A Longitudinal Study of the Feline Faecal Microbiome Identifies Changes into Early Adulthood Irrespective of Sexual Development

Gut microbiota in cats with inflammatory bowel disease and low-grade intestinal T-cell lymphoma

In cats and humans, several physiological and environmental factors have been shown to alter the gut microbiota of healthy individuals. Cats share several diseases with humans such as inflammatory bowel diseases and low-grade intestinal T-cell lymphoma. The physiopathology of these chronic enteropathies is poorly understood but may involve disequilibrium of the gut microbiota composition and disruption of normal microbiome activity profiles. These disorders are increasingly diagnosed in the feline species due to improved medicalization and easier access to endoscopy in veterinary practice. This review addresses the current data on the gut microbiota of cats in health and in chronic enteropathies. Such functional analysis will help the advancement of innovative diagnostic tools and targeted therapeutic strategies.

Collaborative Metabolism: Gut Microbes Play a Key Role in Canine and Feline Bile Acid Metabolism

Bile acids, produced by the liver and secreted into the gastrointestinal tract, are dynamic molecules capable of impacting the overall health of dogs and cats in many contexts. Importantly, the gut microbiota metabolizes host primary bile acids into chemically distinct secondary bile acids. This review explores the emergence of new literature connecting microbial-derived bile acid metabolism to canine and feline health and disease. Moreover, this review highlights multi-omic methodologies for translational research as an area for continued growth in veterinary medicine aimed at accelerating microbiome science and medicine as it pertains to bile acid metabolism in dogs and cats.

Validation of method for faecal sampling in cats and dogs for faecal microbiome analysis

BACKGROUND

Reproducible and reliable studies of cat and dog faecal microbiomes are dependent on many methodology-based variables including how the faecal stools are sampled and stored prior to processing. The current study aimed to establish an appropriate method for sampling and storing faecal stools from cats and dogs which may also be applied to privately-owned pets. The approach investigated the effects of storing faeces for up to 12 h at room temperature and sampling from various locations within the stool in terms of microbial diversity, relative taxa abundances and DNA yield. Faeces were collected from 10 healthy cats and 10 healthy dogs and stored at room temperature (20 °C). Samples were taken from various locations within the stool (the first emitted part (i), the middle (ii) and the last emitted end (iii), at either surface or core) at 0, 0.5, 1, 2, 3, 6 and 12 h, stabilised and stored at -80 °C. DNA was extracted from all samples, using Illumina NovaSeq.

RESULTS

Faecal bacterial composition of dogs and cats shown no statistically significant differences in alpha diversity. Bacteroidetes, Firmicutes, Proteobacteria and Actinobacteria were the most prevalent phyla. Cat and dog samples were characterized by a dominance of Prevotella, and a lack of Fusobacterium in feline stools. Room temperature storage of cat and dog faecal samples generally had no significant effect on alpha diversity, relative taxa abundance or DNA yield for up to 12 h. Sampling from regions i, ii or iii of the stool at the surface or core did not significantly influence the outcome. However, surface cat faecal samples stored at room temperature for 12 h showed a significant increase in two measures of alpha diversity and there was a tendency for a similar effect in dogs. When comparing samples with beta diversity measures, it appeared that for dog and cat samples, individual effect has the strongest impact on the observed microbial diversity (R2 0.64 and 0.88), whereas sampling time, depth and horizontal locations significantly affected the microbial diversity but with less impact.

CONCLUSION

Cat and dog faeces were stable at room temperature for up to 12 h, with no significant changes in alpha diversity, relative taxa abundance and DNA concentration. Beta diversity analysis demonstrated that despite an impact of the sampling storing time and the surface of the sampling, we preserved the identity of the microbial structure linked to the individual. Finally, the data suggest that faecal stools stored for > 6 h at room temperature should be sampled at the core, not the surface.

Impact of Early Weaning on Development of the Swine Gut Microbiome

Considering that pigs are naturally weaned between 12 and 18 weeks of age, the common practice in the modern swine industry of weaning as early as between two and four weeks of age increases challenges during this transition period. Indeed, young pigs with an immature gut are suddenly separated from the sow, switched from milk to a diet consisting of only solid ingredients, and subjected to a new social hierarchy from mixing multiple litters. From the perspective of host gut development, weaning under these conditions causes a regression in histological structure as well as in digestive and barrier functions. While the gut is the main center of immunity in mature animals, the underdeveloped gut of early weaned pigs has yet to contribute to this function until seven weeks of age. The gut microbiota or microbiome, an essential contributor to the health and nutrition of their animal host, undergoes dramatic alterations during this transition, and this descriptive review aims to present a microbial ecology-based perspective on these events. Indeed, as gut microbial communities are dependent on cross-feeding relationships, the change in substrate availability triggers a cascade of succession events until a stable composition is reached. During this process, the gut microbiota is unstable and prone to dysbiosis, which can devolve into a diseased state. One potential strategy to accelerate maturation of the gut microbiome would be to identify microbial species that are critical to mature swine gut microbiomes, and develop strategies to facilitate their establishment in early post-weaning microbial communities.

