The response of canine faecal microbiota to increased dietary protein is influenced by body condition

Cross-comparison of gut metagenomic profiling strategies

The rapid advancements in sequencing technologies and bioinformatics have enabled metagenomic research of complex microbial systems, but reliable results depend on consistent laboratory and bioinformatics approaches. Current efforts to identify best practices often focus on optimizing specific steps, making it challenging to understand the influence of each stage on microbial population analysis and compare data across studies. This study evaluated DNA extraction, library construction methodologies, sequencing platforms, and computational approaches using a dog stool sample, two synthetic microbial community mixtures, and various sequencing data sources. Our work, the most comprehensive evaluation of metagenomic methods to date. We developed a software tool, termed minitax, which provides consistent results across the range of platforms and methodologies. Our findings showed that the Zymo Research Quick-DNA HMW MagBead Kit, Illumina DNA Prep library preparation method, and the minitax bioinformatics tool were the most effective for high-quality microbial diversity analysis. However, the effectiveness of pipelines or method combinations is sample-specific, making it difficult to identify a universally optimal approach. Therefore, employing multiple approaches is crucial for obtaining reliable outcomes in microbial systems.

Comprehensive profile of the companion animal gut microbiome integrating reference-based and reference-free methods

The gut microbiome of companion animals is relatively underexplored, despite its relevance to animal health, pet owner health, and basic microbial community biology. Here, we provide the most comprehensive analysis of the canine and feline gut microbiomes to date, incorporating 2639 stool shotgun metagenomes (2272 dog and 367 cat) spanning 14 publicly available datasets (n = 730) and 8 new study populations (n = 1909). These are compared with 238 and 112 baseline human gut metagenomes from the Human Microbiome Project 1-II and a traditionally living Malagasy cohort, respectively, processed in a manner identical to the animal metagenomes. All microbiomes were characterized using reference-based taxonomic and functional profiling, as well as de novo assembly yielding metagenomic assembled genomes clustered into species-level genome bins. Companion animals shared 184 species-level genome bins not found in humans, whereas 198 were found in all three hosts. We applied novel methodology to distinguish strains of these shared organisms either transferred or unique to host species, with phylogenetic patterns suggesting host-specific adaptation of microbial lineages. This corresponded with functional divergence of these lineages by host (e.g. differences in metabolic and antibiotic resistance genes) likely important to companion animal health. This study provides the largest resource to date of companion animal gut metagenomes and greatly contributes to our understanding of the "One Health" concept of a shared microbial environment among humans and companion animals, affecting infectious diseases, immune response, and specific genetic elements.

Effects of dietary fiber and biotic supplementation on apparent total tract macronutrient digestibility and the fecal characteristics, metabolites, and microbiota of healthy adult dogs

Dietary fibers and biotics have been shown to support gastrointestinal health in dogs, but are usually tested individually. There is value in testing fiber-biotic combinations that are commonly used commercially. Therefore, this study was conducted to determine the apparent total tract macronutrient digestibility (ATTD) of diets supplemented with fibers or biotics and to evaluate their effects on the fecal characteristics, metabolites, microbiota, and immunoglobulin A (IgA) concentrations of dogs. Twelve healthy adult female beagle dogs (age = 6.2 ± 1.6 yr; body weight = 9.5 ± 1.1 kg) were used in a replicated 3 × 3 Latin square design to test three treatments: 1) control diet based on rice, chicken meal, tapioca starch, and cellulose + a placebo treat (CT); 2) diet based on rice, chicken meal, garbanzo beans, and cellulose + a placebo treat (GB); 3) diet based on rice, chicken meal, garbanzo beans, and a functional fiber/prebiotic blend + a probiotic-containing treat (GBPP). In each 28-d period, a 22-d diet adaptation was followed by a 5-d fecal collection phase. Fasted blood samples were collected on day 28. Data were analyzed using the Mixed Models procedure of SAS 9.4, with P < 0.05 being significant and P < 0.10 being trends. ATTD of dry matter (DM), organic matter, and energy were lower (P < 0.001) and DM fecal output was higher (P < 0.01) in dogs fed GBPP than CT or GB, whereas ATTD of crude protein was higher (P < 0.001) in dogs fed CT and GBPP than GB. ATTD of fat was higher (P < 0.001) and wet fecal output was lower (P < 0.01) in dogs fed CT than GB or GBPP. Fecal DM% was higher (P < 0.001) in dogs fed CT than GBPP or GB, and higher in dogs fed GBPP than GB. Fecal short-chain fatty acid concentrations were higher (P < 0.001) in dogs fed GB than CT or GBPP, and higher in dogs fed GB than GBPP. Fecal IgA concentrations were higher (P < 0.01) in dogs fed GB than CT. Fecal microbiota populations were affected by diet, with alpha diversity being higher (P < 0.01) in dogs fed GB than CT, and beta diversity shifting following dietary fiber and biotic supplementation. The relative abundance of 24 bacterial genera was altered in dogs fed GB or GBPP than CT. Serum triglyceride concentrations were lower in dogs fed GB than GBPP or CT. Our results demonstrate that legume-based dietary fibers, with or without prebiotics and probiotics, reduce ATTD, increase stool output, beneficially shift fecal metabolites and microbiota, and reduce blood lipids in adult dogs.

