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Review Article| Volume 51, ISSUE 3, P605-621, May 2021

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The Gut Microbiome of Dogs and Cats, and the Influence of Diet

Open AccessPublished:February 27, 2021DOI:https://doi.org/10.1016/j.cvsm.2021.01.002

      Keywords

      Key points

      • The gut microbiome is a functional organ, and dietary substrates are converted by different intestinal bacteria to metabolically active compounds that influence the host.
      • Butyrate, for example, can be produced from either fiber or protein, suggesting that both increased fiber and increased protein in the diet may bring similar benefits and have the largest impact on the intestinal microbiome and metabolome composition.
      • Although fiber and protein content appear to be main influencers of microbiome composition in both dogs and cats, the ideal fiber and protein intake to promote a healthy microbiome needs to be determined.
      • Diet-induced changes in the microbiome of healthy dogs are less marked compared with microbiome changes associated with disease.

      Background

      The gut microbiome is composed of bacteria, archaea, viruses, and eukaryotic organisms that reside in the gastrointestinal (GI) tract. The bacterial component is the largest and provides essential digestive functions, such as fermentation of fibers. The gut microbiome also contributes to host metabolism, protects against pathogens, and educates the immune system. Expanding knowledge of microbiome functions has revealed several remote connections leading to the coinage of terms such as the gut-brain axis, gut-skin axis, and others.
      Many diseases, systemic or localized, are associated with dysbiosis. Gut dysbiosis is defined as changes in the composition of the gut microbiome that impact its function.
      • Zeng M.Y.
      • Inohara N.
      • Nunez G.
      Mechanisms of inflammation-driven bacterial dysbiosis in the gut.
      The increase in abundance of facultative anaerobic bacteria of the family Enterobacteriaceae is a hallmark of dysbiosis,
      • Rivera-Chavez F.
      • Lopez C.A.
      • Baumler A.J.
      Oxygen as a driver of gut dysbiosis.
      seen also in dogs.
      • Vazquez-Baeza Y.
      • Hyde E.R.
      • Suchodolski J.S.
      • et al.
      Dog and human inflammatory bowel disease rely on overlapping yet distinct dysbiosis networks.
      The composition of the gut microbiota also has significant effects on immune function, and regulating the local production of antibodies,
      • Tizard I.R.
      • Jones S.W.
      The microbiota regulates immunity and immunologic diseases in dogs and cats.
      and the differentiation of intestinal helper T (Th) cell precursors. Intestinal inflammation also can be triggered by gut dysbiosis in different diseases through bile acid dysmetabolism,
      • Duboc H.
      • Rajca S.
      • Rainteau D.
      • et al.
      Connecting dysbiosis, bile-acid dysmetabolism and gut inflammation in inflammatory bowel diseases.
      • Guard B.C.
      • Honneffer J.B.
      • Jergens A.E.
      • et al.
      Longitudinal assessment of microbial dysbiosis, fecal unconjugated bile acid concentrations, and disease activity in dogs with steroid-responsive chronic inflammatory enteropathy.
      • Giaretta P.R.
      • Rech R.R.
      • Guard B.C.
      • et al.
      Comparison of intestinal expression of the apical sodium-dependent bile acid transporter between dogs with and without chronic inflammatory enteropathy.
      or through the decreased production of anti-inflammatory molecules, such as short-chain fatty acids (SCFAs)
      • Minamoto Y.
      • Minamoto T.
      • Isaiah A.
      • et al.
      Fecal short-chain fatty acid concentrations and dysbiosis in dogs with chronic enteropathy.
      • Duscha A.
      • Gisevius B.
      • Hirschberg S.
      • et al.
      Propionic acid shapes the multiple sclerosis disease course by an immunomodulatory mechanism.
      • Park M.J.
      • Pilla R.
      • Panta A.
      • et al.
      Reproductive senescence and ischemic stroke remodel the gut microbiome and modulate the effects of estrogen treatment in female rats.
      and indoles.
      • Bansal T.
      • Alaniz R.C.
      • Wood T.K.
      • et al.
      The bacterial signal indole increases epithelial-cell tight-junction resistance and attenuates indicators of inflammation.
      ,
      • Waclawikova B.
      • El Aidy S.
      Role of microbiota and tryptophan metabolites in the remote effect of intestinal inflammation on brain and depression.
      Although outside of the scope of this review, recent work has associated dysbiosis with obesity,
      • Kieler I.N.
      • Shamzir Kamal S.
      • Vitger A.D.
      • et al.
      Gut microbiota composition may relate to weight loss rate in obese pet dogs.
      ,
      • Bermudez Sanchez S.
      • Pilla R.
      • Sarawichitr B.
      • et al.
      Fecal microbiota in client-owned obese dogs changes after weight loss with a high-fiber-high-protein diet.
      metabolic diseases,
      • Montoya-Alonso J.A.
      • Bautista-Castano I.
      • Pena C.
      • et al.
      Prevalence of canine obesity, obesity-related metabolic dysfunction, and relationship with owner obesity in an obesogenic region of Spain.
      ,
      • Jergens A.E.
      • Guard B.C.
      • Redfern A.
      • et al.
      Microbiota-related changes in unconjugated fecal bile acids are associated with naturally occurring, insulin-dependent diabetes mellitus in dogs.
      cancer,
      • Zitvogel L.
      • Daillere R.
      • Roberti M.P.
      • et al.
      Anticancer effects of the microbiome and its products.
      neurologic disfunctions,
      • Wu J.
      • Zhang Y.
      • Yang H.
      • et al.
      Intestinal microbiota as an alternative therapeutic target for epilepsy.
      ,
      • Jeffery N.D.
      • Barker A.K.
      • Alcott C.J.
      • et al.
      The association of specific constituents of the fecal microbiota with immune-mediated brain disease in dogs.
      and many others, both in dogs and in humans. However, caution should be taken when interpreting those findings, as a causation effect is yet to be proven, and the dysbiosis may be a symptom of the disease process rather than its cause.
      The gut microbiome is responsive to nutrients. Changes in bacterial taxa often require large changes in dietary macronutrients; but alterations in bacterial-derived metabolites and, therefore, microbiota function may already occur due to the addition of micronutrients, and this is an emerging area of current microbiome research. Some bacterial species ferment different types of fiber and carbohydrates, and others are strongly proteolytic. Therefore, changes in the diet that affect the availability of such substrates in the gut will result in alterations of the microbiome and metabolome. Due to its resilience, dietary-induced changes in microbiome composition are maintained only by long-term maintenance of a specific diet. A good example is a study
      • Allaway D.
      • Haydock R.
      • Lonsdale Z.N.
      • et al.
      Rapid reconstitution of the faecal microbiome after extended diet-induced changes indicate a stable gut microbiome in healthy adult dogs.
      in which healthy dogs were fed diets containing only purified amino acids and easily digestible starch for 32 weeks. At the end of the trial, dogs returned to the control diet, and microbiome composition quickly returned to baseline.
      • Allaway D.
      • Haydock R.
      • Lonsdale Z.N.
      • et al.
      Rapid reconstitution of the faecal microbiome after extended diet-induced changes indicate a stable gut microbiome in healthy adult dogs.
      Microbiome changes are individualized,
      • Johnson A.J.
      • Vangay P.
      • Al-Ghalith G.A.
      • et al.
      Daily sampling reveals personalized diet-microbiome associations in humans.
      as the microbiome is an intrinsically redundant ecosystem, in which many unrelated species occupy the same niche.
      • Lozupone C.A.
      • Stombaugh J.I.
      • Gordon J.I.
      • et al.
      Diversity, stability and resilience of the human gut microbiota.
      This has a significant evolutionary advantage, because if only a single species performed an essential function, any aggression to the microbiome (such as antibiotic treatment) affecting that species would deprive the host of that function. Therefore, multiple species are necessary for microbiome resilience, and higher species richness is considered an indicator of a healthy microbiome.
      • Lozupone C.A.
      • Stombaugh J.I.
      • Gordon J.I.
      • et al.
      Diversity, stability and resilience of the human gut microbiota.
      The GI tract regions are colonized with different bacterial populations. The composition varies according to luminal conditions, with a predominance of oxygen-tolerating bacteria in the small, and an abundance of strict anaerobes in the large intestine.
      • Honneffer J.B.
      • Steiner J.M.
      • Lidbury J.A.
      • et al.
      Variation of the microbiota and metabolome along the canine gastrointestinal tract.
      ,
      • Ritchie L.E.
      • Steiner J.M.
      • Suchodolski J.S.
      Assessment of microbial diversity along the feline intestinal tract using 16S rRNA gene analysis.
      Because sampling from the proximal intestine is difficult, most clinical studies focus on fecal microbiota, and the abundance of most relevant bacterial species for gut health in dogs can be reliably measured in feces.
      • Vazquez-Baeza Y.
      • Hyde E.R.
      • Suchodolski J.S.
      • et al.
      Dog and human inflammatory bowel disease rely on overlapping yet distinct dysbiosis networks.
      When analyzing the microbiome along the GI tract of cats, samples clustered by individual cat rather than by site of collection, indicating that fecal samples are also representative of the cat microbiome.
      • Ritchie L.E.
      • Steiner J.M.
      • Suchodolski J.S.
      Assessment of microbial diversity along the feline intestinal tract using 16S rRNA gene analysis.