Comparison of the Effects of Enzymolysis Seaweed Powder and Saccharomyces boulardii on Intestinal Health and Microbiota Composition in Kittens

Kittens are prone to intestinal health problems as their intestines are not completely developed. Seaweed is rich in plant polysaccharides and bioactive substances that are highly beneficial to gut health. However, the effects of seaweed on cat gut health have not been assessed. This study compared the effects of dietary supplementation with enzymolysis seaweed powder and Saccharomyces boulardii on the intestinal health of kittens. In total, 30 Ragdoll kittens (age: 6 months; weight: 1.50 ± 0.29 kg) were assigned to three treatment groups for a 4-week feeding trial. The dietary treatment given was as follows: (1) basal diet (CON); (2) CON + enzymolysis seaweed powder (20 g/kg of feed) mixed evenly with the diet (SE); and (3) CON + Saccharomyces boulardii (2 × 10¹⁰ CFU/kg of feed) mixed evenly with the diet (SB). Compared with the CON and SB groups, dietary supplementation with the enzymolysis seaweed powder improved the immune and antioxidant capacity and also reduced the intestinal permeability and inflammation levels of kittens. The relative abundance of Bacteroidetes, Lachnospiraceae, Prevotellaceae, and Faecalibacterium in the SE group was higher than those in the CON and SB groups (p ≤ 0.05), while the relative abundance of Desulfobacterota, Sutterellaceae, and Erysipelatoclostridium in the SB group was lower than that in the SE group (p ≤ 0.05). Moreover, enzymolysis seaweed powder did not alter the level of intestinal SCFAs in kittens. Conclusively, supplementing kitten diet with enzymolysis seaweed powder can promote intestinal health by enhancing the gut barrier function and optimizing the microbiota composition. Our findings provide new perspectives on the application of enzymolysis seaweed powder.

Yeast Cell Wall Compounds on The Formation of Fermentation Products and Fecal Microbiota in Cats: An In Vivo and In Vitro Approach

The effects of yeast cell wall compounds (YCWs) being added to cat food on hindgut fermentation metabolites and fecal microbiota were assessed in in vivo Experiment 1 (Exp. 1) and in vitro Experiments 2 and 3 (Exp. 2 and 3). In Exp. 1, the cats' diets were supplemented with two dietary concentrations (46.2 and 92.4 ppm) of YCWs (YCW-15 and YCW-30, respectively), and a negative control diet with no compound in three groups (six cats per group) was used to assess the fecal score, pH, digestibility, fermentation products, and microbiota. In Exp. 2, feces from the cats that were not supplemented with YCWs (control) were used as an inoculum. A blend of pectin, amino acids, and cellulose was used as a substrate, and the YCW compound was added at two levels (5 and 10 mg). In Exp. 3, feces from cats fed YCWs were used as an inoculum to test three different substrates (pectin, amino acids, and cellulose). In Exp. 2 and 3, the gas production, pH, and fermentation products (ammonia, SCFAs, and BCFAs) were assessed. YCW-30 resulted in a higher digestibility coefficient of the crude protein, organic matter (OM) (p < 0.05), and energy of the diet (p < 0.10). Regarding the fermentation products, YCW-15 showed a trend toward higher concentrations of propionate, acetate, lactate, ammonia, isobutyrate, and valerate, while YCW-30 showed a trend (p < 0.10) toward higher levels of butyrate and pH values. The bacteroidia class and the genus Prevotella were increased by using YCW-30 and the control. At the gender level, decreased (p < 0.01) Megasphaera was observed with YCW inclusion. The microbiota differed (p < 0.01) among the groups in their Shannon indexes. For beta diversity, YCW-30 showed higher indexes (p = 0.008) than the control. The microbiota metabolic profile differed in the pathway CENTFERM-PWY; it was more expressed in YCW-30 compared to the control. In Exp. 2, the YCWs showed a higher ratio (p = 0.006) of the fermentation products in the treatments with additives with a trend towards a high dose of the additive (10 mg). In Exp. 3, the effects of the substrates (p < 0.001), but not of the YCWs, on the fermentation products were observed, perhaps due to the low dietary concentrations we used. However, the marked responses of the fermentation products to the substrates validated the methodology. We could conclude that the YCWs, even at low dietary concentrations, affected fecal SCFA production, reduced the fecal pH, and modulated the fecal microbiota in the cats. These responses were more pronounced under in vitro conditions.

Effects of weight loss and feeding specially formulated diets on the body composition, blood metabolite profiles, voluntary physical activity, and fecal metabolites and microbiota of overweight cats

Feline obesity is a common and preventable disease, posing a myriad of health risks and detriments. Specially formulated diets and restricted feeding may serve as an intervention strategy to promote weight loss and improve feline health. In this study, our objective was to determine the effects of restricted feeding and weight loss on body composition, voluntary physical activity, blood hormones and metabolites, and fecal microbiota of overweight cats. Twenty-two overweight adult spayed female and neutered male cats [body weight (BW) = 5.70 ± 1.0 kg; body condition score (BCS) = 7.68 ± 0.6; age = 4 ± 0.4 yr] were used in a weight loss study. A control diet (OR) was fed during a 4-wk baseline to identify intake needed to maintain BW. After baseline (week 0), cats were allotted to OR or a test diet (FT) and fed to lose ~1.0% BW/wk for 24 wk. At baseline and 6, 12, 18, and 24 wk after weight loss, dual-energy x-ray absorptiometry scans were performed and blood samples were collected. Voluntary physical activity was measured at weeks 0, 8, 16, and 24. Fecal samples were collected at weeks 0, 4, 8, 12, 16, 20, and 24. Change from baseline data were analyzed statistically using the Mixed Models procedure of SAS, with P < 0.05 considered significant. Restricted feeding of both diets led to weight and fat mass loss, lower BCS, and lower blood triglyceride and leptin concentrations. Cats fed the FT diet had a greater reduction in blood triglycerides and cholesterol than cats fed the OR diet. Restricted feeding and weight loss reduced fecal short-chain fatty acid, branched-chain fatty acid, phenol, and indole concentrations. Fecal valerate concentrations were affected by diet, with cats fed the OR diet having a greater reduction than those fed the FT diet. Fecal bacterial alpha diversity was not affected, but fecal bacterial beta diversity analysis showed clustering by diet. Restricted feeding and weight loss affected relative abundances of 7 fecal bacterial genera, while dietary intervention affected change from baseline relative abundances of 2 fecal bacterial phyla and 20 fecal bacterial genera. Our data demonstrate that restricted feeding promoted controlled and safe weight and fat loss, reduced blood lipids and leptin concentrations, and shifted fecal metabolites and microbiota. Some changes were also impacted by diet, highlighting the importance of ingredient and nutrient composition in weight loss diets.