Faecal metabolome responses to an altered dietary protein:carbohydrate ratio in adult dogs

High-protein diets may aid weight loss and weight maintenance programs in both humans and dogs, although the effect of dietary protein levels on gut metabolism and functionality has not been studied in depth. The current study aimed to investigate the effect of an altered dietary protein:carbohydrate ratio on gut function in adult dogs by means of faecal metabolomic fingerprinting. More specifically, functional metabolic differences in dogs fed a high-protein/low-carbohydrate (HPLC) vs. low-protein/high-carbohydrate (LPHC) diet were studied by equally allocating twelve clinically healthy (6 lean and 6 obese) Beagles into two groups in a cross-over design, with each group receiving two isocaloric diets for four weeks. The faecal metabolome revealed that different protein:carbohydrate ratio can influence host and/or gut microbiome metabolism and function, while no effect was observed on the body condition. Targeted analysis demonstrated that the HPLC diet significantly increased the concentration of indole, spermidine, and pipecolinic acid and decreased the concentration of azelaic acid, D-fructose, mannose, and galactose (p < 0.05). Multivariate modelling (OPLS-DA) of the untargeted faecal metabolome revealed distinctly different metabolomic profiles following the HPLC vs. LPHC diet, with 18 altered pathways. The HPLC diet influenced amino acid and lipid metabolism, potentially promoting weight loss and immune function, whereas the LPHC diet affected carbohydrate fermentation and may promote anti-oxidative function.

Programming of metabolic and autoimmune diseases in canine and feline: linkage to the gut microbiome

Metabolic and autoimmune disorders have long represented challenging health problems because of their growing prevalence in companion animals. The gut microbiome, made up of trillions of microorganisms, is implicated in multiple physiological and pathological processes. Similar to human beings, the complicated microbiome harbored in the gut of canines and felines emerges as a key factor determining a wide range of normal and disease conditions. Evidence accumulated from recent findings on canine and feline research uncovered that the gut microbiome is actively involved in host metabolism and immunity. Notably, the composition, abundance, activity, and metabolites of the gut microbiome are all elements that shape clinical outcomes concerning metabolism and immune function. This review highlights the implications of the gut microbiome for metabolic disorders (obesity, diabetes, and hepatic lipidosis) and autoimmune diseases (inflammatory bowel disease, osteoarthritis, asthma, and myasthenia gravis) in canine and feline animals, providing novel strategies and therapeutic targets for the prevention and treatment of pet diseases.

Relationship of Acylcarnitines to Myocardial Ischemic Remodeling and Clinical Manifestations in Chronic Heart Failure

BACKGROUND

Progressive myocardial remodeling (MR) in chronic heart failure (CHF) leads to aggravation of systolic dysfunction (SD) and clinical manifestations. Identification of metabolomic markers of these processes may help in the search for new therapeutic approaches aimed at achieving reversibility of MR and improving prognosis in patients with CHF.

METHODS

To determine the relationship between plasma acylcarnitine (ACs) levels, MR parameters and clinical characteristics, in patients with CHF of ischemic etiology (n = 79) and patients with coronary heart disease CHD (n = 19) targeted analysis of 30 ACs was performed by flow injection analysis mass spectrometry.

RESULTS

Significant differences between cohorts were found for the levels of 11 ACs. Significant positive correlations (r > 0.3) between the medium- and long-chain ACs (MCACs and LCACs) and symptoms (CHF NYHA functional class (FC); r = 0.31-0.39; p < 0.05); negative correlation (r = -0.31-0.34; p < 0.05) between C5-OH and FC was revealed. Positive correlations of MCACs and LCACs (r = 0.31-0.48; p < 0.05) with the left atrium size and volume, the right atrium volume, right ventricle, and the inferior vena cava sizes, as well as the pulmonary artery systolic pressure level were shown. A negative correlation between C18:1 and left ventricular ejection fraction (r = -0.31; p < 0.05) was found. However, a decrease in levels compared to referent values of ACs with medium and long chain lengths was 50% of the CHF-CHD cohort. Carnitine deficiency was found in 6% and acylcarnitine deficiency in 3% of all patients with chronic heart disease.

CONCLUSIONS

ACs may be used in assessing the severity of the clinical manifestations and MR. ACs are an important locus to study in terms of altered metabolic pathways in patients with CHF of ischemic etiology and SD. Further larger prospective trials are warranted and needed to determine the potential benefits to treat patients with CV diseases with aberrate AC levels.

The Effect of Dietary Protein Concentration on the Fecal Microbiome and Serum Concentrations of Gut-Derived Uremic Toxins in Healthy Adult Cats

The purpose of this study was to evaluate the effect of feeding healthy adult cats with foods containing variable protein concentrations on the fecal microbiome and serum concentrations of the gut-derived uremic toxins indoxyl sulfate, p-cresol sulfate (pCS), and trimethylamine-n-oxide. Twenty healthy young adult cats were randomized into two groups and fed either a low-protein diet (LPD; 7.4 g/100 kcal ME) or a high-protein diet (HPD; 11.0 g/100 kcal ME) for a 12-week period. Serum uremic toxin concentrations were measured via liquid chromatography tandem mass spectrometry, and the fecal microbiome was characterized using shallow sequence shotgun metagenomics. Cats that consumed the HPD had higher pCS concentrations at 8 weeks (p = 0.028) when compared to baseline. After 12 weeks, cats fed the HPD had higher fecal alpha diversity indices at both the taxonomic and functional levels and lower fecal Bifidobacterium relative abundance compared to those cats fed the LPD. In conclusion, a change in diet and dietary protein concentration shifted the fecal microbial community and microbial function. Feeding cats a high amount of protein increased serum concentrations of the uremic toxin pCS; however, the effect was short-lived.

