What is the role of each bacteria in the microbiome?

Let's take a look at the most commonly found bacteria in your dogs’ gut, what they do, and what happens if their levels become too high or too low.


6 min read
Dr Joe Inglis BVSc MRCVS
Head of Veterinary Sciences

In many of our other blog posts we have been looking at the microbiome as a whole. Now we are going to look at the most commonly found bacteria in your dog's gut and see what it does, and what happens if their levels become too high or too low. This is the sort of information you will be receiving in your BIOME9 report, but your report will be individualised depending on what is going on with your pet specifically.



Bacteroides are involved in several functions including carbohydrate metabolism, immune system regulation and inflammation control. They also play a role in the metabolism of bile acids and affect the absorption of both fats taken in through the diet, as well as vitamins which are fat soluble. 

If Bacteroides are too low, your dog’s ability to ferment and digest fibre and carbohydrates may be impaired, as well as their ability to produce short chain fatty acids. This will have widespread implications throughout the body. Low levels have also been linked with chronic intestinal inflammation, including IBD (Inflammatory Bowel Disease). However, certain individual Bacteroides species have been linked with remission of IBD.

If Bacteroides are too high, your dog could be at risk of chronic diarrhoea and obesity (higher levels are found in overweight dogs). 


Prevotella play an important role in the defence against the growth of harmful bacteria, help to keep inflammation in check, ferment fibre and carbohydrates, and produce important energy sources.  

Low levels of Prevotella may lead to various gastrointestinal issues, including chronic intestinal inflammation and acute diarrhoea. 

High levels have been seen in dogs with a higher body condition score, resulting in further issues of inflammation and longevity secondary to obesity.


Alloprevotella helps to digest complex carbohydrates and proteins. They have also been linked to maintaining a healthy weight.

Low levels may lead to impaired energy metabolism and predispose your dog to low and unhealthy amounts of fat with a poor body condition score.

High levels of Alloprevotella may predispose your dog to increased body weight, higher fat levels and an irregularly high energy metabolism. 



Fusobacterium play an important role in the digestion of protein to create amino acids, used for multiple purposes in your dog's health and wellbeing. 

Low levels of Fusobacterium may predispose your dog to multicentric lymphoma, as well as acute diarrhoea and chronic intestinal inflammation. Low levels are commonly found in IBD, along with decreased Folate and Cobalamin (B12). 

Increased levels of Fusobacterium may predispose your dog to acute diarrhoea and acute haemorrhagic diarrhoea syndrome. Higher levels may also predispose your dog to obesity (but increases have been seen in pets at their ideal weight), may induce inflammation within the gastrointestinal tract, and can prove potentially infectious. 



Lactobacillus are key fibre degraders and have beneficial probiotic capabilities. These bacteria have been reported to reduce the production of, or inactivate, toxins produced by the likes of Salmonella, pathogenic E.coli and Clostridium perfringens. They also play a role in the metabolism of bile acids and affect the absorption of both fats taken in through the diet, as well as vitamins which are fat soluble. 

If Lactobacillus are too low, your dog may not be able to adequately utilise nutrients from fibrous food. Defence against disease causing bacteria and toxins may also be impaired if these bacteria are not maintained within the healthy range.

If Lactobacillus is too high, your dog may be at risk of gastrointestinal disorders including both acute and chronic diarrhoea. 


Although there are some disease-causing bacteria within this group, some species of Clostridium are in fact good bacteria, helping with important functions within the gut and even contributing to vitamin production. They also play a role in the metabolism of bile acids and affect the absorption of both fats taken in through the diet, as well as vitamins which are fat soluble. 

Low levels may result in reduced essential vitamin and butyrate production, and have been linked with chronic intestinal inflammation. 

High levels of Clostridium may lead to the development of gastrointestinal illnesses, including acute uncomplicated diarrhoea and acute haemorrhagic diarrhoea. 

Ensuring dietary fibre is high and looking to include lean meat, such as chicken or turkey, helps ensure harmful clostridium growth is limited.  


Faecalibacterium is a carbohydrate fermenting genus thought to contribute to regulation of the immune system and promotion of overall gut health. This includes strengthening the gut wall barrier and protecting against pathogens, reducing inflammation and producing vital energy for the gut, through production of butyrate and anti-inflammatory peptides. 

Low levels of Faecalibacterium may predispose your dog to developing acute haemorrhagic diarrhoea, acute uncomplicated diarrhoea, IBD and generalised gut inflammation due to fewer anti-inflammatory compounds being produced. Decreases in folate and cobalamin (B12) can also occur. Low levels of this bacteria have also been found in canine lymphoma, compared to healthy dogs. 

Dogs with higher levels may increase their risk of disease development by the likes of Salmonella and pathogenic E. coli, due to irregularly high levels of short chain fatty acids (e.g. butyrate) being produced. However, increases have been found in healthy dogs too.  



Suterrella help with the day-to-day functioning of the immune system.