Environmental risk factors in puppies and kittens for developing chronic disorders in adulthood: A call for research on developmental programming

Many dogs and cats are affected by chronic diseases that significantly impact their health and welfare and relationships with humans. Some of these diseases can be challenging to treat, and a better understanding of early-life risk factors for diseases occurring in adulthood is key to improving preventive veterinary care and husbandry practices. This article reviews early-life risk factors for obesity and chronic enteropathy, and for chronic behavioral problems, which can also be intractable with life-changing consequences. Aspects of early life in puppies and kittens that can impact the risk of adult disorders include maternal nutrition, establishment of the gut microbiome, maternal behavior, weaning, nutrition during growth, growth rate, socialization with conspecifics and humans, rehoming and neutering. Despite evidence in some species that the disorders reviewed here reflect the developmental origins of health and disease (DOHaD), developmental programming has rarely been studied in dogs and cats. Priorities and strategies to increase knowledge of early-life risk factors and DOHaD in dogs and cats are discussed. Critical windows of development are proposed: preconception, gestation, the suckling period, early growth pre-neutering or pre-puberty, and growth post-neutering or post-puberty to adult size, the durations of which depend upon species and breed. Challenges to DOHaD research in these species include a large number of breeds with wide genetic and phenotypic variability, and the existence of many mixed-breed individuals. Moreover, difficulties in conducting prospective lifelong cohort studies are exacerbated by discontinuity in pet husbandry between breeders and subsequent owners, and by the dispersed nature of pet ownership.

Randomized placebo-controlled trial of feline-origin Enterococcus hirae probiotic effects on preventative health and fecal microbiota composition of fostered shelter kittens

Introduction

Diarrhea is the second most common cause of mortality in shelter kittens. Studies examining prevention strategies in this population are lacking. Probiotics are of particular interest but studies in cats are largely limited to healthy adults or those with induced disease. Only one study in domestic cats describes the use of host-derived bacteria as a probiotic. We previously identified Enterococcus hirae as a dominant species colonizing the small intestinal mucosa in healthy shelter kittens. Oral administration of a probiotic formulation of kitten-origin E. hirae (strain 1002-2) mitigated the increase in intestinal permeability and fecal water loss resulting from experimental enteropathogenic E. coli infection in purpose-bred kittens. Based on these findings, we hypothesized that administration of kitten-origin E. hirae to weaned fostered shelter kittens could provide a measurable preventative health benefit.

Methods

We conducted a randomized, placebo-controlled, blinded clinical trial to determine the impact of a freeze-dried E. hirae probiotic on body weight gain, incidence of diarrhea, carriage of potential diarrheal pathogens, and composition of the intestinal microbiota in weaned fostered shelter kittens.

Results

One-hundred thirty kittens completed the study. Fifty-eight kittens received the probiotic and 72 received the placebo. There were no significant differences in age, weight upon initiation of the study, number of days in the study, average daily gain in body weight, or weight at completion of the study. Kittens treated with E. hirae were 3.4 times less likely to develop diarrhea compared to kittens treated with placebo (odds ratio = 0.294, 95% CI 0.109-0.792, p = 0.022). A significant impact of E. hirae was not observed on the presence or abundance of 30 different bacterial, viral, protozoal, fungal, algal, and parasitic agents in feces examined by qPCR. With exception to a decrease in Megamonas, administration of the E. hirae probiotic did not alter the predominant bacterial phyla present in feces based on 16S rRNA gene amplicon sequencing.

Discussion

Decreased incidence of diarrhea associated with preventative administration of E. hirae to foster kittens supports a rationale for use of E. hirae for disease prevention in this young population at high risk for intestinal disease though additional studies are warranted.

The Kitty Microbiome Project: Defining the Healthy Fecal "Core Microbiome" in Pet Domestic Cats

Here, we present a taxonomically defined fecal microbiome dataset for healthy domestic cats (Felis catus) fed a range of commercial diets. We used this healthy reference dataset to explore how age, diet, and living environment correlate with fecal microbiome composition. Thirty core bacterial genera were identified. Prevotella, Bacteroides, Collinsella, Blautia, and Megasphaera were the most abundant, and Bacteroides, Blautia, Lachnoclostridium, Sutterella, and Ruminococcus gnavus were the most prevalent. While community composition remained relatively stable across different age classes, the number of core taxa present decreased significantly with age. Fecal microbiome composition varied with host diet type. Cats fed kibble had a slightly, but significantly greater number of core taxa compared to cats not fed any kibble. The core microbiomes of cats fed some raw food contained taxa not as highly prevalent or abundant as cats fed diets that included kibble. Living environment also had a large effect on fecal microbiome composition. Cats living in homes differed significantly from those in shelters and had a greater portion of their microbiomes represented by core taxa. Collectively our work reinforces the findings that age, diet, and living environment are important factors to consider when defining a core microbiome in a population.