Obese dogs exhibit different fecal microbiome and specific microbial networks compared with normal weight dogs

Canine obesity is a major health concern that predisposes dogs to various disorders. The fecal microbiome has been attracting attention because of their impact on energy efficiency and metabolic disorders of host. However, little is known about specific microbial interactions, and how these may be affected by obesity in dogs. The objective of this study was to investigate the differences in fecal microbiome and specific microbial networks between obese and normal dogs. A total of 20 beagle dogs (males = 12, body weight [BW]: 10.5 ± 1.08 kg; females = 8, BW: 11.3 ± 1.71 kg; all 2-year-old) were fed to meet the maintenance energy requirements for 18 weeks. Then, 12 beagle dogs were selected based on body condition score (BCS) and divided into two groups: high BCS group (HBCS; BCS range: 7-9, males = 4, females = 2) and normal BCS group (NBCS; BCS range: 4-6, males = 4, females = 2). In the final week of the experiment, fecal samples were collected directly from the rectum, before breakfast, for analyzing the fecal microbiome using 16S rRNA gene amplicon sequencing. The HBCS group had a significantly higher final BW than the NBCS group (P < 0.01). The relative abundances of Faecalibacterium, Phascolarctobacterium, Megamonas, Bacteroides, Mucispirillum, and an unclassified genus within Ruminococcaceae were significantly higher in the HBCS group than those in the NBCS group (P < 0.05). Furthermore, some Kyoto Encyclopedia of Genes and Genomes (KEGG) modules related to amino acid biosynthesis and B vitamins biosynthesis were enriched in the HBCS group (P < 0.10), whereas those related to carbohydrate metabolism were enriched in the NBCS group (P < 0.10). Microbial network analysis revealed distinct co-occurrence and mutually exclusive interactions between the HBCS and NBCS groups. In conclusion, several genera related to short-chain fatty acid production were enriched in the HBCS group. The enriched KEGG modules in the HBCS group enhanced energy efficiency through cross-feeding between auxotrophs and prototrophs. However, further studies are needed to investigate how specific networks can be interpreted in the context of fermentation characteristics in the lower gut and obesity in dogs.

The impact of protein source and grain inclusion on digestibility, fecal metabolites, and fecal microbiome in adult canines

This study was conducted to determine the effect of animal protein inclusion rate and grain-free or grain-inclusive diets on macronutrient digestibility, fecal characteristics, metabolites, and microbiota in mixed-breed hounds and Beagles. Four experimental extruded kibble diets were made with varying amounts of animal protein and carbohydrates: 1) high animal protein, grain-inclusive (HA-GI), 2) low animal protein, grain-free (LA-GF), 3) low animal protein, grain-inclusive (LA-GI), and 4) high animal protein, grain-free (HA-GF). Thirty-two Beagles and 33 mixed-breed hounds were assigned to 1 of the 4 treatment groups in a completely randomized design that lasted 180 d. All diets were similar in chemical composition and well-digested by the animals. In general, for fecal metabolites, mixed-breed hounds had a greater concentration of total short-chain fatty acid (SCFA) and ammonia and lower indole concentration than Beagles (P < 0.05). In mixed-breed hounds, LA-GF had a greater (P < 0.05) total SCFA concentration than HA-GI and LA-GI; however, this was not observed in Beagles. There were greater concentrations of ammonia, phenol, and indole in HA-GI than in LA-GF (P < 0.05). Breed-affected fecal primary bile acid (BA) concentration, as mixed-breed hounds had a greater concentration of cholic acid (CA) than Beagles (P < 0.05). Mixed-breed hounds fed LA-GF resulted in greater CA concentrations than HA-GI and LA-GI (P < 0.05). Dogs who consumed LA-GF had lower fecal secondary BA content than the other groups (P < 0.05). The distribution of the fecal microbiota community differed in LA-GF compared with the other groups, with lower α-diversity. However, dogs fed LA-GF had the largest difference in composition with greater Selenomonadaceae, Veillonellaceae, Lactobacillaceae, Streptococcus, Ligilactobacillus, Megamonas, Collinsella aerofaciens, and Bifidobacterium sp. than the other groups. A significant breed effect was noted on nutrient digestibility, fecal metabolites, and microbiota. A treatment effect was observed in LA-GF as it resulted in greater fecal SCFA, lower protein fermentative end products, greater fecal primary BAs, lower fecal secondary BA concentrations, and shifts in fecal microbiota.

Determining the protocol requirements of in-home dog food digestibility testing

In-home pet food testing has the benefit of yielding data which is directly applicable to the pet population. Validated and standardised in-home test protocols need to be available, and here we investigated key protocol requirements for an in-home canine food digestibility protocol. Participants were recruited via an online survey. After meeting specific inclusion criteria, sixty dogs of various breeds and ages received, during 14 consecutive days, a relatively low and high digestible complete dry extruded food containing titanium (Ti) dioxide. Both foods were given for 7 d in a cross-over design. Owners collected faeces daily allowing daily faecal Ti concentrations and digestibility of nitrogen (N), dry matter (DM), crude ash, organic matter (OM), crude fat (Cfat), starch and gross energy (GE) to be determined. Faecal Ti and digestibility values for all nutrients were not different (P > 0·05) from the second day onwards after first consumption for both foods. One day of faecal collection yielded reliable digestibility values with additional collection days not reducing the confidence interval around the mean. Depending on the accepted margin of error, the food and the nutrient of interest, the minimal required sample size was between 9 and 43 dogs. Variation in digestibility values could in part be explained by a dog's neuter status (N, crude ash) and age (crude ash, Cfat) but not sex and body size. Future studies should focus on further identifying and controlling sources of variation to improve the in-home digestibility protocol and reduce the number of dogs required.

The Nexus of Diet, Gut Microbiota and Inflammatory Bowel Diseases in Dogs

Canine inflammatory bowel diseases (IBD) are of increasing interest in veterinary medicine. They refer to complex and debilitating conditions of dogs' gastrointestinal tract. Although little evidence for causal inferences is currently available, it is believed that IBD pathophysiology entails intricate interactions between environmental factors, the intestinal immune system, and the microbial communities that colonize the gut. To better understand the mechanisms underlying these disorders, leveraging factors associated with the development of these diseases is imperative. Of these factors, emerging evidence supports the role of dietary patterns as key players influencing the composition and function of gut microbes, with subsequent effects on health and disease. In this review, we particularly focus on addressing IBD in dogs and discuss how specific nutrients may elicit or relieve gut inflammation. Gaining mechanistic insights into such interplay and the underpinning mechanisms is key to inferring dietary recommendations, and setting up new and promising therapeutics.