      Methods for microbial analysis

      Microbiological culture is useful for the subset of bacteria that are culturable, but molecular methods have largely replaced culture due to their ability to capture nonculturable bacteria.
      • Blake A.B.
      • Suchodolski J.S.
      Importance of gut microbiota for the health and disease of dogs and cats.
      Molecular methods, such as 16S ribosomal RNA (rRNA) gene sequencing and DNA shotgun sequencing, aim to measure the diversity of species present in the sample. That is accomplished by either amplifying and sequencing a fragment of a conserved region of the 16S rRNA gene, or by sequencing all available DNA in the sample (shotgun sequencing). Shotgun sequencing has the advantage of going beyond bacterial identification by also sequencing functional genes; however, it requires larger amounts of DNA from the sample, and is more expensive. Quantitative polymerase chain reaction (qPCR) is a quick, affordable, and reproducible method to quantify specific taxa that have been identified as clinically relevant.
      Most studies focus on 16S rRNA gene sequencing, which generates phylogenetical data, and methods for sequencing and data analysis are in constant evolution.
      • Pilla R.
      • Suchodolski J.S.
      The role of the canine gut microbiome and metabolome in health and gastrointestinal disease.
      Indeed, this is one disadvantage of these methods: different sequencing and/or data analysis methods may generate differences in the results, which prevents the development of reference intervals. When reviewing the literature, a wide variation in percentages of specific bacterial taxa can be seen, making comparisons between studies difficult.
      Another limitation of most microbiome studies is that investigators typically compare the effects of environmental factors (eg, diet, storage, antibiotic treatment, breed influences, geography) with a control group or with its own baseline within the study, and often with a small sample size. Therefore, when changes (eg, due to diets) are observed, it is difficult to extrapolate the magnitude of these changes, and how they compare against a normal microbiota in a large reference population. Because of its high reproducibility, qPCR allows the development of reference intervals for specific taxa. One example is the canine fecal dysbiosis index (DI), a qPCR-based assay that quantifies 7 bacterial taxa, which are then combined into one single number.
      • AlShawaqfeh M.K.
      • Wajid B.
      • Minamoto Y.
      • et al.
      A dysbiosis index to assess microbial changes in fecal samples of dogs with chronic inflammatory enteropathy.
      Reference intervals for this assay have been established based on 120 healthy dogs from different countries and fed different commercial diets (https://tx.ag/DysbiosisGI). The DI can be used as a marker for normal microbiota, and is useful to track changes in microbiota over time in response to therapy in dogs.
      • Pilla R.
      • Suchodolski J.S.
      The role of the canine gut microbiome and metabolome in health and gastrointestinal disease.
      ,
      • Chaitman J.
      • Ziese A.L.
      • Pilla R.
      • et al.
      Fecal microbial and metabolic profiles in dogs with acute diarrhea receiving either fecal microbiota transplantation or oral metronidazole.
      The reference intervals for the 7 bacteria allow for comparison of effect sizes between studies, and whether changes in the microbiota fall within or outside the normal range (Fig. 1).
      Figure thumbnail gr1
      Fig. 1The canine qPCR-based fecal DI (A) and key bacterial taxa Faecalibacterium (B) and Fusobacterium (C), both butyrate producers through different pathways (from carbohydrate and protein/amino acids, respectively), for different diet types, in comparison with chronic enteropathy
      • Minamoto Y.
      • Minamoto T.
      • Isaiah A.
      • et al.
      Fecal short-chain fatty acid concentrations and dysbiosis in dogs with chronic enteropathy.
      and metronidazole administration.
      • Pilla R.
      • Gaschen F.P.
      • Barr J.W.
      • et al.
      Effects of metronidazole on the fecal microbiome and metabolome in healthy dogs.
      The gray areas indicate reference intervals, which allow comparison across studies and to a large reference population. Dots in red indicate dogs that also had a low abundance of C hiranonis, a beneficial bacterium that converts primary to secondary bile acids in the canine intestine. Dogs with chronic enteropathy and healthy dogs receiving metronidazole have a dysbiosis that is, associated with decreased Faecalibacterium, Fusobacterium, and C hiranonis. Lack of the latter results in abnormal bile acid metabolism. In contrast, dogs fed a raw food diet,
      • Schmidt M.
      • Unterer S.
      • Suchodolski J.S.
      • et al.
      The fecal microbiome and metabolome differs between dogs fed Bones and Raw Food (BARF) diets and dogs fed commercial diets.
      high in protein and fat, and low in fiber, have an increased fecal DI mostly driven due to low Faecalibacterium and increased E coli (not shown). The vegetable protein
      • Bresciani F.
      • Minamoto Y.
      • Suchodolski J.S.
      • et al.
      Effect of an extruded animal protein-free diet on fecal microbiota of dogs with food-responsive enteropathy.
      and hydrolyzed protein diet
      • Pilla R.
      • Gaschen F.P.
      • Barr J.W.
      • et al.
      Effects of metronidazole on the fecal microbiome and metabolome in healthy dogs.
      fed for 60 and 42 days, respectively, have similar macronutrient composition to commercial adult dog diets, despite the uniqueness of some ingredients. Accordingly, the fecal DI, and abundances of Faecalibacterium and Fusobacterium remained within normal reference intervals.