The Faecal Microbiome of the Wild European Badger Meles meles: A Comparison Against Other Wild Omnivorous Mammals from Across the Globe

Here we investigate the faecal microbiome of wild European badgers Meles meles using samples collected at post-mortem as part of the All Wales Badger Found Dead study. This is the first published characterisation of the badger microbiome. We initially undertook a sex-matched age comparison between the adult and cub microbiomes, based on sequencing the V3–V4 region of the 16S rRNA gene. Analysis used the QIIME 2 pipeline utilising DADA2 and the Silva database for taxonomy assignment. Fusobacteria appeared to be more abundant in the microbiomes of the cubs than the adults although no significant difference was seen in alpha or beta diversity between the adult and cub badger microbiomes. Comparisons were also made against other wild, omnivorous, mammals’ faecal microbiomes using publicly available data. Significant differences were seen in both alpha and beta diversity between the microbiomes from different species. As a wildlife species of interest to the disease bovine tuberculosis, knowledge of the faecal microbiome could assist in identification of infected badgers. Our work here suggests that, if comparisons were made between the faeces of bTB infected and non-infected badgers, age may not have a significant impact on the microbiome.

The Resemblance between Bacterial Gut Colonization in Pigs and Humans

Thorough understanding of the initial colonization process of human intestines is important to optimize the prevention of microbiota-associated diseases, and also to further improve the current microbial therapies. In recent years, therefore, colonization of the human gut has gained renewed interest. However, due to a lack of standardization of life events that might influence this early colonization process in humans, many generally accepted insights are based on deduction and assumption. In our review, we compare knowledge on colonization in humans with research in piglets, because the intestinal tract of pigs is remarkably similar to that of humans and the early-life events are more standardized. We assess potential similarities and challenge some concepts that have been widely accepted in human microbiota research. Bacterial colonization of the human gut is characterized by successive waves in a progressive process, to a complex gut microbiota community. After re-analyzing available data from piglets, we found that the bacterial colonization process is very similar in terms of the wave sequence and functionality of each wave. Moreover, based on the piglet data, we found that, in addition to external factors such as suckling and nutrition, the bacterial community itself appears to have a major influence on the colonization success of additional bacteria in the intestine. Thus, the colonization process in piglets might rely, at least in part, on niche dependency, an ecological principle to be considered in the intestinal colonization process in humans.

The fascinating microbes and their impact on neonatal dogs and cats - A review

Recent literature data indicate that canine and feline neonates are not born in a sterile environment as it was stated previously. The acquisition, colonisation and maintenance of the early life microbiota of healthy fetuses is a rapidly developing research area. In humans, the natural healthy infant microbiome plays an essential role in health and its assembly is determined by the maternal-offspring exchanges of microbes. Even though this topic is becoming more and more important in dogs and cats, the exact role of the neonatal microbiome is not yet fully known in animals. This review summarises the current knowledge of the normal physiological neonatal microbiome in healthy puppies and kittens.

Mutual Links between the Endocannabinoidome and the Gut Microbiome, with Special Reference to Companion Animals: A Nutritional Viewpoint

There is growing evidence that perturbation of the gut microbiome, known as “dysbiosis”, is associated with the pathogenesis of human and veterinary diseases that are not restricted to the gastrointestinal tract. In this regard, recent studies have demonstrated that dysbiosis is linked to the pathogenesis of central neuroinflammatory disorders, supporting the existence of the so-called microbiome-gut-brain axis. The endocannabinoid system is a recently recognized lipid signaling system and termed endocannabinoidome monitoring a variety of body responses. Accumulating evidence demonstrates that a profound link exists between the gut microbiome and the endocannabinoidome, with mutual interactions controlling intestinal homeostasis, energy metabolism and neuroinflammatory responses during physiological conditions. In the present review, we summarize the latest data on the microbiome-endocannabinoidome mutual link in health and disease, focalizing the attention on gut dysbiosis and/or altered endocannabinoidome tone that may distort the bidirectional crosstalk between these two complex systems, thus leading to gastrointestinal and metabolic diseases (e.g., idiopathic inflammation, chronic enteropathies and obesity) as well as neuroinflammatory disorders (e.g., neuropathic pain and depression). We also briefly discuss the novel possible dietary interventions based not only on probiotics and/or prebiotics, but also, and most importantly, on endocannabinoid-like modulators (e.g., palmitoylethanolamide) for intestinal health and beyond.

The Serum and Fecal Metabolomic Profiles of Growing Kittens Treated with Amoxicillin/Clavulanic Acid or Doxycycline

Simple Summary

This study investigated the impact of antibiotic treatment οn the serum and fecal metabolome (the collection of all small molecules produced by the gut bacteria and the host) of young cats. Thirty 2-month-old cats with an upper respiratory tract infection were treated with either amoxicillin/clavulanic acid for 20 days or doxycycline for 28 days. In addition, another 15 control cats that did not receive antibiotics were included. Blood was collected on days 0 (before treatment), 20/28 (last day of treatment), and 300 (10 months after the end of treatment), while feces were collected on days 0, 20/28, 60, 120, and 300. Seven serum and fecal metabolites differed between cats treated with antibiotics and control cats at the end of treatment period. Ten months after treatment, no metabolites differed from healthy cats, suggesting that amoxicillin/clavulanic acid or doxycycline treatment only temporarily affects the abundance of the serum and fecal metabolome.

