The Canine Fecal Microbiome

The debate over whether commercial processed dog food versus raw or home-prepared dog food is better for a companion dog sparks heated, passionate discussions. Kibble-based diets typically have more grains or substitutes for grains such as potatoes or peas, whereas home-prepared or raw diets generally are more meat based.

Up until recently, most evidence has been based upon pet companion caregiver personal experiences, and is considered as anecdotal. Passion should be taken out of the equation and replaced with science. One scientific approach is comparing the two sides of the argument by examining canine fecal microbiota, or simply put – gut bacteria.

The Two Sides of the Argument

In a snapshot, advocates for commercial processed dog food say that most of these foods are regulated and have undergone rigorous testing by experts in veterinary or animal nutrition. They believe that the kibble or canned processing kills pathogens, and that the nutrients lost by processing are replaced with vitamin and mineral additives. They also purport that home-prepared meals are often nutritionally incomplete.

Advocates for home cooking and raw foods agree that one of the dangers of these more avant garde food choices for dogs is that they may not be nutritionally complete. However, they encourage companion dog caregivers to research and seek out a veterinary or animal nutritionist to ensure the meals are balanced. They also prefer that most of the added vitamins and minerals are derived naturally.

In regards to pathogens, raw or home-prepared food advocates argue that most commercial raw foods go through a kill-step process and point to human dishes like beef tartare that are not cooked. Heat-based home cooking (baking, boiling) kills pathogens too.

They also point to the numerous recalls of commercial foods due to nutrient deficiencies or toxicities, or salmonella and other bacterial contamination. They acknowledge that contamination with Salmonella spp and other pathogenic bacteria (e.g. E.coli) does occur with raw foods as well, but that these bacteria rarely cause illness in healthy dogs. The primary purpose of human and pet food recalls is to protect human health. As well, they contend that if the fresh food for their dogs is purchased in a grocery store or market, it is deemed human-grade, so that this contamination would happen regardless of the ingredient sourcing. Food recalls should happen as one pet food manufacturer was recently implicated in an outbreak of multidrug-resistant Salmonella in humans.

One of the possible explanations overlooked by both sides here is how the types of ingredients and processing of them may affect the diversity of the gut microbiome.

Background for Fecal Microbiota Testing

Bloodwork Results

Veterinarians Susan Wynn and I, Jean Dodds, compared the laboratory blood lresults and developed a set of expected reference ranges for healthy raw-fed dogs vs. kibble-fed dogs. Our theory was that the difference in bloodwork, if present, was a result of the longstanding use of reference ranges that were based on dogs fed a kibble-based diet.

Although the bloodwork results were mostly the same between the two groups, there were notable exceptions. We concluded that the normal blood reference ranges for raw-fed dogs needed to be revised for these exceptions and differentiated from the reference norms of dogs fed kibble-based diets.

We examined the blood urea nitrogen (BUN) and creatinine data further as these levels were higher in raw-fed dogs. An increased ratio between the two could have been due to a condition called albuminuria or proteinuria, the presence of too much protein in the urine. This spillage into the urine can occur with high dietary protein intake and/or increased leaking of protein through a damaged glomerular kidney filtration system.

Of the 37 dogs screened, 32 were negative for microalbuminuria, and five were positive (two low and three medium positive). Two of the five positive dogs had low-grade urinary tract infections and follow up testing was negative, after their infections resolved. The remaining dogs were lost to follow-up. In conclusion, a diet of raw ingredients did not cause leakage of albumin into the urine in the healthy dogs tested.

2012 Microbiome Study of Dogs with Acute Diarrhea or Inflammatory Bowel Disease

In 2012, Jan Suchodolski and his research team published one of the most cited studies about the fecal microbiome in canines. The team did not compare raw-fed dogs to kibble-fed dogs, but rather set the stage for comparison studies. They decided to examine the microbiome of dogs with inflammatory bowel disease (IBD) or acute diarrhea. Their data suggested that reduced amounts of bacterial species and microbial diversity were more prevalent in the diseased groups.

The Comparison Studies of 2017

In early 2017, two important and highly controlled comparison studies were published of fecal microbiota in dogs fed kibble foods versus raw.

Sandri et al.

  • Study Title – “Raw meat based diet influences fecal microbiome and end products of fermentation in healthy dogs”
  • Location – Italy
  • Dogs – 8 healthy adult Boxers
  • Duration – 28 days
  • Control – 4 dogs were placed on a meat-based diet for 14 days and the other 4 on a control (kibble) diet. Each group’s diet was then switched to the other.
  • Kibble Diet – Not specified
  • Kibble Diet Composition – Crude Protein (Dry Matter – DM): 26.7%; Crude Fat (DM): 10.6%; Crude Fiber (DM): 2.8%
  • Meat Diet – 70% beef meat. 30% a mix of rice flour, chickpeas flour, oat flakes, dry ground carrots, algae-derived Omega 3 fatty acids, and mineral-vitamin complex
  • Meat Diet Composition – Crude Protein (DM): 26.2%; Crude Fat (DM): 18.2%; Crude Fiber (DM): .7%
  • AAFCO Nutrient Requirements – Not specified
  • Fecal Output Determination – Better apparent digestibility based on fecal score in dogs on the meat diet.
  • Conclusions – Shannon Biodiversity Index significantly increased in the meat diet group compared to the reference diet group. The administration of meat diet promoted a more balanced growth of bacterial communities and a positive change in the readouts of healthy gut functions in comparison to kibble diet.