Characterization of intestinal microbiota in normal weight and overweight Border Collie and Labrador Retriever dogs

Obesity in dogs is an emerging issue that affects canine health and well-being. Its development is ascribed to several factors, including genetic predisposition and dietary management, and recent evidence suggests that intestinal microbiota may be involved as well. Previous works have shown obesity to be linked to significant changes in gut microbiota composition in humans and mice, but only limited information is available on the role played by canine gut microbiota. The aim of this exploratory study was to investigate whether composition of canine faecal microbiota may be influenced by overweight condition and breed. All the enrolled companion dogs were young adults, intact, healthy, and fed commercial extruded pet food; none had received antibiotics, probiotics or immunosuppressant drugs in the previous six months. Labrador Retriever (LR) and Border Collie (BC) were chosen as reference breeds and Body Condition Score (BCS) on a 9-point scale as reference method for evaluating body fat. The faecal microbial communities of 15 lean (BCS 4-5/9; 7 LRs and 8 BCs) and 14 overweight (BCS > 5/9; 8 LRs and 6 BCs) family dogs were analysed using 16S rRNA gene sequencing. Moreover, for each dog, the daily intake of energy (kcal/d) and dietary macronutrients (g/d) were calculated according to an accurate feeding history collection. Firmicutes and Bacteroidetes resulted the predominant phyla (51.5 ± 10.0% and 33.4 ± 8.5%, respectively) in all dogs. Bioinformatic and statistical analysis revealed that no bacterial taxon differed significantly based on body condition, except for genus Allisonella (p < 0.05); BC gut microbiota was richer (p < 0.05) in bacteria belonging to phyla Actinobacteria (family Coriobacteriaceae in particular) and Firmicutes (Allobaculum and Roseburia genera). No remarkable differences were recorded either for diversity indices (i.e., alpha diversity, p > 0.10) or for divergence within the sample set (i.e., beta diversity, p > 0.05). PERMANOVA tests performed on single factors demonstrated the tendency of dietary protein to influence the recruited dogs' microbiota beta-diversity at amplicon sequence variant level (p = 0.08). In conclusion, the faecal microbiota of dogs involved in this exploratory study showed no major variations based on body condition. However, our findings suggested that certain bacterial taxa previously acknowledged in obesity-related studies may be detected in dissimilar amounts depending on canine breed.

Analysis and Comparison of Gut Microbiome in Young Detection Dogs

The detection dogs are well-known for their excellent capabilities to sense different kinds of smells, which can play an important role in completing various searching and rescuing missions. The recent studies have demonstrated that the excellent olfactory function of detection dogs might be related with the gut microbes via the bidirectional communications between the gastrointestinal tract and the brain. In this study, the gut microbial communities of three types of breeds of detection dogs (Springer Spaniel, Labrador Retriever, and German Shepherd) were studied and compared. The results revealed that the richness and the diversity of gut microbiome German Shepherd dogs were significantly higher than the Labrador Retriever dogs and the Springer Spaniel dogs. At the phylum level, the most predominant gut microbial communities of the detection dogs were comprised of Fusobacteriota, Bacteroidetes, Firmicutes, Proteobacteria, Campilobacterota, and Actinobacteriota. At the genus level the most predominant gut microbial communities were comprised of Fusobacterium, Megamonas, Prevotella, Alloprevotella, Bacteroides, Haemophilus, Anaerobiospirillum, Helicobacter, Megasphaera, Peptoclostridium, Phascolarctobacterium, and Streptococcus. However, the gut microbial communities of the three dogs group were also obviously different. The mean relative abundance of Fusobacterium, Prevotella, Alloprevotella, Megamonas, Bacteroides, and Phascolarctobacterium presented significant differences in the three groups. According to the portraits and characteristics of the gut microbiome in young detection dogs, multiple kinds of nutritional interventions could be applied to manipulate the gut microbiota, with the aim of improving the health states and the olfactory performances.

Composition and short-term stability of gut microbiota in lean and spontaneously overweight healthy Labrador retriever dogs

Background

The gut microbiota and its metabolic end-products act in close collaboration with the nutrient metabolism of the animal. A relationship between excess adiposity and alterations in gut microbiota composition has been identified in humans and rodents, but data are scarce for overweight dogs. This study compared composition and temporal variations of gut microbiota in healthy lean and spontaneously overweight dogs. The analysis was based on three individual fresh faeces samples from each dog during a 10-day period. Twenty-seven healthy and intact male Labrador retriever dogs were included, 12 of which were classified as lean (body condition score (BCS) 4–5 on a 9-point scale) and 15 as overweight (BCS 6–8). Gut microbiota was analysed by Illumina sequencing of the V3-V4 region of the 16S rRNA gene.

Results

Lean and overweight groups of dogs were not separated by principal coordinate analysis (PCoA), analysis of similarity (one-way ANOSIM, P = 0.99) or species indicator analysis (IndVal) using operational taxonomic units (OTU) data. Gut microbial taxa at phylum, family or genus level did not differ between lean and overweight dogs in mixed-model repeated measures analyses. Short-term stability, evaluated by similarity index, did not differ between lean and overweight dogs over the 10-day period. Pooled Firmicutes/Bacteroidetes (F/B) ratio was 3.1 ± 3.7 in overweight dogs and 2.1 ± 1.2 in lean dogs (P = 0.83). Individual dogs, irrespective of body condition (lean or overweight), displayed variation in mean alpha diversity (Chao-1 index range 122–245, Shannon index range 2.6–3.6) and mean similarity index (range 44–85%).

Conclusions

Healthy lean and spontaneously overweight Labrador retriever dogs had comparable gut microbiota composition and short-term stability over a 10-day sampling period. There were no alterations in microbial diversity or in relative abundance of specific taxa at phylum, family or genus level in overweight compared to lean dogs. Our findings suggest that there are few detectable differences in gut microbiota composition between healthy spontaneously overweight and lean dogs by the current method. Future application of metagenomic or metabolomic techniques could be used to investigate microbial genes or microbial end-products that may differ even when microbiota compositional analyses fail to detect a significant difference between lean and overweight dogs.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13028-022-00628-z.