Abstract

The long-term impact of antibiotics on the serum and fecal metabolome of kittens has not yet been investigated. Therefore, the objective of this study was to evaluate the serum and fecal metabolome of kittens with an upper respiratory tract infection (URTI) before, during, and after antibiotic treatment and compare it with that of healthy control cats. Thirty 2-month-old cats with a URTI were randomly assigned to receive either amoxicillin/clavulanic acid for 20 days or doxycycline for 28 days, and 15 cats of similar age were enrolled as controls. Fecal samples were collected on days 0, 20/28, 60, 120, and 300, while serum was collected on days 0, 20/28, and 300. Untargeted and targeted metabolomic analyses were performed on both serum and fecal samples. Seven metabolites differed significantly in antibiotic-treated cats compared to controls on day 20/28, with two differing on day 60, and two on day 120. Alterations in the pattern of serum amino acids, antioxidants, purines, and pyrimidines, as well as fecal bile acids, sterols, and fatty acids, were observed in antibiotic-treated groups that were not observed in control cats. However, the alterations caused by either amoxicillin/clavulanic acid or doxycycline of the fecal and serum metabolome were only temporary and were resolved by 10 months after their withdrawal.

Short- and long-term effects of amoxicillin/clavulanic acid or doxycycline on the gastrointestinal microbiome of growing cats

Antibiotic treatment in early life influences gastrointestinal (GI) microbial composition and function. In humans, the resultant intestinal dysbiosis is associated with an increased risk for certain diseases later in life. The objective of this study was to determine the temporal effects of antibiotic treatment on the GI microbiome of young cats. Fecal samples were collected from cats randomly allocated to receive either amoxicillin/clavulanic acid (20 mg/kg q12h) for 20 days (AMC group; 15 cats) or doxycycline (10 mg/kg q24h) for 28 days (DOX group;15 cats) as part of the standard treatment of upper respiratory tract infection. In addition, feces were collected from healthy control cats (CON group;15 cats). All cats were approximately two months of age at enrolment. Samples were collected on days 0 (baseline), 20 or 28 (AMC and DOX, respectively; last day of treatment), 60, 120, and 300. DNA was extracted and sequencing of the 16S rRNA gene and qPCR assays were performed. Fecal microbial composition was different on the last day of treatment for AMC cats, and 1 month after the end of antibiotic treatment for DOX cats, compared to CON cats. Species richness was significantly greater in DOX cats compared to CON cats on the last day of treatment. Abundance of Enterobacteriales was increased, and that of Erysipelotrichi was decreased in cats of the AMC group on the last day of treatment compared to CON cats. The abundance of the phylum Proteobacteria was increased in cats of the DOX group on days 60 and 120 compared to cats of the CON group. Only minor differences in abundances between the treatment groups and the control group were present on day 300. Both antibiotics appear to delay the developmental progression of the microbiome, and this effect is more profound during treatment with amoxicillin/clavulanic acid and one month after treatment with doxycycline. Future studies are required to determine if these changes influence microbiome function and whether they have possible effects on disease susceptibility in cats.

Developmental intestinal microbiome alterations in canine fading puppy syndrome: a prospective observational study

Fading puppy syndrome (FPS) is a fatal condition in neonatal dogs. Intestinal microbial alterations, although never investigated, may be involved in its pathophysiology. The study examined the occurrence of FPS and its associations with dam, puppy, and husbandry characteristics, compared the intestinal microbial diversity of healthy puppies and those with FPS, and examined whether intestinal microbiomes are predictive of FPS. Day 1 and 8 post-partum (PP) rectal swabs were collected from healthy puppies and puppies which later developed FPS. Microbial compositional structure, including alpha and beta diversities and relative abundance of specific taxa were compared between groups, and microbial data was applied to a machine-learning model to assess the predictive performance of microbial indices of FPS or death. FPS occurred in 22/165 puppies (13%), with a 100% mortality rate. FPS was associated (P < 0.001) with decreased Day 1 PP puppy activity. Day 1 (P = 0.003) and 8 (P = 0.005) PP rectal beta diversities were different in puppies with FPS vs healthy ones. Increased Proteobacteria/Firmicutes ratio, increased relative abundance of Pasteurellaceae, and decreased relative abundance of Clostridia and Enterococcus were associated with FPS. A machine-learning model showed that Day 1 PP rectal microbiome composition accurately predicted FPS-related death. We found that specific rectal microbial phenotypes are associated with FPS, reflecting the significant role of microbiome alterations in this phenomenon. These findings may serve as useful microbial indices for early diagnosis of puppies at risk of FPS and may provide specific therapeutic targets.

White and Red Sorghum as Primary Carbohydrate Sources in Extruded Diets of Felines

The research objectives were to evaluate the effect of dietary supplementation of white (WSH) and red (RSH) sorghum grains on gastrointestinal health of felines through the determination of apparent total tract macronutrient digestibility (ATTD), fecal characteristics, fermentative end-products, and microbiota, compared with a traditional corn-based diet. We hypothesize that inclusion of RSH and WSH, respectively, would be well-accepted by cats, and the RSH and WSH diets would be comparable to corn when added as the main carbohydrate source in extruded diets. Three diets containing 30% corn, 30% WSH, or 30% RSH were formulated to meet or exceed the AAFCO (2018) nutrient profiles for cats during growth. Nine male cats (0.8 ± 0.00 yr) were randomly assigned to one of the three dietary treatments using a triplicated 3 × 3 Latin square design. Experimental periods consisted of 14 d (10 d of diet adaption and 4 d of total and fresh fecal collections). The ATTD of dry matter (DM) did not differ amongst treatments, organic matter was greatest (P < 0.05) for both sorghum diets (86.4%) and lowest for the corn diet (84.2%), crude protein was comparable among diets ranging from 84.5 to 86.6%, acid hydrolyzed fat was high among diets varying between 91.4 and 92.8%, and total dietary fiber was greatest (P < 0.05) for the WSH diet (56.0%) with the corn diet being lowest (44.7%). Digestible energy was greatest (P < 0.05) for the WSH diet (4.66 kcal/g) and lowest for the corn diet (4.54 kcal/g), with the RSH diet being intermediate (4.64; P > 0.05). Fecal pH (6.3–6.5) and most fecal metabolites did not differ among diets except for phenol/indole concentrations that were significantly lower (P < 0.05) in cats fed the RSH diet (1.5 μmole/g DM) than for cats fed the corn diet (2.1 μmole/g DM). Bacteroidetes, Firmicutes, Fusobacteria, and Proteobacteria were the major phyla observed in the microbiota of feces of cats fed the three experimental diets, with no differences seen amongst all treatments. Data indicate that dietary supplementation of these varieties of WSH and RSH as carbohydrate sources were well-tolerated by the cat.