      Core microbiota

      Key bacterial species are consistently present in fecal samples of healthy dogs, indicating the presence of a core fecal bacterial community. Table 1 shows some of the most relevant bacterial taxa in fecal samples of dogs. The fecal microbiome of healthy dogs is co-dominated by 3 phyla: Firmicutes, Bacteroidetes, and Fusobacterium.
      • Middelbos I.S.
      • Vester Boler B.M.
      • Qu A.
      • et al.
      Phylogenetic characterization of fecal microbial communities of dogs fed diets with or without supplemental dietary fiber using 454 pyrosequencing.
      ,
      • Hand D.
      • Wallis C.
      • Colyer A.
      • et al.
      Pyrosequencing the canine faecal microbiota: breadth and depth of biodiversity.
      Within this core bacterial community, many major taxa belong to phylum Firmicutes, including Clostridia and Bacilli,
      • Garcia-Mazcorro J.F.
      • Lanerie D.J.
      • Dowd S.E.
      • et al.
      Effect of a multi-species synbiotic formulation on fecal bacterial microbiota of healthy cats and dogs as evaluated by pyrosequencing.
      ,
      • Garcia-Mazcorro J.F.
      • Dowd S.E.
      • Poulsen J.
      • et al.
      Abundance and short-term temporal variability of fecal microbiota in healthy dogs.
      many of which are SCFA producers, such as Faecalibacterium. Bacteroidetes is another abundant phylum in fecal samples from dogs, including Prevotella and Bacteroides, which are highly variable in abundance between dogs.
      • Vazquez-Baeza Y.
      • Hyde E.R.
      • Suchodolski J.S.
      • et al.
      Dog and human inflammatory bowel disease rely on overlapping yet distinct dysbiosis networks.
      Table 1Relevant bacterial taxa in the fecal microbiome of dogs, organized according to the Greengenes database taxonomy
      • DeSantis T.Z.
      • Hugenholtz P.
      • Larsen N.
      • et al.
      Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB.
      PhylumClassFamilyGenus/Species
      ActinobacteriaCoriobacteriiaCoriobacteriaceaeCollinsella
      BacteroidetesBacteroidetesPrevotellaceaePrevotella
      BacteroidaceaeBacteroides
      FirmicutesClostridiaClostridiaceaeClostridium
      RuminococcaceaeFaecalibacterium prausnitzii
      PeptostreptococcaceaePeptostreptococcus
      LachnospiraceaeBlautia
      VeillonellaceaeMegamonas
      BacilliStreptococcaceaeStreptococcus
      LactobacillaceaeLactobacillus
      TuricibacteraceaeTuricibacter
      FusobacteriaFusobacteriiaFusobacteriaceaeFusobacterium
      ProteobacteriaBetaproteobacteriaAlcaligenaceaeSutterella
      GammaproteobacteriaEnterobacteriaceaeE. coli
      The genus Fusobacterium is typically associated with health in dogs. This is in contrast to people, in which Fusobacterium nucleatum is a pathogen associated with colorectal cancer.
      • Amitay E.L.
      • Werner S.
      • Vital M.
      • et al.
      Fusobacterium and colorectal cancer: causal factor or passenger? Results from a large colorectal cancer screening study.
      In the GI tract of dogs, other Fusobacterium species, such as Fusobacterium mortiferum and Fusobacterium perfoetens, are typically observed,
      • Kim D.H.
      • Jeong D.
      • Kang I.B.
      • et al.
      Modulation of the intestinal microbiota of dogs by kefir as a functional dairy product.
      and these seem to play a different role.
      • Vazquez-Baeza Y.
      • Hyde E.R.
      • Suchodolski J.S.
      • et al.
      Dog and human inflammatory bowel disease rely on overlapping yet distinct dysbiosis networks.
      Fusobacteria are severely impacted by antibiotic treatment
      • Manchester A.C.
      • Webb C.B.
      • Blake A.B.
      • et al.
      Long-term impact of tylosin on fecal microbiota and fecal bile acids of healthy dogs.
      and GI diseases,
      • Pilla R.
      • Suchodolski J.S.
      The role of the canine gut microbiome and metabolome in health and gastrointestinal disease.
      and their recovery is slower than other phyla.
      • Pilla R.
      • Gaschen F.P.
      • Barr J.W.
      • et al.
      Effects of metronidazole on the fecal microbiome and metabolome in healthy dogs.
      Therefore, in dogs Fusobacteria may be a therapeutic target for specific food ingredients that can increase their abundance.
      Proteobacteria and Actinobacteria are also commonly identified and are typically colonizers of the small intestine, and in physiologic conditions will present in smaller numbers in fecal samples. For example, members of the family Enterobacteriaceae (eg, Escherichia coli) are facultative anaerobes, which allows them to take advantage of the oxygen available in the small intestine. Although part of the normal microbiome in small numbers, an increase of Enterobacteriaceae in fecal samples is a hallmark of dysbiosis
      • Vazquez-Baeza Y.
      • Hyde E.R.
      • Suchodolski J.S.
      • et al.
      Dog and human inflammatory bowel disease rely on overlapping yet distinct dysbiosis networks.
      and is associated with many diseases, both within and outside of the GI tract.
      • Minamoto Y.
      • Minamoto T.
      • Isaiah A.
      • et al.
      Fecal short-chain fatty acid concentrations and dysbiosis in dogs with chronic enteropathy.
      ,
      • Xenoulis P.G.
      • Palculict B.
      • Allenspach K.
      • et al.
      Molecular-phylogenetic characterization of microbial communities imbalances in the small intestine of dogs with inflammatory bowel disease.
      ,
      • Suchodolski J.S.
      • Xenoulis P.G.
      • Paddock C.G.
      • et al.
      Molecular analysis of the bacterial microbiota in duodenal biopsies from dogs with idiopathic inflammatory bowel disease.
      The literature on the fecal microbiome of healthy cats is less extensive. The fecal microbiome of cats is dominated in most studies by Firmicutes,
      • Ritchie L.E.
      • Steiner J.M.
      • Suchodolski J.S.
      Assessment of microbial diversity along the feline intestinal tract using 16S rRNA gene analysis.
      ,
      • Barry K.A.
      • Middelbos I.S.
      • Vester Boler B.M.
      • et al.
      Effects of dietary fiber on the feline gastrointestinal metagenome.
      • Eshar D.L.
      • Lee C.
      • Weese J.S.
      Comparative molecular analysis of fecal microbiota of bobcats (Lynx rufus) and domestic cats (Felis catus).
      • Handl S.
      • Dowd S.E.
      • Garcia-Mazcorro J.F.
      • et al.
      Massive parallel 16S rRNA gene pyrosequencing reveals highly diverse fecal bacterial and fungal communities in healthy dogs and cats.
      • Garcia-Mazcorro J.F.
      • Barcenas-Walls J.R.
      • Suchodolski J.S.
      • et al.
      Molecular assessment of the fecal microbiota in healthy cats and dogs before and during supplementation with fructo-oligosaccharides (FOS) and inulin using high-throughput 454-pyrosequencing.
      • Marsilio S.
      • Pilla R.
      • Sarawichitr B.
      • et al.
      Characterization of the fecal microbiome in cats with inflammatory bowel disease or alimentary small cell lymphoma.
      followed by smaller percentages of Proteobacteria, Actinobacteria, Bacteroidetes, and Fusobacteria. One study compared the fecal microbiome of dogs and cats fed species-appropriate commercial diets, and found that cats had a larger number of species than dogs,
      • Handl S.
      • Dowd S.E.
      • Garcia-Mazcorro J.F.
      • et al.
      Massive parallel 16S rRNA gene pyrosequencing reveals highly diverse fecal bacterial and fungal communities in healthy dogs and cats.
      hinting at a higher diversity; however, more studies are needed to confirm that finding.
      Although changes in microbiome composition can be important, they do not reflect changes in microbiome function. Recent studies are going beyond describing “Who is there?” and investigate the more pressing question of “What are they doing?” The study of bacterial metabolites through fecal metabolomics has revealed some major pathways regulated by bacteria, such as SCFA production, bile acid deconjugation and dehydroxylation, production of neurotransmitters such as serotonin and gamma-aminobutyric acid (GABA), and anti-inflammatory compounds such as indoles. Diet can influence bacterial metabolites, which can remotely affect organs such as the brain, skin, or muscle.

      Effects of diets on microbiota in dogs

      Most microbiome studies in dogs have evaluated effects of extruded diets, which represent up to 95% of the dog food market. Extruded diets typically include a high carbohydrate load, but high-protein low-carbohydrate alternatives are available. Also increasingly popular are raw diets, frozen or freeze-dried, which are typically meat based and include low carbohydrate percentages. A small but increasing percentage of owners feed homemade diets, either raw or cooked.
      Studies have shown that gut microbiome profiles in different species reflect their diet composition, especially when large macronutrient differences such as carnivore versus herbivore diets are considered.
      • Bresciani F.
      • Minamoto Y.
      • Suchodolski J.S.
      • et al.
      Effect of an extruded animal protein-free diet on fecal microbiota of dogs with food-responsive enteropathy.
      • De Filippo C.
      • Cavalieri D.
      • Di Paola M.
      • et al.
      Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa.
      • David L.A.
      • Maurice C.F.
      • Carmody R.N.
      • et al.
      Diet rapidly and reproducibly alters the human gut microbiome.
      In omnivore species, including humans, the short-term consumption of diets composed entirely of animal or plant products is enough to alter the microbial community structure and overwhelm interindividual differences in microbial gene expression.
      • David L.A.
      • Maurice C.F.
      • Carmody R.N.
      • et al.
      Diet rapidly and reproducibly alters the human gut microbiome.
      In humans, the consumption of an animal-based diet increased the dietary intake of fat and protein, and decreased fiber intake to nearly zero. Such changes led to an increase in the abundance of bile-tolerant microorganisms and decreases the levels of Firmicutes, which includes species known to metabolize dietary plant polysaccharides.
      For the canine gut microbiome, the ingredients seem to be less important than the overall macronutrient content. One study found that an extruded diet prepared exclusively with plant sources of protein did not significantly alter the microbiome of dogs when compared with a traditional (mixed animal and plant) extruded diet with similar macronutrient content.
      • Bresciani F.
      • Minamoto Y.
      • Suchodolski J.S.
      • et al.
      Effect of an extruded animal protein-free diet on fecal microbiota of dogs with food-responsive enteropathy.
      Major shifts in macronutrient composition were tested in a study in healthy dogs, which included 4 dry prescription diets formulated for weight loss, for renal disease, to be low-fat, or anallergenic.
      • Mori A.
      • Goto A.
      • Kibe R.
      • et al.
      Comparison of the effects of four commercially available prescription diet regimens on the fecal microbiome in healthy dogs.
      The weight loss diet had the most drastic changes in macronutrients (higher protein and fiber) and resulted in the largest shift in microbiome composition. Increased protein content was associated with increased Fusobacteria. The abundance of SCFA producers Bacteroides, Prevotella, and Faecalibacterium was significantly increased in dogs fed the weight loss diet, and Faecalibacterium was increased in the low-fat diet. The weight-loss (28.1% fiber) and low-fat (8.6% fiber) diets both included soluble and insoluble fiber (beet pulp, fructooligosaccharide [FOS], and psyllium), and the increase in those genera is likely related to increased fiber content and different fiber types.
      Different fibers have been studied for their prebiotic properties, and induce specific changes in the microbiome (Table 2). Most fibers act by enriching fiber-fermenting SCFA-producing Firmicutes.
      • Middelbos I.S.
      • Vester Boler B.M.
      • Qu A.
      • et al.
      Phylogenetic characterization of fecal microbial communities of dogs fed diets with or without supplemental dietary fiber using 454 pyrosequencing.
      ,
      • Panasevich M.R.
      • Serao M.C.R.
      • de Godoy M.R.C.
      • et al.
      Potato fiber as a dietary fiber source in dog foods.
      • Panasevich M.R.
      • Kerr K.R.
      • Dilger R.N.
      • et al.
      Modulation of the faecal microbiome of healthy adult dogs by inclusion of potato fibre in the diet.
      • Alexander C.
      • Cross T.L.
      • Devendran S.
      • et al.
      Effects of prebiotic inulin-type fructans on blood metabolite and hormone concentrations and faecal microbiota and metabolites in overweight dogs.
      • Myint H.
      • Iwahashi Y.
      • Koike S.
      • et al.
      Effect of soybean husk supplementation on the fecal fermentation metabolites and microbiota of dogs.
      • Beloshapka A.N.
      • Dowd S.E.
      • Suchodolski J.S.
      • et al.
      Fecal microbial communities of healthy adult dogs fed raw meat-based diets with or without inulin or yeast cell wall extracts as assessed by 454 pyrosequencing.
      Inulin-type fructans can increase SCFA,
      • Panasevich M.R.
      • Serao M.C.R.
      • de Godoy M.R.C.
      • et al.
      Potato fiber as a dietary fiber source in dog foods.
      including acetate, butyrate and propionate, total fecal bile acids,
      • Alexander C.
      • Cross T.L.
      • Devendran S.
      • et al.
      Effects of prebiotic inulin-type fructans on blood metabolite and hormone concentrations and faecal microbiota and metabolites in overweight dogs.
      and decrease Enterobacteriaceae.
      • Alexander C.
      • Cross T.L.
      • Devendran S.
      • et al.
      Effects of prebiotic inulin-type fructans on blood metabolite and hormone concentrations and faecal microbiota and metabolites in overweight dogs.
      ,
      • Beloshapka A.N.
      • Dowd S.E.
      • Suchodolski J.S.
      • et al.
      Fecal microbial communities of healthy adult dogs fed raw meat-based diets with or without inulin or yeast cell wall extracts as assessed by 454 pyrosequencing.
      Table 2Main effects of different types of fiber in the fecal microbiome and metabolome of dogs
      Fiber TypeMain FindingsMethodReferences
      Beet pulp
      Down arrows indicate decreased abundance
      Erysipelotrichi and Fusobacteria