Differences in the composition and predicted functions of the intestinal microbiome of obese and normal weight adult dogs

Obesity is a multifactorial nutritional disorder highly prevalent in dogs, observed in developed and developing countries. It is estimated that over 40% of the canine population suffers from obesity, which manifests in an increased risk of chronic osteoarticular, metabolic, and cardiovascular diseases. The intestinal microbiome of obese animals shows increases in the abundance of certain members capable of extracting energy from complex polysaccharides. The objective of this study was to compare the composition and predicted function of the intestinal microbiome of Chilean obese and normal weight adult dogs. Twenty clinically healthy dogs were classified according to their body condition score (BCS) as obese (n = 10) or normal weight (n = 10). DNA was extracted from stool samples, followed by next-generation sequencing of the 16S rRNA V3-V4 region and bioinformatics analysis targeting microbiome composition and function. Significant differences were observed between these groups at the phylum level, with anincrease in Firmicutes and a decrease in Bacteroidetes in obese dogs. Microbiome compositions of these animals correlated with their BCS, and obese dogs showed enrichment in pathways related to transport, chemotaxis, and flagellar assembly. These results highlight the differences in the gut microbiome between normal weight and obese dogs and prompt further research to improve animal health by modulating the gut microbiome.

The Fecal Microbiota of Dogs Switching to a Raw Diet Only Partially Converges to That of Wolves

The genomic signature of dog domestication reveals adaptation to a starch-rich diet compared with their ancestor wolves. Diet is a key element to shape gut microbial populations in a direct way as well as through coevolution with the host. We investigated the dynamics in the gut microbiota of dogs when shifting from a starch-rich, processed kibble diet to a nature-like raw meat diet, using wolves as a wild reference. Six healthy wolves from a local zoo and six healthy American Staffordshire Terriers were included. Dogs were fed the same commercial kibble diet for at least 3 months before sampling at day 0 (DC), and then switched to a raw meat diet (the same diet as the wolves) for 28 days. Samples from the dogs were collected at day 1 (DR1), week 1 (DR7), 2 (DR14), 3 (DR21), and 4 (DR28). The data showed that the microbial population of dogs switched from kibble diet to raw diet shifts the gut microbiota closer to that of wolves, yet still showing distinct differences. At phylum level, raw meat consumption increased the relative abundance of Fusobacteria and Bacteroidetes at DR1, DR7, DR14, and DR21 (q < 0.05) compared with DC, whereas no differences in these two phyla were observed between DC and DR28. At genus level, Faecalibacterium, Catenibacterium, Allisonella, and Megamonas were significantly lower in dogs consuming the raw diet from the first week onward and in wolves compared with dogs on the kibble diet. Linear discriminant analysis effect size (LEfSe) showed a higher abundance of Stenotrophomonas, Faecalibacterium, Megamonas, and Lactobacillus in dogs fed kibble diet compared with dogs fed raw diet for 28 days and wolves. In addition, wolves had greater unidentified Lachnospiraceae compared with dogs irrespective of the diets. These results suggested that carbohydrate-fermenting bacteria give way to protein fermenters when the diet is shifted from kibble to raw diet. In conclusion, some microbial phyla, families, and genera in dogs showed only temporary change upon dietary shift, whereas some microbial groups moved toward the microbial profile of wolves. These findings open the discussion on the extent of coevolution of the core microbiota of dogs throughout domestication.

Gut Microbiota Influence Lipid Metabolism of Skeletal Muscle in Pigs

Gut microbiota is recognized as a strong determinant of host physiology including fat metabolism and can transfer obesity-associated phenotypes from donors to recipients. However, the relationship between gut microbiota and intramuscular fat (IMF) is still largely unknown. Obese Jinhua pigs (JP) have better meat quality that is associated with higher IMF content than lean Landrace pigs (LP). The present study was conducted to test the contribution of gut microbiota to IMF properties by transplanting fecal microbiota of adult JP and LP to antibiotics-treated mice. Similar to JP donors, the mice receiving JP's microbiota (JM) had elevated lipid and triglyceride levels and the lipoprotein lipase activity, as well as reduced mRNA level of angiopoietin-like 4 (ANGPTL4) in the gastrocnemius muscles, compared to those in mice receiving LP's microbiota (LM). High-throughput 16S rRNA sequencing confirmed that transplantation of JP and LP feces differently reconstructed the gut microbiota in both jejunum and colon of mouse recipients. In colonic samples, we observed an elevated ratio of Firmicutes to Bacteroidetes and increased abundance of genus Romboutsia in JM, which were positively correlated with obesity. Furthermore, the abundance of Akkermansia decreased in JM, which is positively correlated with lean. Colonic concentrations of acetate (P = 0.047) and butyrate (P = 0.014) were significantly lower in JM than in LM, and consistently, the terminal genes for butyrate synthesis, butyryl CoA: acetate CoA transferase were less abundant in colonic microbiota of JM. Taken together, these gut microbiota of obese JP intrinsically promotes IMF accumulation and can transfer the properties to mouse recipients. Manipulation of intestinal microbiota will, therefore, have the potential to improve the meat quality and flavor of pigs and even to ameliorate the metabolic syndrome in human.

Identification of Enterotype and Its Effects on Intestinal Butyrate Production in Pigs

Simple Summary

Enterotype (ET) is defined based on different gut microbial community composition. It has been considered as a critical factor strongly associated with the porcine feed efficiency and growth characteristic. However, little is known about whether the ET clustering depends on the pig breeds and the effects of the different enterotypes on the butyrate metabolism in pigs. Therefore, we studied Jinhua pig’s enterotype by using 16S rRNA high throughput sequencing, and then analyzed the interaction between enterotype and butyrate production. Results showed that we identified three ETs driven by discriminative genera dominated by Lactobacillus, Clostridium sensu stricto 1, and Bacteroides, respectively. Significant differences in the fecal contents of butyrate production and butyrate-producing bacteria were observed among ETs. These findings present a first overview of the enterotypes clustering in Jinhua pigs and provide new insights into the relationship between the different ETs and intestinal butyrate production.