Supplemental selenium source on gut health: insights on fecal microbiome and fermentation products of growing puppies

Selenium is an essential trace element that can modulate the gut microbiome with an impact on host health. The present study aimed to evaluate the effects of organic (selenium-enriched yeast) vs inorganic (sodium selenite) selenium source on fecal end-fermentation products and gut microbiome of puppies from 20 to 52 weeks of age. Alpha and beta diversity of the gut bacterial community were affected by age but not by gender or selenium source. The relative abundance of taxa was differently affected by age, and the DNA concentration of all selected bacterial groups increased with age, although total volatile fatty acids (VFA), acetate, propionate, caproate and lactate concentrations decreased. Organic selenium was associated with a higher concentration of total VFA, propionate and butyrate, a higher number of DNA copies of Lactobacillus, and a trend to lower DNA copies of Escherichia coli. Effects on fecal microbiome during growth differed with selenium source. Females had higher fecal end-fermentation products related to protein degradation, whereas males had higher DNA concentration of Bifidobacterium. Organic selenium might be beneficial over inorganic for dog food supplementation due to the positive modulation of the gut microbiome observed in puppies.

Best Practices for Microbiome Study Design in Companion Animal Research

The gut microbiome is a community of microorganisms that inhabits an animal host's gastrointestinal tract, with important effects on animal health that are shaped by multiple environmental, dietary, and host-associated factors. Clinical and dietary trials in companion animals are increasingly including assessment of the microbiome, but interpretation of these results is often hampered by suboptimal choices in study design. Here, we review best practices for conducting feeding trials or clinical trials that intend to study the effects of an intervention on the microbiota. Choices for experimental design, including a review of basic designs, controls, and comparison groups, are discussed in the context of special considerations necessary for microbiome studies. Diet is one of the strongest influences on the composition of gut microbiota, so applications specific to nutritional interventions are discussed in detail. Lastly, we provide specific advice for successful recruitment of colony animals and household pets into an intervention study. This review is intended to serve as a resource to academic and industry researchers, clinicians, and veterinarians alike, for studies that test many different types of interventions.

Dysbiosis of fecal microbiota in cats with naturally occurring and experimentally induced Tritrichomonas foetus infection

The protozoal pathogen Tritrichomonas foetus infects the colon of domestic cats and is a major cause of chronic colitis and diarrhea. Treatment failure is common, but antibiotics may improve clinical signs in a subset of cats, leading researchers to question involvement of the colonic microbiota in disease pathogenesis. Studies performed in women with venereal Trichomonas vaginalis infections have revealed that dysbiosis of host microbiota contributes to pathogenicity with similar findings also found in mice with intestinal Tritrichomonas musculis The aim of this study was to characterize differences in the fecal microbiota of cats with and without naturally occurring T. foetus infection and in a group of kittens prior to and after experimentally induced infection. Archived fecal DNA from cats undergoing testing for T. foetus infection (n = 89) and experimentally infected kittens (n = 4; at pre-, 2 weeks, and 9 weeks post-infection) were analyzed by sequencing of 16S rRNA genes. Amongst the naturally infected population, the genera Megamonas and Helicobacter were significantly increased in prevalence and abundance in cats testing positive for T. foetus infection. In the group of four experimentally infected kittens, fecal samples post-infection had significantly lower abundance of genus Dialister and Megamonas and greater abundance of the class Betaproteobacteria and family Succinivibrionaceae. We hypothesize that T. foetus promotes dysbiosis by competition for fermentable substrates used by these bacteria and that metabolic byproducts may contribute to the pathogenesis of colonic inflammation and diarrhea. Future studies are warranted for the measurement of fecal concentrations of microbial and protozoal metabolites in cats with T. foetus infection for the identification of potential therapeutic targets.

Catching a glimpse of the bacterial gut community of companion animals: a canine and feline perspective

Dogs and cats have gained a special position in human society by becoming our principal companion animals. In this context, efforts to ensure their health and welfare have increased exponentially, with in recent times a growing interest in assessing the impact of the gut microbiota on canine and feline health. Recent technological advances have generated new tools to not only examine the intestinal microbial composition of dogs and cats, but also to scrutinize the genetic repertoire and associated metabolic functions of this microbial community. The application of high-throughput sequencing techniques to canine and feline faecal samples revealed similarities in their bacterial composition, with Fusobacteria, Firmicutes and Bacteroidetes as the most prevalent and abundant phyla, followed by Proteobacteria and Actinobacteria. Although key bacterial members were consistently present in their gut microbiota, the taxonomic composition and the metabolic repertoire of the intestinal microbial population may be influenced by several factors, including diet, age and anthropogenic aspects, as well as intestinal dysbiosis. The current review aims to provide a comprehensive overview of the multitude of factors which play a role in the modulation of the canine and feline gut microbiota and that of their human owners with whom they share the same environment.