Low Sutterella could be hindering the immune response within your dog, putting your dog at risk of serious infections. Lower levels have also been found in overweight dogs compared to normal weight ones. 

High levels of Sutterella have been linked with a predisposition to acute diarrhoea, including acute haemorrhagic diarrhoea syndrome, due to inflammation and toxins.

Escherichia coli

Some strains of E.coli are beneficial to dogs and are involved in the production of vitamins, fermentation of carbohydrates, and maintenance of gut homeostasis. However, other strains of E. coli can be pathogenic and cause gastrointestinal disease. 

Low levels of E. coli may result in reduced digestive ability, fermentative capacity and impaired homeostatic control in the gut. Levels tend to be lower when a pet is at their ideal weight. 

High levels could cause inflammation, including various types of colitis and intestinal inflammation, including IBD. This leads to unwanted side effects in your dog, including discomfort and digestive problems. High levels have been linked with reduced B12 levels, often found in chronic gastrointestinal disease. Levels seem to be increased in congestive heart failure.



Collinsella has a role in maintaining the health of the intestinal lining (and so how permeable the gut is), as well as regulating inflammation in the gut. 

Dogs experiencing issues such as diarrhoea often have elevated levels of Collinsella. High levels have been linked to cases of IBD. High levels may also predispose your dog to disease, especially in cases where other bacteria are in dysbiosis and the gut wall barrier is weakened, as these bacteria have the potential to act as pathogens given the right circumstances. This could lead to impaired cholesterol absorption in the gut, reduced short term energy storage and increased fat production. High levels have also been linked with aggression and obesity.



These bacteria are important in keeping your dog energetic and healthy, as well as helping with water and mineral absorption. It is also involved in the biosynthesis pathway of vitamin B12.

Low levels of Phascolarctobacterium may lead to increased gut wall permeability and reduced immune function, as well as low levels of B12.

High levels have been linked to canine obesity and so, higher levels may indicate or predispose your dog to obesity. 


Megamonas are vital in the immune system and help protect against harmful bacteria.

Low levels have been linked to dogs with idiopathic IBD and other intestinal inflammatory conditions. Lower levels have also been found after weight loss.

High levels of Megamonas will lead to a shift in the energy sources being produced which may lead to further dysbiosis. Increased levels have been found in arthritic dogs, as well as those with atopic skin disease. 

There are obviously other bacteria that are present within the microbiome, but these are some of the main players in your dog's gut health and so overall health. Studying your dog's microbiome and trying to improve their health, through adjusting each bacteria to its optimum levels within the biome, will help to optimise their gut and overall health. 


Huang Z, Pan Z, Yang R, Bi Y, Xiong X. The canine gastrointestinal microbiota: early studies and research frontiers. Gut Microbes. 2020 Jul 3;11(4):635-654. doi: 10.1080/19490976.2019.1704142. Epub 2020 Jan 28. PMID: 31992112; PMCID: PMC7524387.

Alessandri G, Argentini C, Milani C, Turroni F, Cristina Ossiprandi M, van Sinderen D, Ventura M. Catching a glimpse of the bacterial gut community of companion animals: a canine and feline perspective. Microb Biotechnol. 2020 Nov;13(6):1708-1732. doi: 10.1111/1751-7915.13656. Epub 2020 Aug 30. PMID: 32864871; PMCID: PMC7533323.

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Frequently asked questions

  • The microbiome is the name given to the collection of microbes, mostly bacteria, but also fungi and protozoa, that exist within your dog’s gut. It is a diverse and complex microbial community which can directly affect health and wellbeing. We know that 90% of a human’s body cells are microbes, with only 10% being human cells – it’s just that human cells are markedly larger than the microbes. It’s similar for our four-legged friends. Testing the microbiome gives us an idea of exactly which bacteria are present in your dog’s gut and this can help indicate existing or future health problems.

  • A healthy diversity within the microbiome has been found to be an accurate indicator of overall health and wellbeing. If your dog appears healthy, but has an imbalance in their microbiome, then this could be an indicator of a potential future health issue. If your dog has any existing health complaints, then improving the health of their microbiome can help to improve immune system health and overall wellbeing, as well as improving disease symptoms.

  • Testing and treatment have the potential to help with a whole range of different health complaints. The immune system is very closely associated with the gut, so any imbalance in the microbiome can influence immune system health, overall vitality and wellbeing. Our supplement recommendations are also tailored to your individual dog, with specific ranges designed to help with gastrointestinal inflammation, joint problems, allergies and skin complaints, to name a few.

  • All you need to do is order a kit online and fill in our questionnaire about your dog and their general health. We will then send the kit out to you by post. You then just need to collect a sample and return it to us, again by post. Once the test is performed, we will email the results directly to you.

  • You do not need to get your vet’s permission to test, or talk to them about performing the test beforehand. We do recommend that you pass on a copy of your test results to your regular vets, as it may help them in understanding your pet’s current health, and any future complaints they may have.

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