      Up arrows indicate increased abundance
      Firmicutes and Clostridia
      16S rRNA seq.Middelbos et al,
      • Middelbos I.S.
      • Vester Boler B.M.
      • Qu A.
      • et al.
      Phylogenetic characterization of fecal microbial communities of dogs fed diets with or without supplemental dietary fiber using 454 pyrosequencing.
      2010
      Inulin-type fructans
      Up arrows indicate increased abundance
      Firmicutes, Erysipelotrichaceae, and Turicibacteraceae
      16S rRNA seq.Alexander et al,
      • Alexander C.
      • Cross T.L.
      • Devendran S.
      • et al.
      Effects of prebiotic inulin-type fructans on blood metabolite and hormone concentrations and faecal microbiota and metabolites in overweight dogs.
      2018
      Inulin
      Down arrows indicate decreased abundance
      Enterobacteriaceae

      Up arrows indicate increased abundance
      Megamonas and Lactobacillus
      16S rRNA seq.Beloshapka et al,
      • Beloshapka A.N.
      • Dowd S.E.
      • Suchodolski J.S.
      • et al.
      Fecal microbial communities of healthy adult dogs fed raw meat-based diets with or without inulin or yeast cell wall extracts as assessed by 454 pyrosequencing.
      2013
      Potato fiber
      Down arrows indicate decreased abundance
      Prevotella and Fusobacterium

      Up arrows indicate increased abundance
      Faecalibacterium, Lachnospira, fecal acetate, propionate and butyrate
      16S rRNA seq.Panasevich et al,
      • Panasevich M.R.
      • Serao M.C.R.
      • de Godoy M.R.C.
      • et al.
      Potato fiber as a dietary fiber source in dog foods.
      2013; Panasevich et al,
      • Panasevich M.R.
      • Kerr K.R.
      • Dilger R.N.
      • et al.
      Modulation of the faecal microbiome of healthy adult dogs by inclusion of potato fibre in the diet.
      2015
      Soybean husk
      Down arrows indicate decreased abundance
      Clostridium cluster XI

      Up arrows indicate increased abundance
      Total lactobacilli, Faecalibacterium, Bacteroides-Prevotella-Porphyromonas, and Clostridium cluster XIVa
      qPCRMyint et al,
      • Myint H.
      • Iwahashi Y.
      • Koike S.
      • et al.
      Effect of soybean husk supplementation on the fecal fermentation metabolites and microbiota of dogs.
      2017
      Yeast cell wall
      Up arrows indicate increased abundance
      Bifidobacterium
      16S rRNA seq.Beloshapka et al,
      • Beloshapka A.N.
      • Dowd S.E.
      • Suchodolski J.S.
      • et al.
      Fecal microbial communities of healthy adult dogs fed raw meat-based diets with or without inulin or yeast cell wall extracts as assessed by 454 pyrosequencing.
      2013
      Abbreviations: qPCR, quantitative polymerase chain reaction; rRNA seq., ribosomal RNA sequencing.
      Up arrows indicate increased abundance
      Down arrows indicate decreased abundance
      A few studies
      • Bermingham E.N.
      • Maclean P.
      • Thomas D.G.
      • et al.
      Key bacterial families (Clostridiaceae, Erysipelotrichaceae and Bacteroidaceae) are related to the digestion of protein and energy in dogs.
      • Schmidt M.
      • Unterer S.
      • Suchodolski J.S.
      • et al.
      The fecal microbiome and metabolome differs between dogs fed Bones and Raw Food (BARF) diets and dogs fed commercial diets.
      • Kim J.
      • An J.U.
      • Kim W.
      • et al.
      Differences in the gut microbiota of dogs (Canis lupus familiaris) fed a natural diet or a commercial feed revealed by the Illumina MiSeq platform.
      have evaluated the impact of meat-based raw diets on the gut microbiome of healthy dogs. Meat-based raw diets are typically very different in macronutrient content compared with control diets, with higher protein and lower carbohydrate and fiber. Dogs fed raw diets showed overall decreases in Firmicutes
      • Schmidt M.
      • Unterer S.
      • Suchodolski J.S.
      • et al.
      The fecal microbiome and metabolome differs between dogs fed Bones and Raw Food (BARF) diets and dogs fed commercial diets.
      and Bacteroidetes,
      • Bermingham E.N.
      • Maclean P.
      • Thomas D.G.
      • et al.
      Key bacterial families (Clostridiaceae, Erysipelotrichaceae and Bacteroidaceae) are related to the digestion of protein and energy in dogs.
      as shown in Table 3. Most decreased bacteria are associated with SCFA production from dietary carbohydrate,
      • Vital M.
      • Gao J.
      • Rizzo M.
      • et al.
      Diet is a major factor governing the fecal butyrate-producing community structure across Mammalia, Aves and Reptilia.
      indicating a decrease in carbohydrate fermentation due to decreased intake. Proteobacteria, Fusobacteria, and protein-associated genera increased in abundance.
      • Bermingham E.N.
      • Maclean P.
      • Thomas D.G.
      • et al.
      Key bacterial families (Clostridiaceae, Erysipelotrichaceae and Bacteroidaceae) are related to the digestion of protein and energy in dogs.
      ,
      • Schmidt M.
      • Unterer S.
      • Suchodolski J.S.
      • et al.
      The fecal microbiome and metabolome differs between dogs fed Bones and Raw Food (BARF) diets and dogs fed commercial diets.
      One study with 6 dogs fed a raw diet for more than 1 year found increased microbiome diversity,
      • Kim J.
      • An J.U.
      • Kim W.
      • et al.
      Differences in the gut microbiota of dogs (Canis lupus familiaris) fed a natural diet or a commercial feed revealed by the Illumina MiSeq platform.
      and an increased abundance of Clostridium perfringens and Fusobacterium varium, both known to produce butyrate from protein,
      • Vital M.
      • Gao J.
      • Rizzo M.
      • et al.
      Diet is a major factor governing the fecal butyrate-producing community structure across Mammalia, Aves and Reptilia.
      suggesting an adaptation to the diet.
      Table 3Summary of findings from studies that evaluated the effect of high-protein diets on the fecal microbiome of dogs
      DietMain FindingsTime on diet, nReference
      Bones and raw foods (BARF)Bifidobacterium and Faecalibacterium;

      ↑ Fusobacteria, Escherichia coli, Streptococcus, and Clostridium
      4 wk to 9 y, n = 27Schmidt et al,
      • Schmidt M.
      • Unterer S.
      • Suchodolski J.S.
      • et al.
      The fecal microbiome and metabolome differs between dogs fed Bones and Raw Food (BARF) diets and dogs fed commercial diets.
      2018
      Red meatFaecalibacterium, Peptostreptococcus, Bacteroides, and Prevotella