Abstract

Gut microbiota is thought to play a crucial role in nutrient digestion for pigs, especially in processing indigestible polysaccharides in the diets to produce short-chain fatty acids (SCFAs). However, the link between microbiota community structure and phenotypic performances are poorly understood. In the present study, the fecal samples of 105 Jinhua pigs at 105 days of age were clustered into three enterotypes (ETs, ET1, ET2, and ET3) that are subpopulations of distinct bacterial community composition by using 16S rRNA high throughput sequencing. The α-diversity indices (the OTU number and Shannon index) were significantly different among the ETs (p < 0.001). At the genus level, the ET1 group was over-represented by Lactobacillus (17.49%) and Clostridium sensu stricto 1 (11.78%), the ET2 group was over-represented by Clostridium sensu stricto 1 (17.49%) and Bifidobacterium (11.78%), and the ET3 group was over-represented by Bacteroides (18.17%). Significant differences in the fecal contents of butyrate were observed among ETs, with the highest level detected in ET3 and the lowest in ET2 (p < 0.05). Consistently, more copies of the terminal genes for butyrate synthesis, butyrate kinase (Buk) and butyryl coenzyme A (CoA): acetate CoA transferase (But) were detected by qPCR in the fecal samples of the ET3 group as compared to other two groups (p < 0.05). In addition, of the two genes, But was demonstrated to be more relevant to the butyrate content (R = 0.7464) than Buk (R = 0.4905) by correlation analysis. In addition, based on the taxonomic analysis, we found that Faecalibacterium was the most relevant butyrate-producing genera with fecal butyrate contents in Jinhua pigs, followed by Butyricicoccus, Eubacterium, Butyricimonas, Blautia, and Anaerostipes, all of which showed significantly higher richness in ET3 than as compared to ET1 and ET2 (p < 0.05). Collectively, this work presents a first overview of the enterotypes clustering in Jinhua pigs and will help to unravel the functional implications of ETs for the pig’s phenotypic performance and nutrient metabolism.

Effects of High-Fat Diet at Two Energetic Levels on Fecal Microbiota, Colonic Barrier, and Metabolic Parameters in Dogs

Increased consumption of energy-rich foods is a key factor in overweight, obesity, and associated metabolic disorders. This would be, at least in part, related to microbiota disturbance. In rodent models of obesity, microbiota disruption has been associated with alteration of the intestinal barrier, endotoxemia, inflammation grade, and insulin sensitivity. The aim of the present study was to assess the effects of a high-fat diet (HFD), fed at two energetic levels, on microbiota, intestinal barrier, and inflammatory and metabolic parameters in dogs. A HFD (33% fat as fed, 4,830 kcal/kg) was given to 24 healthy Beagle dogs at 100% (HF-100; n = 8) and at 150% (HF-150; n = 16) of their maintenance energy requirements for 8 weeks. Analysis of similarity revealed a significant difference in gut microbiota β-diversity following the diet compared to week 0 in both groups while α-diversity was lower only in the HF-150 group. Firmicutes/Bacteroidetes ratio was higher in the HF-150 group compared to the HF-100 group at weeks 2 and 8. A reduction in insulin sensitivity was observed over time in the HF150 group. Neither endotoxemia nor inflammation was observed in either group, did not find supporting data for the hypothesis that the microbiota is involved in the decline of insulin sensitivity through metabolic endotoxemia and low-grade inflammation. Colonic permeability was increased at week 4 in both groups and returned to initial levels at week 8, and was associated with modifications to the expression of genes involved in colonic barrier function. The increase in intestinal permeability may have been caused by the altered intestinal microbiota and increased expression of genes encoding tight junction proteins might indicate a compensatory mechanism to restore normal permeability. Although simultaneous changes to the microbiota, barrier permeability, inflammatory, and metabolic status have not been observed, such a causal link cannot be excluded in dogs overfed on a HFD. Further studies are necessary to better understand the link between HFD, intestinal microbiota and the host.

Decreases in Circulating Concentrations of Short-Chain Acylcarnitines are Associated with Systolic Function Improvement After Decompensated Heart Failure

Impaired fatty acid metabolism is associated with heart failure (HF) prognosis. However, specific changes in acylcarnitine profiles and their potential clinical value have not been well explored in patients recovering from acute decompensation.This study recruited 79 HF patients hospitalized because of acute decompensation with a left ventricular ejection fraction (LVEF) of < 40% and 51 normal controls. Patients were dichotomized into two groups, namely, the "improved (IMP) " and the "non-improved (NIMP) " groups, as defined by the changes in LVEF from baseline to 12 months after discharge. Mass spectrometry was used to quantify the acylcarnitine concentrations at baseline and 6 and 12 months after discharge. The IMP and NIMP groups contained 42 and 37 patients, respectively. At baseline, HF patients had higher plasma concentrations of specific long-, medium-, and short-chain acylcarnitines compared to normal controls. From baseline to 12 months post-discharge, the IMP group showed significant decreases in long- and short-chain acylcarnitine concentrations, but significant increases in medium-chain acylcarnitines. In the NIMP group, none of the acylcarnitines significantly decreased, and significant increases were noted in long-, medium-, and short-chain acylcarnitines. Generalized estimating equations demonstrated that nine acylcarnitines could discriminate the IMP group from the NIMP group, including three long-chain (C18:1, C16, and C16:1) and six short-chain acylcarnitines (C5, C5-OH, C4, C4:1-DC, C3, and C2). After adjusting for age, the six short-chain acylcarnitines remained significant. Changes in short-chain acylcarnitine profiles are independently associated with the improvement in cardiac systolic function after acute decompensation.

