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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 levels 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 dogs. 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 processing complex molecules in the intestine down to more simple ones. Bacteroides has been shown to be more abundant in dogs fed a kibble diet.


Clostridiaceae is an incredibly diverse family of bacteria that can be found in the mammalian gut. Clostridiaceae appears to play an important role in the breakdown of proteins within the canine 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 study, for example, found no difference in Clostridiaceae levels between healthy individuals and individuals with diarrhea.


Clostridiales is an order of bacteria within the Clostridia class. Low abundance of Clostridiales has been associated with a liver disease called Primary Sclerosing Cholangitis, or PSC, in which inflammation in the bile ducts leads to scarring and, over time, serious liver damage. PSC is strongly associated with one form of Irritable Bowel Disease. Researchers have observed that this particular order of bacteria, when found in the mammalian gut, correlates significantly with the health of the individual. In addition to its association with overall gut health, Clostridiales is known to be found in great abundance in the human belly button.


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 end products that can be more easily utilized by the host. However, an overgrowth of the Collinsella genus in particular can be problematic: in cats, elevated levels of Collinsella compared to healthy individuals is associated with diarrhea. In addition, in humans, individuals with Crohn’s disease, a chronic inflammatory bowel disease, showed elevated levels of Collinsella when compared to their unaffected relatives.


Erysipelotrichia is a class of bacteria commonly found in the mammalian gut. In mice, Erysipelotrichia is in much greater abundance in obese individuals compared to healthy individuals.


Fusobacterium is a bacterial pathogen which can colonize the mammalian gut. It is increasingly being associated with a number of chronic diseases, including Irritable Bowel Disease. Some studies have even identified individual species of Fusobacterium that have the potential to serve as biomarkers for the disease, meaning that their mere presence could identify IBD-affected individuals.


Lachnospiracaea is a family of bacteria that is commonly found in the mammalian gut. One of their primary functions is producing butyric acid, a strong-smelling acid that is used for cell processes in many places throughout the mammalian body. Importantly for digestive health, recent studies have indicated that butyric acid can be used as a therapy for irritable bowel syndrome. It has anti-inflammatory properties and also makes the environment less tolerable to harmful species of bacteria. Though Lachnospiracaea’s production of butyric acid is beneficial to the gut, at least one species within the family has been linked to the development of obesity and diabetes.


The Lactobacillus genus of bacteria is one member of the Firmicute phylum, which is the most predominant phylum found in the gut microbiota of healthy individuals. Individuals with IBS 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 IBS such as pain due to inflammation of the internal organs (also known as visceral pain). Experts believe that Lactobacillus can positively affect 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 that is used by 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 cats had much higher levels of the genus Megamonas compared to cats with diarrhea. However, an increased abundance in certain species within the genus Megamonas has been linked specifically to IBD.


Methanobrevibacter is a genus within the Methanobacteria class. The organisms making up this genus are not members of the bacterial kingdom; instead, they are members of the kingdom Archaea. This class of organisms holds 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. Methanobrevibacter increases the amount of nutrients absorbed from food, resulting in an increase in the host’s energy intake and weight gain. In addition, it is the methanogen most closely associated with IBS-C, or constipation-predominant Irritable Bowel Syndrome.


Odoribacter is a genus of bacteria belonging to the Bacteroidetes phylum. Their primary role in the gut is to break down proteins and carbohydrates for the host organism. One study carried out in rats indicated that higher levels of Odoribacter were correlated with lower levels of adiposity, or severe obesity. Similarly, individuals diagnosed with Metabolic Syndrome (a cluster of symptoms that together increase one’s risk for heart disease, stroke, and diabetes) proved to have lower levels of Odoribacter. The findings of these studies are consistent with the popularized viewpoint that higher levels of Bacteroidetes (the phylum encompassing the Odoribacter bacteria) are correlated with lower body weights.


Prevotella is a group of common commensal bacteria found living in the dog digestive tract. It is associated with the oral cavity and the gut of animals. In humans, Prevotella has been found to be associated with plant-rich diets; however, it has also been linked with chronic inflammatory conditions.


Ruminococcaceae is a genus of bacteria that belongs to the Firmicutes phylum, which makes up a large portion of the canine gut microbiome. Individuals suffering from acute hemorrhagic diarrhea had significant decreases in Ruminococcaceae when compared to healthy individuals.


Bacteria belonging to the Shigella genus are known as enteric pathogens. “Enteric” indicates that when present, these bacteria tend to reside in the intestines of their host. “Pathogen,” naturally, identifies the genus’ 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 type of IBS in which the onset of symptoms directly follows an episode of gastroenteritis. Most of the research conducted on Shigella has been done in humans; however, its method of sabotaging cells remains fairly consistent across many species, including cats and dogs.

Staphylococcus aureus

Staphylococcus aureus is a pathogenic species of bacteria that is a member of the Firmicutes phylum. 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. In humans, increases in bacteria belonging to the Succinivibrionaceae family were associated with elevated levels of lead in the blood, suggesting that one function of this family may be to facilitate greater lead uptake.


Sutterella is a genus of bacteria that is normally found in the gastrointestinal tract of mammals. Dogs with acute hemorrhagic diarrhea have been shown to have significant increases in Sutterella residing within their gut. Though many studies in the past have drawn connections between Sutterella and Irritable Bowel Disease, more recent research has shown that it is typically present in roughly equal numbers in healthy individuals and those with IBD. Interestingly, in humans, an overabundance of Sutterella has been linked to autism in children.