      Fusobacterium, Lactobacillus, and Clostridium
      9 wk, n = 7Bermingham et al,
      • Bermingham E.N.
      • Maclean P.
      • Thomas D.G.
      • et al.
      Key bacterial families (Clostridiaceae, Erysipelotrichaceae and Bacteroidaceae) are related to the digestion of protein and energy in dogs.
      2017
      Raw diet↑ Richness, evenness, Clostridium perfringens, Clostridium hiranonis, Dorea, and Fusobacterium variumAt least 1 y, n = 6Kim et al,
      • Kim J.
      • An J.U.
      • Kim W.
      • et al.
      Differences in the gut microbiota of dogs (Canis lupus familiaris) fed a natural diet or a commercial feed revealed by the Illumina MiSeq platform.
      2017
      Kibble with boiled beefFaecalibacterium prausnitzii

      Clostridium hiranonis, Dorea, Slackia, and unidentified Clostridiaceae
      1 wk per combination, n = 11Herstad et al,
      • Herstad K.M.V.
      • Gajardo K.
      • Bakke A.M.
      • et al.
      A diet change from dry food to beef induces reversible changes on the faecal microbiota in healthy, adult client-owned dogs.
      2017
      Although Clostridiaceae can be associated with GI disease, it has been suggested that their increase when protein-rich diets are fed to dogs may not be detrimental to their health,
      • Bermingham E.N.
      • Maclean P.
      • Thomas D.G.
      • et al.
      Key bacterial families (Clostridiaceae, Erysipelotrichaceae and Bacteroidaceae) are related to the digestion of protein and energy in dogs.
      but are rather associated with protein digestion. In addition, Clostridiaceae were also found to positively correlate with protein digestibility and firmer fecal scores, and negatively correlate with fecal protein content (ie, more Clostridiaceae results in less undigested protein in feces) and less fecal output.
      • Bermingham E.N.
      • Maclean P.
      • Thomas D.G.
      • et al.
      Key bacterial families (Clostridiaceae, Erysipelotrichaceae and Bacteroidaceae) are related to the digestion of protein and energy in dogs.
      Clostridium hiranonis is a bacterial species associated with normal bile acid (BA) metabolism,
      • Guard B.C.
      • Honneffer J.B.
      • Jergens A.E.
      • et al.
      Longitudinal assessment of microbial dysbiosis, fecal unconjugated bile acid concentrations, and disease activity in dogs with steroid-responsive chronic inflammatory enteropathy.
      ,
      • Herstad K.M.V.
      • Gajardo K.
      • Bakke A.M.
      • et al.
      A diet change from dry food to beef induces reversible changes on the faecal microbiota in healthy, adult client-owned dogs.
      and was found to increase in 2 studies with higher protein diets.
      • Kim J.
      • An J.U.
      • Kim W.
      • et al.
      Differences in the gut microbiota of dogs (Canis lupus familiaris) fed a natural diet or a commercial feed revealed by the Illumina MiSeq platform.
      ,
      • Herstad K.M.V.
      • Gajardo K.
      • Bakke A.M.
      • et al.
      A diet change from dry food to beef induces reversible changes on the faecal microbiota in healthy, adult client-owned dogs.
      C hiranonis is often decreased in dogs with gastrointestinal disease, and after treatment with antibiotics (see Fig. 1). A study
      • Schmidt M.
      • Unterer S.
      • Suchodolski J.S.
      • et al.
      The fecal microbiome and metabolome differs between dogs fed Bones and Raw Food (BARF) diets and dogs fed commercial diets.
      reported normal BA metabolism in healthy dogs fed bones and raw foods (BARF) diets, with no significant difference from kibble-fed controls (see Fig. 1). BA metabolism is an important pathway not only for lipid digestion, but also for regulation of intestinal inflammation, and is commonly altered in chronic gastrointestinal diseases.
      • Guard B.C.
      • Honneffer J.B.
      • Jergens A.E.
      • et al.
      Longitudinal assessment of microbial dysbiosis, fecal unconjugated bile acid concentrations, and disease activity in dogs with steroid-responsive chronic inflammatory enteropathy.
      ,
      • Giaretta P.R.
      • Rech R.R.
      • Guard B.C.
      • et al.
      Comparison of intestinal expression of the apical sodium-dependent bile acid transporter between dogs with and without chronic inflammatory enteropathy.
      Bifidobacterium, Lactobacillus, and Faecalibacterium are considered beneficial in omnivores, and the effect of diet on their abundances is often investigated.
      • Turroni F.
      • van Sinderen D.
      • Ventura M.
      Genomics and ecological overview of the genus Bifidobacterium.
      Their benefit is due to their role in carbohydrate fermentation resulting in butyrate. The role of butyrate, an SCFA, in intestinal health is undisputed, as butyrate is the preferred energy source for colonocytes.
      • Rivera-Chavez F.
      • Zhang L.F.
      • Faber F.
      • et al.
      Depletion of butyrate-producing clostridia from the gut microbiota drives an aerobic luminal expansion of salmonella.
      However, butyrate can be found in fecal samples of all mammals regardless of their food sources. Therefore, in mammals that consume little to no carbohydrates, alternative pathways for butyrate production must be present. In a study comparing high-fat with high-starch diets in dogs, acetate, butyrate, and propionate levels were not different between dogs fed either diet, indicating that the production of SCFA in dogs is not exclusively dependent on carbohydrate content.
      • Schauf S.
      • de la Fuente G.
      • Newbold C.J.
      • et al.
      Effect of dietary fat to starch content on fecal microbiota composition and activity in dogs.
      Supporting that hypothesis, another study
      • Herstad K.M.V.
      • Gajardo K.
      • Bakke A.M.
      • et al.
      A diet change from dry food to beef induces reversible changes on the faecal microbiota in healthy, adult client-owned dogs.
      found that the addition of minced meat to a dry food diet actually led to a small increase in fecal butyrate and isovalerate.
      A recent study has highlighted that in carnivores, Clostridiaceae, and in particular C perfringens, are associated with the butyrate kinase butyrate-synthesis pathway, which allows the production of butyrate from protein.
      • Vital M.
      • Gao J.
      • Rizzo M.
      • et al.
      Diet is a major factor governing the fecal butyrate-producing community structure across Mammalia, Aves and Reptilia.
      Another bacterium known to produce butyrate from protein sources is F varium,
      • Potrykus J.
      • White R.L.
      • Bearne S.L.
      Proteomic investigation of amino acid catabolism in the indigenous gut anaerobe Fusobacterium varium.
      which was more abundant in a group of dogs fed meat-based raw diets for more than 1 year, suggesting an adaptation of the microbiome to the long-term diet.
      • Kim J.
      • An J.U.
      • Kim W.
      • et al.
      Differences in the gut microbiota of dogs (Canis lupus familiaris) fed a natural diet or a commercial feed revealed by the Illumina MiSeq platform.
      In addition, members of the Fusobacteriaceae family have been found to be more abundant in other carnivore species (cats,
      • Bermingham E.N.
      • Young W.
      • Kittelmann S.
      • et al.
      Dietary format alters fecal bacterial populations in the domestic cat (Felis catus).
      ,
      • Bermingham E.N.
      • Young W.
      • Butowski C.F.
      • et al.
      The fecal microbiota in the domestic cat (Felis catus) is influenced by interactions between age and diet; a five year longitudinal study.
      wolves,
      • Wu X.
      • Zhang H.
      • Chen J.
      • et al.
      Analysis and comparison of the wolf microbiome under different environmental factors using three different data of Next Generation Sequencing.
      ,
      • Lyu T.
      • Liu G.
      • Zhang H.
      • et al.
      Changes in feeding habits promoted the differentiation of the composition and function of gut microbiotas between domestic dogs (Canis lupus familiaris) and gray wolves (Canis lupus).
      other carnivora
      • Vital M.
      • Gao J.
      • Rizzo M.
      • et al.
      Diet is a major factor governing the fecal butyrate-producing community structure across Mammalia, Aves and Reptilia.
      ,
      • Menke S.
      • Meier M.
      • Mfune J.K.E.
      • et al.
      Effects of host traits and land-use changes on the gut microbiota of the Namibian black-backed jackal (Canis mesomelas).
      ), and dogs fed high-protein raw diets.
      • Bermingham E.N.
      • Maclean P.
      • Thomas D.G.
      • et al.
      Key bacterial families (Clostridiaceae, Erysipelotrichaceae and Bacteroidaceae) are related to the digestion of protein and energy in dogs.
      ,
      • Schmidt M.
      • Unterer S.
      • Suchodolski J.S.
      • et al.
      The fecal microbiome and metabolome differs between dogs fed Bones and Raw Food (BARF) diets and dogs fed commercial diets.
      ,
      • Sandri M.
      • Dal Monego S.
      • Conte G.
      • et al.
      Raw meat based diet influences faecal microbiome and end products of fermentation in healthy dogs.
      Those findings bring into question whether bacteria that specialize in carbohydrate fermentation bring the same benefits described in omnivores to the carnivore GI tract.
      • Bermingham E.N.
      • Maclean P.
      • Thomas D.G.
      • et al.
      Key bacterial families (Clostridiaceae, Erysipelotrichaceae and Bacteroidaceae) are related to the digestion of protein and energy in dogs.
      It is possible that in carnivores the butyrate production may be at least partially accomplished by other bacterial species such as members of the Clostridiaceae and Fusobacteriaceae families, which could be the reason for their increase in dogs fed raw diets.
      Another bacteria-derived metabolite that can be affected by diet is GABA, a neurotransmitter, and its precursor gamma-hydroxybutyric acid (GHB).
      • Schmidt M.
      • Unterer S.
      • Suchodolski J.S.
      • et al.
      The fecal microbiome and metabolome differs between dogs fed Bones and Raw Food (BARF) diets and dogs fed commercial diets.
      BARF diets have also been found to increase fecal levels of GABA and GHB.
      • Schmidt M.
      • Unterer S.
      • Suchodolski J.S.
      • et al.
      The fecal microbiome and metabolome differs between dogs fed Bones and Raw Food (BARF) diets and dogs fed commercial diets.
      Ketogenic diets in mice have also led to microbiome-mediated increases in GABA,
      • Olson C.A.
      • Vuong H.E.
      • Yano J.M.
      • et al.
      The gut microbiota mediates the anti-seizure effects of the ketogenic diet.
      and it is possible that the high fat and low carbohydrate content of BARF diets trigger similar changes. Both GABA and GHB are quickly absorbed from the GI tract when administered orally,
      • Mason P.E.
      • Kerns 2nd, W.P.
      Gamma hydroxybutyric acid (GHB) intoxication.
      ,
      • Thwaites D.T.
      • Basterfield L.
      • McCleave P.M.
      • et al.
      Gamma-Aminobutyric acid (GABA) transport across human intestinal epithelial (Caco-2) cell monolayers.
      and fermented foods rich in GABA-producing bacteria (Lactobacillus and Bifidobacterium) are available in Japan for the treatment of hypertension.
      • Barrett E.
      • Ross R.P.
      • O'Toole P.W.
      • et al.
      gamma-Aminobutyric acid production by culturable bacteria from the human intestine.
      ,
      • Iwatani S.
      • Yamamoto N.
      Functional food products in Japan: a review.
      The BARF diet also resulted in increased abundance of lactic acid bacteria such as Lactobacillales and Steptococcus,
      • Schmidt M.
      • Unterer S.
      • Suchodolski J.S.
      • et al.
      The fecal microbiome and metabolome differs between dogs fed Bones and Raw Food (BARF) diets and dogs fed commercial diets.
      which both of which can produce GABA.
      • Dhakal R.
      • Bajpai V.K.
      • Baek K.H.
      Production of gaba (gamma - Aminobutyric acid) by microorganisms: a review.
      The connection between the gut and the brain has been studied in many diseases, in dogs and other species, and ketogenic diets have been shown to be beneficial for dogs with neurologic diseases.
      • Molina J.
      • Jean-Philippe C.
      • Conboy L.
      • et al.
      Efficacy of medium chain triglyceride oil dietary supplementation in reducing seizure frequency in dogs with idiopathic epilepsy without cluster seizures: a non-blinded, prospective clinical trial.
      ,
      • Law T.H.
      • Davies E.S.
      • Pan Y.
      • et al.
      A randomised trial of a medium-chain TAG diet as treatment for dogs with idiopathic epilepsy.
      Recent studies
      • Ma D.
      • Wang A.C.
      • Parikh I.
      • et al.
      Ketogenic diet enhances neurovascular function with altered gut microbiome in young healthy mice.
      ,
      • Xie G.
      • Zhou Q.
      • Qiu C.Z.
      • et al.
      Ketogenic diet poses a significant effect on imbalanced gut microbiota in infants with refractory epilepsy.
      have shown that ketogenic diets impact microbiome composition, which may be one of the mechanisms by which they reduce seizure frequency.