Varying Protein Levels Influence Metabolomics and the Gut Microbiome in Healthy Adult Dogs

The optimal ranges of protein for healthy adult dogs are not known. This study evaluated the impact of long-term consumption of foods containing low, medium, and high levels of protein on serum, urine, and fecal metabolites, and gut microbiome in beagles. Following maintenance on a prefeed food for 14 days, dogs (15 neutered males, 15 spayed females, aged 2–9 years, mean initial weight 11.3 kg) consumed the low (18.99%, dry matter basis), medium (25.34%), or high (45.77%) protein foods, each for 90 days, in a William’s Latin Square Design sequence. In serum and/or urine, metabolites associated with inflammation (9,10-dihydroxyoctadecanoic acid (DiHOME)), 12,13-DiHOME) and kidney dysfunction (urea, 5-hydroxyindole sulfate, 7-hydroxyindole sulfate, p-cresol sulfate) increased with higher protein levels in food, while one-carbon pathway metabolites (betaine, dimethylglycine, sarcosine) decreased. Fecal pH increased with protein consumed, and levels of beneficial indoles and short-chain fatty acids decreased while branched-chain fatty acids increased. Beta diversity of the fecal microbiome was significantly different, with increased abundances of proteolytic bacteria with higher protein food. Feeding dogs a high amount of protein leads to a shift to proteolytic gut bacteria, higher fecal pH, and is associated with increased levels of metabolites linked with inflammation and kidney dysfunction.

The canine gastrointestinal microbiota: early studies and research frontiers

The canine gut microbiota is a complex microbial population that is potentially related to metabolism, immunologic activity and gastrointestinal (GI) diseases. Early studies revealed that the canine gut microbiota was dynamic, and bacterial populations in the adjacent gut segments were similar, with anaerobes predominating. Metagenomics analysis revealed that nutrient contents in the diet modulated bacterial populations and metabolites in the canine gut. Further research revealed significant correlations between dietary factors and canine gut core microbiomes. Canine GI diseases are closely correlated with gut microbiota dysbiosis and metabolic disorders. Probiotic-related therapies can effectively treat canine GI diseases. Recent studies have revealed that the canine gut microbiota is similar to the human gut microbiota, and dietary factors affect both. Studying canine intestinal microorganisms enables clarifying changes in the canine intestinal bacteria under different conditions, simulating human diseases in dog models, and conducting in-depth studies of the interactions between intestinal bacteria and disease.

The Effects of Nutrition on the Gastrointestinal Microbiome of Cats and Dogs: Impact on Health and Disease

The gastrointestinal (GI) microbiome of cats and dogs is increasingly recognized as a metabolically active organ inextricably linked to pet health. Food serves as a substrate for the GI microbiome of cats and dogs and plays a significant role in defining the composition and metabolism of the GI microbiome. The microbiome, in turn, facilitates the host's nutrient digestion and the production of postbiotics, which are bacterially derived compounds that can influence pet health. Consequently, pet owners have a role in shaping the microbiome of cats and dogs through the food they choose to provide. Yet, a clear understanding of the impact these food choices have on the microbiome, and thus on the overall health of the pet, is lacking. Pet foods are formulated to contain the typical nutritional building blocks of carbohydrates, proteins, and fats, but increasingly include microbiome-targeted ingredients, such as prebiotics and probiotics. Each of these categories, as well as their relative proportions in food, can affect the composition and/or function of the microbiome. Accumulating evidence suggests that dietary components may impact not only GI disease, but also allergies, oral health, weight management, diabetes, and kidney disease through changes in the GI microbiome. Until recently, the focus of microbiome research was to characterize alterations in microbiome composition in disease states, while less research effort has been devoted to understanding how changes in nutrition can influence pet health by modifying the microbiome function. This review summarizes the impact of pet food nutritional components on the composition and function of the microbiome and examines evidence for the role of nutrition in impacting host health through the microbiome in a variety of disease states. Understanding how nutrition can modulate GI microbiome composition and function may reveal new avenues for enhancing the health and resilience of cats and dogs.

Microbial Community and Short-Chain Fatty Acid Mapping in the Intestinal Tract of Quail

Simple Summary

Quail is an economically important type of poultry, valued for its high meat quality and abundant egg nutrition. It is also an important laboratory research animal, widely used in developmental biology and toxicology tests. Since the gut microbiota plays a vital role in the host’s growth and health, we investigated the microbiota inhabiting the duodenum, jejunum, ileum, cecum, and colorectum of quail in the present study, using 16S rRNA gene sequencing and qPCR. The concentrations of short-chain fatty acids (SCFAs) were evaluated using gas chromatography. We found that the microbiota in the cecum was different from other intestinal sections and the enriched inhabitants of SCFA-producing bacterial genera made cecum the core locations of SCFA production in quail. The results of this study will provide fundamental data for further quail microbiology and functional studies.

Abstract

Quail is raised throughout China for egg and meat production. To deeply understand the gastrointestinal microbial composition and metabolites of quail, the present study characterized the microbiota inhabiting five intestinal locations of eight-week-old quail using 16S rRNA gene sequencing and qPCR, and evaluated the concentrations of short-chain fatty acids (SCFAs) in each individual location using gas chromatography. The results showed that Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Deferribacteres were the five most abundant phyla in the intestinal tract of quail. Firmicutes was largely dominant (>95%) in the small intestine, whereas Bacteroidetes increased significantly in the cecum (19.19%) and colorectum (8.09%). At the genus level, Lactobacillus was predominant in almost all sections (>50%) except in the cecum (7.26%), where Megamonas, Faecalibacterium, and Bacteroides were dominant. qPCR data indicated that the population sizes of both the total bacteria and proportions of the Firmicutes, Bacteroidetes, and Bacteroides group increased going from the proximal toward the distal end of the intestine in quail. The SCFA-producing bacterial genera Bacteroides, Faecalibacterium, Alistipes, Blautia, Parabacteroides, and Clostridium were of higher richness in the cecum and colorectum, where, accordingly, more SCFAs were produced. These findings will be helpful for the future study of quail microbiology, as well as its relationship with productive performance and health.

