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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 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 used to characterize the diversity in your pet’s sample identifies bacteria all the way to the genus (plural “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 typically found in the gut of healthy carnivores. One important role this group plays is preventing harmful microbes from multiplying in the gut: they do this by taking up resources that, if left unutilized, would provide a breeding ground for disease-causing pathogens. In addition, Bacteroides actively secrete compounds that help make the gut environment more hospitable to themselves and other beneficial bacteria. Bacteroides is also responsible for converting complex carbohydrates into compounds more easily utilized by the host organism.


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 Irritable Bowel Syndrome (IBS). It 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 carry out the fermentation process, they produce a number of compounds called short-chain fatty acids. It is thought that short-chain fatty acids may reduce the risk of developing certain gastrointestinal disorders, including Inflammatory Bowel Disease (IBD). One of these short-chain fatty acids in particular, 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 Clostridium dificile in humans, have been linked with diarrhea, the family as a whole is not pathogenic.  Colon cancer cells often die upon exposure to strains of dead Clostridiaceae bacteria; it is believed 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, often 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 Clostridiales probiotic supplementation, the allergic reaction will decrease in severity or even disappear completely.


It is thought that the Clostridium genus plays an important role in the maintenance of host gastrointestinal health. Several species belonging to the Clostridium genus have been linked with high-protein, low-carbohydrate diets, which is the diet recommended for healthy weight loss. However, a few species of Clostridium, such as Clostridium perfrigens, have been known to be pathogenic.


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. However, a Collinsella overgrowth is often problematic: elevated levels of Collinsella have been associated with diarrhea and Inflammatory Bowel Disease (IBD).


Increases in Coprococcus levels in the gut have been associated with decreased severity of allergic reactions, suggesting that, conversely, low Coprococcus levels could be used as biomarkers for the presence of food allergies. When examining the microbiomes of those suffering from Inflammatory Bowel Disease (IBD), Coprococcus levels are markedly decreased compared to the microbiomes of healthy individuals.


Dialister is a genus of bacteria that produces large amounts of propionate and lactate, short-chain fatty acids that possess potent anti-inflammatory properties. IBD-affected individuals tend to have lower levels of Dialister than their healthy counterparts.


Dorea is a genus of bacteria whose members are known to be major gas producers, mainly carbon dioxide and hydrogen gases. Though this genus is often found in healthy individuals, when present in elevated numbers there is a greater likelihood of constipation. Elevated levels are also more common in individuals with Multiple Sclerosis, an autoimmune condition, suggesting that the Dorea genus may play a role in immune system activity.


High levels of Erysipelotrichaceae have been associated with metabolic disorders, such as hyperthyroidism, hypothyroidism, Cushing’s syndrome, and diabetes. Erysipelotrichaceae levels also tend to be elevated in individuals with colorectal cancer. At the same time, it is perfectly normal for Erysipelotrichaceae to be present in the gastrointestinal tract in moderate amounts, and its mere presence is no cause for alarm. Animal who consume food that is particularly bioavailable, especially raw food, may have higher levels of Erysipelotrichaceae despite having no gastrointestinal issues whatsoever. This is thought to be due to greater amounts of protein being absorbed into the body.


Eubacteria is a genus of bacteria that tends to be more abundant in individuals who consume a high-fat diet. Additionally, those who regularly engage in physical activity have been shown to have significantly lower levels of this group compared to those who are sedentary. Though Eubacteria have been associated with pathologies such as colorectal cancer, they are present in a large percentage of pets, so their mere presence is not cause for concern.


Faecalibacteria is a genus of bacteria which typically exerts mostly positive effects on the host. Researchers often refer to this group as a “health-promoting” genus, because it has been found to be more abundant in the guts of individuals who lead more active lifestyles. Excessively low levels of Faecalibacteria in the gut is associated with lymphoma as well as Crohn’s disease. However, raw-fed pets have also been shown to have much lower levels of Faecalibacteria in the stool compared to kibble-fed pets, so if your cat or dog eats raw food and has low levels of Faecalibacteria, that is one possible explanation.


Fusobacteria are normally found in the carnivore 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 health conditions, including Inflammatory Bowel Disease (IBD). Some studies have even identified individual species of Fusobacterium that have the potential to serve as biomarkers for the disease, meaning that the mere presence of these species could identify IBD-affected individuals. However, some members of the Fusobacterium genus are not necessarily indicative of gastrointestinal malaise; researchers have shown that Fusobacteria levels are higher in animals fed raw meat compared to animals fed kibble.