      Effects of diets on microbiota in cats

      High-protein/low-carbohydrate diets (HPLC), both extruded and raw, have been studied in cats compared with traditional moderate protein extruded diets. In cats, canned diets are an additional higher protein alternative, which is commonly fed alone or in combination with extruded diets. The use of moist foods in cats is supported by research indicating that their consumption leads to increased water intake,
      • Carciofi A.
      • Bazolli R.
      • Zanni A.
      • et al.
      Influence of water content and the digestibility of pet foods on the water balance of cats.
      ,
      • Buckley C.M.
      • Hawthorne A.
      • Colyer A.
      • et al.
      Effect of dietary water intake on urinary output, specific gravity and relative supersaturation for calcium oxalate and struvite in the cat.
      decreased voluntary energy intake,
      • Buckley C.M.
      • Hawthorne A.
      • Colyer A.
      • et al.
      Effect of dietary water intake on urinary output, specific gravity and relative supersaturation for calcium oxalate and struvite in the cat.
      and decreased urine specific gravity,
      • Buckley C.M.
      • Hawthorne A.
      • Colyer A.
      • et al.
      Effect of dietary water intake on urinary output, specific gravity and relative supersaturation for calcium oxalate and struvite in the cat.
      which may be beneficial for certain health conditions.
      Studies
      • Vester B.M.
      • Dalsing B.L.
      • Middelbos I.S.
      • et al.
      Faecal microbial populations of growing kittens fed high- or moderate-protein diets.
      • Hooda S.
      • Vester Boler B.M.
      • Kerr K.R.
      • et al.
      The gut microbiome of kittens is affected by dietary protein:carbohydrate ratio and associated with blood metabolite and hormone concentrations.
      • Deusch O.
      • O'Flynn C.
      • Colyer A.
      • et al.
      Deep Illumina-based shotgun sequencing reveals dietary effects on the structure and function of the fecal microbiome of growing kittens.
      have evaluated the microbiome of kittens weaned onto HPLC extruded diets compared with kittens weaned onto medium protein/medium carbohydrate (MP/MC) diets. There was some agreement between the studies, and their main findings are summarized in Table 4. Interestingly, species diversity was increased by HPLC,
      • Deusch O.
      • O'Flynn C.
      • Colyer A.
      • et al.
      Deep Illumina-based shotgun sequencing reveals dietary effects on the structure and function of the fecal microbiome of growing kittens.
      and 5 genera that increased in HPLC-fed kittens
      • Hooda S.
      • Vester Boler B.M.
      • Kerr K.R.
      • et al.
      The gut microbiome of kittens is affected by dietary protein:carbohydrate ratio and associated with blood metabolite and hormone concentrations.
      are known butyrate producers: Clostridium and Eubacterium may produce butyrate either from carbohydrate through the but pathway, or from protein through the buk pathway, whereas Faecalibacterium, Ruminococcus, and Blautia are producers through the but pathway.
      • Vital M.
      • Gao J.
      • Rizzo M.
      • et al.
      Diet is a major factor governing the fecal butyrate-producing community structure across Mammalia, Aves and Reptilia.
      Differences between kittens fed either diet affected 194 metabolic pathways, including pathways related to amino acid biosynthesis and metabolism, indicating that the protein:carbohydrate ratio has a significant effect on microbiome function.
      • Deusch O.
      • O'Flynn C.
      • Colyer A.
      • et al.
      Deep Illumina-based shotgun sequencing reveals dietary effects on the structure and function of the fecal microbiome of growing kittens.
      However, the impact of such metabolite differences on overall health is still unknown.
      Table 4Summary of findings from studies that evaluated the effect of high-protein diets in the fecal microbiome of cats
      DietMain FindingsAgeTime on Diet, nReference
      High-protein low-carbohydrate dry foodLactobacillus, Bifidobacterium, and Escherichia coliKitten, weaning diet8 wk, n = 7Vester et al,
      • Vester B.M.
      • Dalsing B.L.
      • Middelbos I.S.
      • et al.
      Faecal microbial populations of growing kittens fed high- or moderate-protein diets.
      2009
      ↓ Actinobacteria, Bifidobacterium, Dialister, Acidaminococcus, Megasphera, and Mitsuokella