Gluconobacter dominates the gut microbiome of the Asian palm civet Paradoxurus hermaphroditus that produces kopi luwak

Coffee beans derived from feces of the civet cat are used to brew coffee known as kopi luwak (the Indonesian words for coffee and palm civet, respectively), which is one of the most expensive coffees in the world owing to its limited supply and strong market demand. Recent metabolomics studies have revealed that kopi luwak metabolites differ from metabolites found in other coffee beans. To produce kopi luwak, coffee beans are first eaten by civet cats. It has been proposed that fermentation inside the civet cat digestive tract may contribute to the distinctively smooth flavor of kopi luwak, but the biological basis has not been determined. Therefore, we characterized the microbiome of civet cat feces using 16S rRNA gene sequences to determine the bacterial taxa that may influence fermentation processes related to kopi luwak. Moreover, we compared this fecal microbiome with that of 14 other animals, revealing that Gluconobacter is a genus that is, uniquely found in feces of the civet cat. We also found that Gluconobacter species have a large number of cell motility genes, which may encode flagellar proteins allowing colonization of the civet gut. In addition, genes encoding enzymes involved in the metabolism of hydrogen sulfide and sulfur-containing amino acids were over-represented in Gluconobacter. These genes may contribute to the fermentation of coffee beans in the digestive tract of civet cats.

Past, Present, and Future of Gastrointestinal Microbiota Research in Cats

The relationship between microbial community and host has profound effects on the health of animals. A balanced gastrointestinal (GI) microbial population provides nutritional and metabolic benefits to its host, regulates the immune system and various signaling molecules, protects the intestine from pathogen invasion, and promotes a healthy intestinal structure and an optimal intestinal function. With the fast development of next-generation sequencing, molecular techniques have become standard tools for microbiota research, having been used to demonstrate the complex intestinal ecosystem. Similarly to other mammals, the vast majority of GI microbiota in cats (over 99%) is composed of the predominant bacterial phyla Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria. Many nutritional and clinical studies have shown that cats' microbiota can be affected by several different factors including body condition, age, diet, and inflammatory diseases. All these factors have different size effects, and some of these may be very minor, and it is currently unknown how important these are. Further research is needed to determine the functional variations in the microbiome in disease states and in response to environmental and/or dietary modulations. Additionally, further studies are also needed to explain the intricate relationship between GI microbiota and the genetics and immunity of its host. This review summarizes past and present knowledge of the feline GI microbiota and looks into the future possibilities and challenges of the field.

Activation of butyrate-producing bacteria as well as bifidobacteria in the cat intestinal microbiota by the administration of 1-kestose, the smallest component of fructo-oligosaccharide

1-kestose is a structural component of fructo-oligosaccharides and is composed of 2 fructose residues bound to sucrose through β2-1 bonds. In the present study, the influence of the ingestion of 1-kestose on the intestinal microbiota was investigated in cats. Six healthy cats were administered 1 g/day of 1-kestose for 8 weeks followed by a 2-week wash-out period. Fecal samples were collected from cats after 0, 4, 8, and 10 weeks. The intestinal microbiota was examined by a 16S rRNA gene metagenomic analysis and real-time PCR. Short-chain fatty acids were measured by GC/MS. The results suggested that the intestinal bacterial community structure in feline assigned to this study was divided into 2 types: one group mainly composed of the genus Lactobacillus (GA) and the other mainly composed of the genus Blautia with very few bacteria of Lactobacillus (GB). Furthermore, the number of Bifidobacterium slightly increased after the administration of 1-kestose (at 4 and 8 weeks) (P<0.1). The administration of 1-kestose also increased the abundance of Megasphaera, the butyric acid-producing bacteria, at 4 and 8 weeks (P<0.1). Furthermore, an increase in butyric acid levels was observed after the administration of 1-kestose for 4 weeks (P<0.1). These results suggest that 1-kestose activated butyrate-producing bacteria as well as bifidobacteria and propose its potential as a new generation prebiotic.

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.

Comparative analysis of the gut microbiota of the blue fox (Alopex lagopus) and raccoon dog (Nyctereutes procyonoides)

The goal of this study is to compare the gut microbiota of domestic blue fox (Alopex lagopus) and raccoon dog (Nyctereutes procyonoides) to provide better understanding of their intestinal gut microbiota. We analyzed the structure of fecal microbes in 40 blue foxes and 40 raccoon dogs that were raised under same conditions, using high-throughput Illumina sequencing targeting the V3-V4 region of the 16S rRNA gene. In total, 295,146 sequence reads were obtained. The average number of operational taxonomical units in the two group samples was 194 to 286. Firmicutes (blue fox 73.40%, raccoon dog 46.90%) and Bacteroidetes (blue fox 21.92%, raccoon dog 44.25%) were the most abundant phyla in the gut of blue fox and raccoon dog. At the genus level, Prevotella (blue fox 16.89%, raccoon dog 36.22%), Blautia (blue fox 9.02%, raccoon dog 13.72%), and Peptostreptococcaeae_incertae_sedi (blue fox 22.41%, raccoon dog 2.84%) were commonly presented in the gut of two kinds of animal. Principal coordinates analysis showed that the microbial communities were different between blue fox and raccoon dog. The Firmicutes-to-Bacteroidetes ratio was higher in blue foxes (3:1) than in raccoon dogs (1:1). Moreover, Peptostreptococcaeae_incertae_sedi and Prevotella, were more abundant in the gut of blue fox, whereas the abundance of Prevotella and Blautia were higher in the gut of raccoon dog. In conclusion, the present study revealed the difference of the gut microbial composition between blue fox and raccoon dog under the same diet conditions.

