics, so it tends to be deficient or even absent in animals who have recently undergone antibiotic treatment.


The Lactobacillus genus of bacteria is one category within the Firmicute phylum, which is the most predominant phylum found in the gut microbiome of many healthy individuals. Individuals with IBD have been shown to have lower levels of Lactobacillus compared to healthy controls. Increasing the Lactobacillus levels in an individual’s gut, whether naturally or via administration of a probiotic, has the ability to alleviate symptoms of IBD such as pain due to inflammation of the internal organs (also known as visceral pain). Experts believe that Lactobacillus positively affects the gut because these cells produce chemical products with anti-inflammatory properties. One other role Lactobacillus plays in the gut is breaking down sugars into lactic acid, which is a crucial energy source for the body.


Megamonas is a genus of bacteria within the Firmicutes phylum, a phylum which comprises a large part of the mammalian gut microbiome. One study revealed that healthy mammals had much higher levels of the genus Megamonas compared to cats suffering from diarrhea. Indeed, one of the major metabolic products of this group is a compound called propionate, which has been shown to possess potent anti-inflammatory properties. However, an increased abundance of certain species within the Megamonas genus has been linked to IBD.


Methanobrevibacter is a genus within the Methanobacteria class. These organisms are not bacteria; rather, they are members of the kingdom Archaea. They hold the important function of converting hydrogen, H₂, into methane, CH₄. Methane has been shown to delay the rate at which food moves through the gut, allowing more time for nutrients to be absorbed. This leads to an increase in the host’s energy intake and often subsequent weight gain. In addition, it is closely associated with IBS-C, or constipation-predominant Irritable Bowel Syndrome.


Odoribacter is a genus of bacteria normally found in the mammalian gut that helps break down proteins and carbohydrates for the host organism. As it metabolizes these macronutrients, it produces butyric acid, which has anti-inflammatory properties and also makes the gastrointestinal tract less tolerable to disease-causing strains of bacteria. Odoribacter is susceptible to Clindamycin, an antibiotic commonly used in veterinary medicine, so if your pet recently finished a round of Clindamycin, this genus may be deficient or absent.One recent study indicated that higher levels of Odoribacter were correlated with lower levels of obesity.


Parabacteroides is a genus of bacteria normally found in the healthy mammalian gut. One of its main roles is to prevent the invasion and colonization of disease-causing pathogens: it does this by secreting bacteriocins, which are chemicals that are toxic to other strains of bacteria. The intestinal tracts of IBD-affected individuals are often completely devoid of Parabacteroides, suggesting that this genus (along with several others) may help protect the gut from excessive inflammation.


Prevotella is a genus of bacteria commonly found in the digestive tract of healthy mammals. The presence of Prevotella has been shown to promote more efficient processing of glucose, a critical energy source for all body cells. However, studies have linked an overabundance of this group with excessive inflammation; for this reason, researchers suspect it may play a role in chronic inflammatory diseases, including IBD. Individuals consuming diets high in carbohydrates tend to have higher levels of Prevotella, so if your pet has an overabundance of this genus and eats grains, fruits, or vegetables on a regular basis, you may consider decreasing or eliminating them from their diet.


Ruminococcaceae is a family of bacteria which is normally abundant in the mammalian gastrointestinal tract. Several of its metabolic byproducts decrease the permeability of the cells lining the intestine; more permeable intestines tend to be correlated with a higher incidence of disease because pathogens ingested by the host have easier access to the bloodstream. Individuals suffering from acute hemorrhagic diarrhea tend to have decreased levels of Ruminococcaceae compared to healthy individuals.


Bacteria belonging to the Shigella genus are known as enteric pathogens. “Enteric” indicates that these bacteria tend to reside in the intestines of their host. “Pathogen,” naturally, identifies the ability to cause potentially life-threatening disease. Shigella wreaks havoc on the gut microbiome because it depletes the host organism of its supply of very important cells known as “macrophages.” These large cells engulf and destroy pathogens that could otherwise prove fatal to the host.  Due to Shigella’s destructive nature, it is thought to be a common cause of Postinfectious Irritable Bowel Syndrome, or PI-IBS. PI-IBS is a variety of IBS in which symptoms of gastrointestinal distress do not resolve long after an acute infection of the gut.

Staphylococcus aureus

Staphylococcus aureus is a pathogenic species of bacteria that is typically only found in an unhealthy gut. Some strains of this bacterium have become resistant to antibiotics; these strains are referred to as MRSA, or methicillin-resistant Staphylococcus aureus. Those strains which are antibiotic resistant are suspected to be even more inflammatory to immune cells than strains which are not. The presence of any Staphylococcus aureus within the gut has been shown to increase the likelihood of post-infectious Irritable Bowel Syndrome by at least six times. Post-infectious Irritable Bowel Syndrome is a variety of IBS in which symptoms of gastrointestinal distress do not resolve long after an acute infection of the gut.


Succinivibrionaceae is a family of bacteria belonging to the Proteobacteria phylum. Increases in the Proteobacteria phylum have been associated with IBD. Typically, Succinivibrionaceae are found in the guts of ruminates such as cows and sheep. (Ruminates are animals that regurgitate previously swallowed food in order to digest it once again.) Because Succinivibrionaceae plays a role in the digestion of starch, however, these bacteria can be found in the gut of any species that consumes carbohydrates, including dogs and cats.


Sutterella is a genus of bacteria normally found in the gastrointestinal tract of mammals. They are mildly pro-inflammatory, though studies have indicated that they are unlikely to play a significant role in the development of gastrointestinal conditions like Inflammatory Bowel Disease. Rather, members of this genus may help keep immune system responses at an appropriate level.