      ↑ Fusobacteria, Clostridium, Faecalibacterium, Ruminococcus, Blautia, and Eubacterium
      Kitten, weaning diet8 wk, n = 7Hooda et al,
      • Hooda S.
      • Vester Boler B.M.
      • Kerr K.R.
      • et al.
      The gut microbiome of kittens is affected by dietary protein:carbohydrate ratio and associated with blood metabolite and hormone concentrations.
      2013
      ↑ species diversity; Affected 194 metabolic pathways, including amino acid synthesis and metabolismKitten, weaning diet8 wk, n = 6Deusch et al,
      • Deusch O.
      • O'Flynn C.
      • Colyer A.
      • et al.
      Deep Illumina-based shotgun sequencing reveals dietary effects on the structure and function of the fecal microbiome of growing kittens.
      2014
      to 3-day-old chicksPeptococcus, Pseudobutyrivibrio, and unidentified LachnospiraceaeAdult10 d, n = 5Kerr et al,
      • Kerr K.R.
      • Dowd S.E.
      • Swanson K.S.
      Faecal microbiota of domestic cats fed raw whole chicks v. an extruded chicken-based diet.
      2014
      RawClostridium, Fusobacterium, Eubacterium, and molar ratio of butyrateAdult3 wk, n = 12Butowski et al,
      • Butowski C.F.
      • Thomas D.G.
      • Young W.
      • et al.
      Addition of plant dietary fibre to a raw red meat high protein, high fat diet, alters the faecal bacteriome and organic acid profiles of the domestic cat (Felis catus).
      2019
      Raw plus plant fiberClostridium, Fusobacterium, and Eubacterium

      Prevotella
      Adult3 wk, n = 12Butowski et al,
      • Butowski C.F.
      • Thomas D.G.
      • Young W.
      • et al.
      Addition of plant dietary fibre to a raw red meat high protein, high fat diet, alters the faecal bacteriome and organic acid profiles of the domestic cat (Felis catus).
      2019
      Canned↓ Firmicutes, Bacteroides, Lactobacillus, and Streptococcus

      Fusobacterium, Clostridium, unidentified Peptostreptococcaceae and Prevotellaceae
      Kitten, weaning diet9 wk, n = 10Bermingham et al,
      • Bermingham E.N.
      • Kittelmann S.
      • Young W.
      • et al.
      Post-weaning diet affects faecal microbial composition but not selected adipose gene expression in the cat (Felis catus).
      2013
      Lactobacillus, Megasphera, and Olsenella

      ↑ richness, Fusobacteria, Proteobacteria, Clostridium, Blautia, Bacteroides, and unidentified Peptostreptococcaceae
      Adult5 wk, n = 16Bermingham et al,
      • Bermingham E.N.
      • Young W.
      • Kittelmann S.
      • et al.
      Dietary format alters fecal bacterial populations in the domestic cat (Felis catus).
      2013
      Lactobacillus, Bifidobacterium, and Collinsella

      Bacteroides, Clostridium, Fusobacterium, genes involved in vitamin biosynthesis, metabolism and transport
      Kitten, weaning diet9 wk, n = 10Young et al,
      • Young W.
      • Moon C.D.
      • Thomas D.G.
      • et al.
      Pre- and post-weaning diet alters the faecal metagenome in the cat with differences in vitamin and carbohydrate metabolism gene abundances.
      2016
      The literature evaluating raw meat–based diets on the gut microbiome is less extensive in cats. Feeding raw 1-day-old to 3-day-old chicks,
      • Kerr K.R.
      • Dowd S.E.
      • Swanson K.S.
      Faecal microbiota of domestic cats fed raw whole chicks v. an extruded chicken-based diet.
      or raw beef
      • Butowski C.F.
      • Thomas D.G.
      • Young W.
      • et al.
      Addition of plant dietary fibre to a raw red meat high protein, high fat diet, alters the faecal bacteriome and organic acid profiles of the domestic cat (Felis catus).
      to adult cats resulted in increases in genera known to be SCFA-producers
      • Butowski C.F.
      • Thomas D.G.
      • Young W.
      • et al.
      Addition of plant dietary fibre to a raw red meat high protein, high fat diet, alters the faecal bacteriome and organic acid profiles of the domestic cat (Felis catus).
      ,
      • Liu B.
      • Wang W.
      • Zhu X.
      • et al.
      Response of gut microbiota to dietary fiber and metabolic interaction with SCFAs in piglets.
      (see Table 4). Although the butyrate concentration was not increased in cats fed raw beef, the butyrate molar ratio was higher, indicating a shift in the proportions of different SCFAs. However, when plant fiber (2% as fed, inulin and cellulose) was added to raw beef, the microbiome became more similar to that of cats fed the control extruded diet, and fecal acetate:propionate:butyrate ratio was almost identical to that of controls.
      • Butowski C.F.
      • Thomas D.G.
      • Young W.
      • et al.
      Addition of plant dietary fibre to a raw red meat high protein, high fat diet, alters the faecal bacteriome and organic acid profiles of the domestic cat (Felis catus).
      Similarly to raw diets, canned cat food has higher average protein and fat content, and lower carbohydrates content, compared with extruded dry foods. The microbiome of adult cats and kittens fed canned diets is more diverse
      • Bermingham E.N.
      • Young W.
      • Kittelmann S.
      • et al.
      Dietary format alters fecal bacterial populations in the domestic cat (Felis catus).
      ,
      • Bermingham E.N.
      • Kittelmann S.
      • Young W.
      • et al.
      Post-weaning diet affects faecal microbial composition but not selected adipose gene expression in the cat (Felis catus).
      (see Table 4). As with other high-protein diets, many genera enriched by canned diets are associated with butyrate production, and may therefore be beneficial for intestinal health.
      • Butowski C.F.
      • Thomas D.G.
      • Young W.
      • et al.
      Addition of plant dietary fibre to a raw red meat high protein, high fat diet, alters the faecal bacteriome and organic acid profiles of the domestic cat (Felis catus).
      Due to the strict carnivorous nature of cats, hindgut fermentation was considered unimportant.
      • Rochus K.
      • Janssens G.P.
      • Hesta M.
      Dietary fibre and the importance of the gut microbiota in feline nutrition: a review.
      However, several studies have evaluated the impact of dietary fiber on fecal microbiome composition in cats, and their results are summarized in Table 5. Similar to dogs, prebiotic fibers increase SCFA-producing bacterial genera,
      • Barry K.A.
      • Middelbos I.S.
      • Vester Boler B.M.
      • et al.
      Effects of dietary fiber on the feline gastrointestinal metagenome.
      ,
      • Hooda S.
      • Vester Boler B.M.
      • Kerr K.R.
      • et al.
      The gut microbiome of kittens is affected by dietary protein:carbohydrate ratio and associated with blood metabolite and hormone concentrations.
      ,
      • Rochus K.
      • Janssens G.P.
      • Hesta M.
      Dietary fibre and the importance of the gut microbiota in feline nutrition: a review.
      but also Bifidobacterium.
      • Hooda S.
      • Vester Boler B.M.
      • Kerr K.R.
      • et al.
      The gut microbiome of kittens is affected by dietary protein:carbohydrate ratio and associated with blood metabolite and hormone concentrations.
      ,
      • Bermingham E.N.
      • Kittelmann S.
      • Young W.
      • et al.
      Post-weaning diet affects faecal microbial composition but not selected adipose gene expression in the cat (Felis catus).
      ,
      • Young W.
      • Moon C.D.
      • Thomas D.G.
      • et al.
      Pre- and post-weaning diet alters the faecal metagenome in the cat with differences in vitamin and carbohydrate metabolism gene abundances.
      The combination of FOS and galactooligosaccharides also led to increased concentrations of total SCFA, butyrate, and valerate.
      • Kanakupt K.
      • Vester Boler B.M.
      • Dunsford B.R.
      • et al.
      Effects of short-chain fructooligosaccharides and galactooligosaccharides, individually and in combination, on nutrient digestibility, fecal fermentative metabolite concentrations, and large bowel microbial ecology of healthy adults cats.
      Table 5Main effects of different types of fiber in the fecal microbiome and metabolome of cats
      Fiber TypeMain FindingsMethodReferences
      FOSBifidobacteriumqPCRKanakupt et al.
      • Kanakupt K.
      • Vester Boler B.M.
      • Dunsford B.R.
      • et al.
      Effects of short-chain fructooligosaccharides and galactooligosaccharides, individually and in combination, on nutrient digestibility, fecal fermentative metabolite concentrations, and large bowel microbial ecology of healthy adults cats.
      2011
      ↑ Actinobacteria16S rRNA seq.Barry et al,
      • Barry K.A.
      • Middelbos I.S.
      • Vester Boler B.M.
      • et al.
      Effects of dietary fiber on the feline gastrointestinal metagenome.
      2012
      GOSBifidobacteriumqPCRKanakupt et al,
      • Kanakupt K.
      • Vester Boler B.M.
      • Dunsford B.R.
      • et al.
      Effects of short-chain fructooligosaccharides and galactooligosaccharides, individually and in combination, on nutrient digestibility, fecal fermentative metabolite concentrations, and large bowel microbial ecology of healthy adults cats.
      2011
      FOS and GOSBifidobacterium, total SCFA, butyrate and valerateqPCRKanakupt et al,
      • Kanakupt K.
      • Vester Boler B.M.
      • Dunsford B.R.
      • et al.
      Effects of short-chain fructooligosaccharides and galactooligosaccharides, individually and in combination, on nutrient digestibility, fecal fermentative metabolite concentrations, and large bowel microbial ecology of healthy adults cats.
      2011
      FOS and inulin↓ Gammaproteobacteria