Lachnospiraceae is a family of bacteria normally found in the gut of healthy carnivores. One of its primary functions is to produce butyric acid, which has anti-inflammatory properties and also makes the surrounding environment less tolerable to harmful species of bacteria. Higher levels of Lachnospiraceae have been associated with a 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 of bacteria within the Firmicute phylum, which is the most predominant phylum found in the gut microbiome of many healthy individuals. Individuals with Inflammatory Bowel Disease (IBD) have been shown to have lower levels of Lactobacillus compared to healthy individuals. Increasing the Lactobacillus levels in an individual’s gut, whether naturally or via administration of an oral probiotic, has the ability to alleviate symptoms of IBD such as pain due to inflammation of the internal organs. Researchers believe that Lactobacillus positively affects the gut because these cells produce chemicals 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 normally found in the gut of healthy carnivores. One of the major metabolic products of this group is a compound called propionate, which has been shown to possess potent anti-inflammatory properties. In addition to its ability to inhibit inflammation, Megamonas affects the metabolic rate of the host organism. One study revealed that when animals were fed an insufficient amount of food for an extended period of time, those with more Megamonas in their gut were better able to maintain their weights despite the stress.


Methanobrevibacter is a genus within the Methanobacteria class. Unlike all the other groups listed on this page, these organisms are not bacteria; rather, they are members of the kingdom Archaea. They hold the important function of converting hydrogen, H, into methane, CH. 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. When present in excess, it is closely associated with IBS-C, or constipation-predominant Irritable Bowel Syndrome.


Odoribacter is a genus of bacteria that helps break down proteins and carbohydrates for the host organism. As Odoribacter 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.


Oscillospira is a genus of bacteria that tends to be present in greater numbers in healthier host organisms, especially when considering weight and cardiovascular status. This group of bacteria tends to be markedly deficient in IBD-affected individuals, as well as individuals with severe food allergies. Interestingly, among human infants, living with pets during the first few months of life is associated with drastically higher levels of Oscillospira, suggesting that there may be a link between pet ownership and better health!


Parabacteroides is a genus of bacteria that helps prevent the invasion and colonization of disease-causing pathogens: it does this by secreting bacteriocins, unique chemicals that are toxic to other strains of bacteria. Individuals with Inflammatory Bowel Disease (IBD) often lack a healthy population of Parabacteroides in their gut, suggesting that this genus also helps protect against excessive inflammation.


Prevotella is a genus of bacteria commonly found in the digestive tract of healthy carnivores. 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 like IBD. Individuals consuming diets high in carbohydrates tend to have higher levels of Prevotella, so if your pet shows an overabundance of this group and eats grains, fruits, or vegetables on a regular basis, whether on their own or in their kibble, you may consider decreasing or eliminating them from the diet.


Ruminococcaceae is a family of bacteria which is typically present in the carnivore gastrointestinal tract. Several of this group’s metabolic byproducts decrease the permeability of the cells lining the intestine, which reduces the incidence of disease for the host. More permeable intestines tend to cause health issues because pathogens ingested by the host have easier access to the bloodstream, where they can cause issues throughout the body.


Ruminococcus is a genus of bacteria normally found in the carnivore intestinal tract. Bacteria belonging to the Ruminococcus genus are able to easily break down cellulose, an important carbohydrate found in plant cell walls. Carnivores lack the powerful digestive enzymes necessary to break down cellulose, so the presence of Ruminococcus allows them to obtain energy from this ubiquitous compound. When Ruminococcus digests cellulose, it produces succinate and acetate, two short-chain fatty acids which have been shown to have anti-inflammatory effects.


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 their ability to cause potentially life-threatening illness. 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 Post-Infectious 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 bacteria 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 Inflammatory Bowel Disease (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 again.) Because Succinivibrionaceae plays a role in the digestion of starches, 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 that is normally found in the gastrointestinal tract of dogs. They are mildly pro-inflammatory, though the results of several studies have indicated that they are unlikely to play a significant role in the development of GI conditions like Inflammatory Bowel Disease (IBD). Instead, members of this genus may help keep immune system responses at an appropriate level. At the same time, higher levels of Sutterella are associated with a host of health issues including diarrhea and food sensitivities, so moderation is key with this genus.