Biogeography of microbiome and short-chain fatty acids in the gastrointestinal tract of duck

It is generally accepted that domestic ducks are valuable protein sources for humans. The gastrointestinal ecosystem contains enormous and complicated microbes that have a profound effect on the nutrition, immunity, health, and production of domestic ducks. To deeply understand the gastrointestinal microbial composition of domestic ducks, we investigated the microbiomes of 7 different gastrointestinal locations (proventriculus, gizzard, duodenum, jejunum, ileum, cecum, and rectum) and the short-chain fatty acids in 15 healthy muscovy ducks based on 16S rRNA gene sequencing, qPCR, and gas chromatography. As a result, 1 029 735 sequences were identified into 35 phyla and 359 genera. Firmicutes, Proteobacteria, Bacteroidetes, Cyanobacteria, and Actinobacteria were the major phyla, with Bacteroidetes being most abundant in the cecum. The population of the total bacteria and the representatives of the Firmicutes, Bacteroidetes, and Bacteroides groups increased from the proximal to the distal part of the GIT. Bacteroides was the most dominant group in the cecum. Acetate, propionate, and butytrate, as well as gene copies of butyryl-CoA including acetate-CoA transferase and butyrate kinase, were significantly higher in cecum than in other sections. Isobutyrate, valerate, and isovalerate were only found in the cecum. The differences of microbial composition and the short-chain fatty acids of their metabolites among these 7 intestinal locations might be correlated with differences in gut function. All these results provide a reference for the duck gastrointestinal microbiome and a foundation for understanding the types of bacteria that promote health and enhance growth performance and decrease instances of disease in duck breeding.

Akkermansia and Microbial Degradation of Mucus in Cats and Dogs: Implications to the Growing Worldwide Epidemic of Pet Obesity

Akkermansia muciniphila is a mucin-degrading bacterium that has shown the potential to provide anti-inflammatory and anti-obesity effects in mouse and man. We here focus on companion animals, specifically cats and dogs, and evaluate the microbial degradation of mucus and its health impact in the context of the worldwide epidemic of pet obesity. A literature survey revealed that the two presently known Akkermansia spp., A. muciniphila and A. glycaniphila, as well as other members of the phylum of Verrucomicrobia seem to be neither very prevalent nor abundant in the digestive tract of cats and dog. While this may be due to methodological aspects, it suggests that bacteria related to Akkermansia are not the major mucus degraders in these pets and hence other mucus-utilizing taxa may deserve attention. Hence, we will discuss the potential of these endogenous mucus utilizers and dietary interventions to boost these as well as the use of Akkermansia spp. related bacteria or their components as strategies to target feline and canine obesity.

Diagnosis of Feline Food Sensitivity and Intolerance Using Saliva: 1000 Cases

This prospective study assessed the efficacy of a novel saliva-based immunoassay of IgA- and IgM-antibodies in predicting feline food sensitivities and intolerances. Clinical samples were obtained from 1000 cats proven or suspected to have food intolerances. Most were of domestic shorthair breed type, over 10 years of age, and weighed around 5 kg; they were equally distributed between spayed females and neutered males. Saliva was collected after at least an 8-h fast with a dental cotton rope, placed in a double-sleeved saliva collection tube, and sent to the laboratory. Salivary antibodies elicited by 24 common foods were measured with goat anti-canine IgA and IgM. Low reacting foods were lamb, cow milk, pork, turkey, wheat (lowest) and white-colored fish, whereas high reacting foods were millet, white potato, rice (highest) and salmon. Thus, the novel salivary-based food sensitivity and intolerance test, described previously for canines, also provided a reliable and clinically predictive alternative to food elimination trials, serum-based food allergy testing, and skin patch testing in cats. Manufacturers of commercial cat foods and treats, as well as those making homemade diets and treats for cats, should consider avoiding the more highly reactive foods as determined by the present study.

Plasma metabolomics reveals lower carnitine concentrations in overweight Labrador Retriever dogs

Background

The prevalence of overweight is increasing in dogs, but the metabolic events related to this condition are still poorly understood. The purpose of the study was to investigate the postprandial response of plasma metabolites using a meal-challenge test and to identify metabolic variations related to spontaneous overweightness in privately owned dogs.

Results

Twenty-eight healthy male intact Labrador Retriever dogs were included, 12 of which were classified as lean (body condition score (BCS) 4–5 on a 9-point scale) and 16 as overweight (BCS 6–8). After an overnight fast (14–17 h), blood samples were collected and dogs were thereafter fed a high-fat meal. Postprandial blood samples were collected hourly four times. Plasma metabolites were identified by nuclear magnetic resonance. Postprandial metabolomes differed from the fasting metabolome in multivariate discriminant analysis (PLS-DA: Q²Y = 0.31–0.63, cross-validated ANOVA: P ≤ 0.00014) Eleven metabolites, all amino acids, contributed to the separations. Carnitine was identified as a metabolite related to overweight (stepwise logistic regression analysis P ≤ 0.03) and overweight dogs had overall lower carnitine response (mixed model repeated measures analysis P = 0.005) than lean dogs. Notably, mean fasting carnitine concentration in overweight dogs (9.4 ± 4.2 µM) was close to a proposed reference limit for carnitine insufficiency.

Conclusions

A postprandial amino acid response was detected but no time-dependent variations with regards to body condition groups were found. Lower carnitine concentrations were found in overweight compared to lean dogs. The latter finding could indicate a carnitine insufficiency related to spontaneous adiposity and altered lipid metabolism in overweight dogs in this cohort of otherwise healthy Labrador Retrievers.

Electronic supplementary material

The online version of this article (10.1186/s13028-019-0446-4) contains supplementary material, which is available to authorized users.