      ↑ Veillonaceae
      16S rRNA seq.Garcia-Mazcorro et al,
      • Garcia-Mazcorro J.F.
      • Barcenas-Walls J.R.
      • Suchodolski J.S.
      • et al.
      Molecular assessment of the fecal microbiota in healthy cats and dogs before and during supplementation with fructo-oligosaccharides (FOS) and inulin using high-throughput 454-pyrosequencing.
      2017
      InulinFaecalibacterium and Fusobacterium

      Bifidobacterium
      16S rRNA seq.Young et al,
      • Young W.
      • Moon C.D.
      • Thomas D.G.
      • et al.
      Pre- and post-weaning diet alters the faecal metagenome in the cat with differences in vitamin and carbohydrate metabolism gene abundances.
      2016
      CelluloseNo changes16S rRNA seq.Barry et al,
      • Barry K.A.
      • Middelbos I.S.
      • Vester Boler B.M.
      • et al.
      Effects of dietary fiber on the feline gastrointestinal metagenome.
      2012
      Wool hydrolysateNo changes16S rRNA seq.Deb-Choudhury et al,
      • Deb-Choudhury S.
      • Bermingham E.N.
      • Young W.
      • et al.
      The effects of a wool hydrolysate on short-chain fatty acid production and fecal microbial composition in the domestic cat (Felis catus).
      2018
      Pectin↑ Firmicutes16S rRNA seq.Barry et al,
      • Barry K.A.
      • Middelbos I.S.
      • Vester Boler B.M.
      • et al.
      Effects of dietary fiber on the feline gastrointestinal metagenome.
      2012
      Mixed insoluble fibers↓ isobutyric, 2-methylbutyric, and isovaleric acids

      Blautia, Bacteroides, Turicibacter, acetic and propionic acids
      16S rRNA seq.Wernimont et al,
      • Wernimont S.
      • Fritsch D.
      • Jackson M.
      • et al.
      Specialized dietary fibers alter microbiome composition & promote fermentative metabolism in the lower gastrointestinal tract of healthy adult cats (P20-045-19).
      2019
      Inulin and celluloseClostridium, Fusobacterium, and Eubacterium

      Prevotella, Bifidobacterium, Lactobacillus, Megamonas, and unclassified Lachnospiraceae
      16S rRNA seq.Hooda et al,
      • Hooda S.
      • Vester Boler B.M.
      • Kerr K.R.
      • et al.
      The gut microbiome of kittens is affected by dietary protein:carbohydrate ratio and associated with blood metabolite and hormone concentrations.
      2013
      Abbreviations: FOS, fructooligosaccharides; GOS, galactooligosaccharides; qPCR, quantitative polymerase chain reaction; rRNA seq., ribosomal RNA sequencing; SCFA, short-chain fatty acid.

      Diet versus disease effects on the microbiome

      Although diet can change microbiome composition significantly, and result in changes both in metabolic pathways and production of metabolites, those changes are typically much smaller than those that accompany disease.
      • Pilla R.
      • Suchodolski J.S.
      The role of the canine gut microbiome and metabolome in health and gastrointestinal disease.
      In sick animals, and in particular those with gastrointestinal disease (eg, chronic enteropathies), microbiome diversity is quickly reduced, and many core species, such as C hiranonis, Fusobacterium spp, and Faecalibacterium praunitzii, are decreased
      • Guard B.C.
      • Honneffer J.B.
      • Jergens A.E.
      • et al.
      Longitudinal assessment of microbial dysbiosis, fecal unconjugated bile acid concentrations, and disease activity in dogs with steroid-responsive chronic inflammatory enteropathy.
      ,
      • Minamoto Y.
      • Minamoto T.
      • Isaiah A.
      • et al.
      Fecal short-chain fatty acid concentrations and dysbiosis in dogs with chronic enteropathy.
      ,
      • Pilla R.
      • Suchodolski J.S.
      The role of the canine gut microbiome and metabolome in health and gastrointestinal disease.
      ,
      • Chaitman J.
      • Ziese A.L.
      • Pilla R.
      • et al.
      Fecal microbial and metabolic profiles in dogs with acute diarrhea receiving either fecal microbiota transplantation or oral metronidazole.
      (see Fig. 1). Therefore, although dietary manipulations of microbiome composition can likely play a role in fostering a healthy and resilient microbe community, they are in most cases unlikely to generate changes comparable in magnitude to those observed in disease.
      Diet modification, prebiotics, and probiotics are often used, alone or together with medications, to ameliorate clinical signs of diseases including diarrhea. The changes in microbiome composition associated with diarrhea are extensive and have been reviewed elsewhere,
      • Pilla R.
      • Suchodolski J.S.
      The role of the canine gut microbiome and metabolome in health and gastrointestinal disease.
      and are accompanied by functional changes in digestion and motility that modify the luminal environment, further affecting microbiome composition. Hypoallergenic diets, formulated to reduce immunogenicity and facilitate digestion, do not significantly affect the microbiome of healthy dogs,
      • Pilla R.
      • Gaschen F.P.
      • Barr J.W.
      • et al.
      Effects of metronidazole on the fecal microbiome and metabolome in healthy dogs.
      ,
      • Bresciani F.
      • Minamoto Y.
      • Suchodolski J.S.
      • et al.
      Effect of an extruded animal protein-free diet on fecal microbiota of dogs with food-responsive enteropathy.
      but have been associated with improved microbiome composition in dogs with food-responsive diarrhea.
      • Bresciani F.
      • Minamoto Y.
      • Suchodolski J.S.
      • et al.
      Effect of an extruded animal protein-free diet on fecal microbiota of dogs with food-responsive enteropathy.
      ,
      • Kalenyak K.
      • Isaiah A.
      • Heilmann R.M.
      • et al.
      Comparison of the intestinal mucosal microbiota in dogs diagnosed with idiopathic inflammatory bowel disease and dogs with food-responsive diarrhea before and after treatment.
      Similarly, prebiotic fibers can aid recovery of beneficial bacterial populations and restore SCFA production. Probiotics, which are beneficial bacterial species, also can be fed to aid recovery. Although their colonization is typically transient,
      • Garcia-Mazcorro J.F.
      • Lanerie D.J.
      • Dowd S.E.
      • et al.
      Effect of a multi-species synbiotic formulation on fecal bacterial microbiota of healthy cats and dogs as evaluated by pyrosequencing.
      ,
      • Pilla R.
      • Guard B.C.
      • Steiner J.M.
      • et al.
      Administration of a synbiotic containing enterococcus faecium does not significantly alter fecal microbiota richness or diversity in dogs with and without food-responsive chronic enteropathy.
      probiotics can still be metabolically active during their transit, and produce beneficial metabolites that help improve clinical signs.
      • Schmitz S.
      • Suchodolski J.
      Understanding the canine intestinal microbiota and its modification by pro-, pre- and synbiotics - what is the evidence?.
      Probiotics have been reported to have a protective effect on acute diarrhea outbreaks, and to have beneficial effects on mucosal homeostasis,
      • White R.
      • Atherly T.
      • Guard B.
      • et al.
      Randomized, controlled trial evaluating the effect of multi-strain probiotic on the mucosal microbiota in canine idiopathic inflammatory bowel disease.
      speeding disease remission
      • Rossi G.
      • Jergens A.
      • Cerquetella M.
      • et al.
      Effects of a probiotic (SLAB51) on clinical and histologic variables and microbiota of cats with chronic constipation/megacolon: a pilot study.
      in dogs with chronic diarrhea.

      Summary

      The gut microbiome is a functional organ, and is responsive to the nutrient composition of diet. However, major shifts in microbiome composition are only observed with major changes in macronutrient composition, such as high-protein or high-fiber diets. More importantly, changes in bacterial composition may affect the production of metabolites in the gut. Indeed, fiber, starch, and protein content seem to be the key modulating players, and changes in those nutrient profiles cause rapid shifts in microbiome and metabolome composition, likely due to the changes in substrate availability. Because of the redundancy of the microbial communities, key metabolites can be produced by different bacteria. Butyrate, for example, can be produced from either fiber or protein, suggesting that both increased fiber or increased protein in the diet may bring similar benefits; however, the ideal levels of fiber and protein remain to be determined. The microbiome of healthy dogs and cats is resilient and adaptable, and it is capable of quickly restoring itself to baseline composition once the animal returns to its usual diet, indicating that sustained change requires long-term administration of a specific diet. Although diet affects the microbiome and metabolome of healthy dogs, changes associated with disease are of greater magnitude. In those cases, dietary change, prebiotic fibers, and probiotic bacteria can be beneficial to help improve microbial diversity and metabolite production.

      Disclosure

      R. Pilla and J.S. Suchodolski are employed by the Gastrointestinal Laboratory at Texas A&M University, which provides assay for intestinal function and microbiota analysis on a fee-for-service basis.

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