Bermingham et al.

  • Study Title – “Key bacterial families (Clostridiaceae, Erysipelotrichaceae and Bacteroidaceae) are related to the digestion of protein and energy in dogs”
  • Location – New Zealand
  • Dogs – 15 adult dogs
  • Duration – 9 weeks
  • Control – 8 dogs were fed a kibble diet; 7 dogs were fed a raw red meat diet.
  • Kibble Diet – Not specified
  • Kibble Diet Composition – Crude Protein (DM): 29.9%; Crude Fat (DM): 27.1%; Crude Fiber (DM): 6%
  • Meat Diet – 73% beef muscle, 10% beef liver, 5% bone chip, 5% beef tripe, 3.5% beef heart, 3.5% beef kidney, .2% mineral pre-mix
  • Meat Diet Composition – Crude Protein (DM): 76.3%; Crude Fat (DM): 17.9%; Crude Fiber (DM): .6%
  • AAFCO Nutrient Requirements – Both diets formulated to meet nutrient requirements for maintenance according to AAFCO.
  • Fecal Output Determination – Dogs fed the meat diet did not show any signs of intestinal upset, as indicated by the improved fecal score and reduced fecal weight.
  • Conclusions – Observed improved apparent protein and energy digestibility, reduced fecal weight and better fecal consistency in dogs fed the meat diet, but lower volatile fatty acid production. Apparent digestibility of energy and crude protein was also higher in dogs fed the meat diet.

We have shown that the microbiota changes in response to diet in dogs, with Clostridiaceae, Erysipelotrichaceae and Bacteroidaceae apparently central to the relationships between microbiota and intestinal health. The data suggest that when interpreting changes in microbial composition in relation to diet, comparisons to other species may not be valid.

Since Bermingham’s study focused on certain bacterial families, we decided to compare the two studies.

Clostridiaceae was higher in the meat-fed groups in both studies. The increased levels of this bacterial group in the meat-fed groups is of concern, as they have been implicated in compromising the gut health and nutrient digestibility of dogs and humans. Bermingham stated, “Clostridiaceae in the intestinal health of the dog is complex.”

Erysipelotrichaceae was higher in the meat-fed group in Sandri’s study than in Bermingham’s study, but the difference was not statistically significant. Sandri’s meat-based diet also contained a 30% grain mix.

Both studies both demonstrated decreased Bacteroidaceae in their meat-fed groups. For the kibble-based diets, however, the presence of these bacteria was positively correlated with dietary carbohydrate, crude fiber and fecal output, but negatively correlated with crude protein.

Home-Prepared Diet Study of 2018

As we discussed, commercial dog food proponents are concerned that home-prepared foods may not be meet the nutritional standards for dogs and that the bacteria present may be causing intestinal harm in the long-term.

Schmidt et al.

  • Study Title – “The fecal microbiome and metabolome differs between dogs fed Bones and Raw Food (BARF) diets and dogs fed commercial diets”
  • Location – Germany
  • Dogs – 19 commercial-fed adult dogs and 27 BARF fed dogs that lived with their companion pet parents during the study.
  • Duration – Unknown
  • Commercial Diets – Researchers did not try to influence or change diets. Some dogs ate wet food, others ate dry, and others had a combination. These dogs ingested more carbohydrates than the BARF group. One dog was treated with antibiotics four weeks prior to fecal sampling due to a kidney infection. Another dog received antibiotics because of an accident 16 days prior to sample collection. Both dogs were kept in the trial because statistical results were not different compared to the rest of the dogs in the control group. Only one of the other dogs received antibiotics 9 months ago, whereas 14 dogs were not treated with antibiotics for at least 12 months and two dogs had never received antibiotics.
  • Meat Diets/BARF Diets – Researchers did not try to influence or change diets. Some companion pet caregivers gave additional carbohydrates and others did not. Overall, this group of dogs ingested higher amounts of protein. Two dogs received antibiotics during the last 3–5 months, six dogs in the last 6–12 months, 16 dogs were not treated with antibiotics for at least 12 months and two dogs had never received antibiotics.

Clearly, the Schmidt study was not as controlled as the 2017 studies. However, it is useful to assess how pet diets are applied in daily life.

Study Drawbacks

The use of antibiotics in this study introduced a confounding variable. With the exception of one dog, the reason the other dogs received antibiotics is not explained, as these drugs would alter the bacteria present in the gut, and can affect gut recovery time.

Schmidt’s study also did not record fecal score, which is a scale of the firmness (hard or soft) a particular sample of dog feces.

Comparison of Gut Bacterial Levels

Comparing the gut bacterial levels between the three studies is revealing:

  • Enterobacteriaceae – Higher abundance in all meat-fed groups across all studies.
  • Fusobacterium – Higher abundance in all meat-fed groups across all studies. Higher concentrations of Fusobacterium has been implicated in causing human inflammatory bowel disease. However, applying a human dysbiosis index on dogs fails regarding this bacterial family, as it is associated with a healthy microbiomes in dogs. Yet, Fusobacterium was negatively correlated with butyrate (short chain fatty acid) concentrations in Bermingham’s study, indicating that further investigation is required.
  • Erysipelotrichaceae – Lower abundance in meat-fed groups in the Bermingham and Schmidt’s studies. Higher abundance in Sandri’s meat-fed dogs.
  • Ruminococcaceae – Lower abundance in all meat-fed groups across all studies. Positively correlated with carbohydrates in Bermingham’s study; and thought to improve intestinal health in omnivores.
  • Lachnospiraceae – Pretty much equal across all groups in Sandri’s study. Higher abundance in Bermingham’s meat-fed group and in Schmidt’s commercial-fed dogs.
  • Clostridiaceae – Higher abundance in Schmidt’s commercial-fed dogs, and in meat-fed groups for both Sandri and Bermingham’s study. YET…Schmidt’s study found a higher abundance of Clostridium perfringens – which causes a short bout of diarrhea and is considered nonfatal – in the meat-fed groups.

Shannon Diversity Index

Sandri’s study found that meat-fed dogs had a more diverse colony of gut bacteria, whereas Schmidt did not observe any significant differences between meat-fed and commercial-fed dogs.

Dysbiosis Index

Schmidt’s study used a Dysbiosis Index that was created specifically for dogs at Texas A&M University in 2017 after Sandri and Bermingham’s studies were published.

This dysbiosis index analyzed fecal matter of dogs with chronic gastrointestinal problems compared to healthy dogs. According to this index, the major bacteria contributing to intestinal dysbiosis in dogs are increases in E. coli and Streptococcus, and decreases in Ruminococcaceae faecalibacterium. Schmidt’s study stated unequivocally, “The Dysbiosis Index was significantly higher in the raw fed dog group.” Bermingham, as well, noted a decrease of this bacterium in meat-fed dogs.

However, Schmidt’s study did not state if any of the meat-fed dogs displayed gastrointestinal problems. It noted, “Therefore, at this stage it is unknown, whether the changes observed in this study will cause intestinal diseases in the future. Nevertheless, our study was able to show that typical BARF diets may induce some of these alterations in the intestinal microbiota.”


At this point in time, most of us are just beginning to understand the complexities of pet nutrition. Researchers will need to consider not only gut health, but also still need to explore other factors in depth. A partial list includes: the optimal amino acid, carbohydrate and fat contents across all life stages; the role of the microbiome, herbal, spice and phytochemical supplements; trace and ultra-trace mineral contamination, as well as the optimal, vitamin and mineral content.


AlShawaqfeh, MK et al. “A dysbiosis index to assess microbial changes in fecal samples of dogs with chronic inflammatory enteropathy.” FEMS Microbiology Ecology, Volume 93, Issue 11, 1 November 2017, fix136,

Bermingham et al. “Key bacterial families (Clostridiaceae, Erysipelotrichaceae and Bacteroidaceae) are related to the digestion of protein and energy in dogs.” PeerJ 5:e3019, 2017, doi:10.7717/peerj.3019.

Burke, Anna. “Best Dog Food: Choosing What’s Right For Your Dog.” American Kennel Club, 20 Jan. 2019,

Dodds, Jean. “Raw Diets and Bloodwork Results: Should You Be Concerned?” Pet Health Resources, Tumblr, 6 Dec. 2015,

Sandri, Misa et al. “Raw meat based diet influences faecal microbiome and end products of fermentation in healthy dogs” BMC Veterinary Research, vol. 13,1 65. 28 Feb. 2017, doi:10.1186/s12917-017-0981-z.

Schmidt, Milena, et al. “The Fecal Microbiome and Metabolome Differs between Dogs Fed Bones and Raw Food (BARF) Diets and Dogs Fed Commercial Diets.” PLOS One, 15 Aug. 2018, doi:10.1371/journal.pone.0201279.

Suchodolski, Jan, et al. “The Fecal Microbiome in Dogs with Acute Diarrhea and Idiopathic Inflammatory Bowel Disease.” PLOS One, 26 Dec. 2012, doi:10.1371/journal.pone.0051907.

Vázquez-Baeza, Yoshiki, et al. “Dog and Human Inflammatory Bowel Disease Rely on Overlapping Yet Distinct Dysbiosis Networks.” Nature Microbiology, 3 Oct. 2016.

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