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)

Commercial diets high in animal protein and fat are increasingly being developed for pets, however little is understood about the impacts of feeding such diets to domestic cats. The carbohydrate content of these diets is typically low, and dietary fibre is often not included. Dietary fibre is believed to be important in the feline gastrointestinal tract, promoting stool formation and providing a substrate for the hindgut microbiome. Therefore, we aimed to determine the effects of adding plant-based dietary fibre to a high animal protein and fat diet. Twelve domestic short hair cats were fed three complete and balanced diets in a cross-over design for blocks of 21 days: raw meat (Raw), raw meat plus fibre (2%, ‘as is’ inclusion of inulin and cellulose; Raw+Fibre) and a commercially available Kibble diet. A commercially available canned diet was fed for 21 days as a washout phase. Apparent macronutrient digestibility, faecal output, score, pH, organic acid concentrations and bacteriome profiles were determined. Diet significantly affected all faecal parameters measured. The addition of dietary fibre to the raw meat diet was found to reduce apparent macronutrient digestibility, increase faecal output, pH and score. Thirty one bacterial taxa were significantly affected by diet. Prevotella was found to dominate in the Kibble diet, Clostridium and Fusobacterium in the Raw diet, and Prevotella and a group of unclassified Peptostreptococcaceae in the Raw+Fibre diet. Our results show that diets of different macronutrient proportions can strongly influence the faecal microbiome composition and metabolism, as shown by altered organic acid concentrations and faecal pH, in the domestic cat. The addition of 2% of each fibre to the Raw diet shifted faecal parameters closer to those produced by feeding a Kibble diet. These results provide a basis for further research assessing raw red meat diets to domestic cats.

Fecal bacterial microbiota of Canadian commercial mink (Neovison vison): Yearly, life stage, and seasonal comparisons

The gastrointestinal microbiome is known to play a critical role in animal health but has been relatively poorly characterized in commercial mink, an obligate carnivore. Whether the microbiota can be manipulated in mink to improve pelt quality, health, and well-being is unknown. The objectives of this study were to characterize the fecal microbiota of commercial mink, and to evaluate potential changes due to year (2014 vs 2015), life stage (adult female vs weaned kit), season (summer vs winter), and between Canadian farms. Pooled fecal samples were collected from adult females and weaned kits in the summers of 2014 (n = 173) and 2015 (n = 168), and from females in the winter of 2016 (n = 39), a time when females undergo marked calorie restriction, from 49 mink farms in Ontario. Bacterial DNA was extracted and the V4 region of the 16S rRNA gene was amplified. Approximately 22 million sequences were identified following quality control filtering. A total of 31 bacterial phyla were identified; however, only 3 comprised >1% of the total sequences identified, with Firmicutes and Proteobacteria together comprising 95% of the total sequences. Comparisons were made by life stage, season and year; no differences were found in the relative abundance of any taxa between samples collected from adult females and weaned kits from the same year and the greatest number of differences at each taxonomic level were noted between 2014 and 2015. Significantly more operational taxonomic units (OTUs) were found in 2014 than 2015 or 2016 (p<0.05) and samples from 2014 were more even, but less diverse than in 2015 (p = 0.002 and 0.001, respectively). There were significant differences in community population and structure by year and season (all p-values <0.001). The predominant phyla and genera at the farm level were similar from year to year. Together, these indicate that mink environment, season, and time are important factors in the stability of gastrointestinal microbiota, once mink reach maturity.

Evaluation of the impact of dental prophylaxis on the oral microbiota of dogs

Periodontal disease is one of the most commonly diagnosed oral diseases in dogs and can result from undisturbed dental plaque. Dental prophylaxis is a routinely practiced veterinary procedure, but its effects on both the plaque and oral microbiota is not fully understood. The objectives of this study were to evaluate the impact of dental prophylaxis on the composition of the supragingival plaque and composite oral microbiota in clinically healthy dogs and to determine if composite sampling could be used in lieu of sampling the plaque microbiota directly. Thirty dogs received a dental prophylaxis. Supragingival plaque and composite oral samples were collected just prior to, and one week after dental prophylaxis. A subsample of 10 dogs was followed, and additional samples were collected two and five weeks post-prophylaxis. The V4 region of the 16S rRNA gene was used for Illumina MiSeq next-generation sequencing. Results demonstrate that decreases in Treponema as well as increases in Moraxella and Neisseria distinguished the plaque pre- and one week post-prophylaxis timepoints (all P<0.05). Within the oral microbiota, the initially dominant Psychrobacter (20% relative abundance) disappeared one week later (P<0.0001), and Pseudomonas became the dominant taxon one week after treatment (80% relative abundance, P<0.0001). A rapid transition back towards the pre-dental prophylaxis microbiota by five weeks post-treatment was seen for both niches, suggesting the canine oral microbiota is resilient. Direct comparison of the two environments yielded striking differences, with complete separation of groups. Firmicutes (40%) and Spirochaetes (22%) predominated in the plaque while Proteobacteria (58%) was predominant in the oral microbiota. Greater richness was also seen in the plaque microbiota. This study reveals that prophylaxis had a profound impact on both the plaque and oral microbiota, and the longitudinal results help elucidate the pathophysiology of periodontal disease. The results suggest that oral swabs are a poor proxy for plaque samples and highlight the need to study specific oral niches.

The Fecal Microbiota in the Domestic Cat (Felis catus) Is Influenced by Interactions Between Age and Diet; A Five Year Longitudinal Study

In humans, aging is associated with changes in the gastrointestinal microbiota; these changes may contribute to the age-related increase in incidence of many chronic diseases, including Type 2 diabetes. The life expectancies of cats are increasing, and they are also exhibiting the same types of diseases. While there are some studies investigating the impacts of diets on gastrointestinal microbiota in young cats, the impacts of aging in older cats has not been explored. We followed a cohort of related kittens, maintained on two commercial diets (kibbled and canned) from weaning (8 weeks) to 5 years of age (260 weeks). We hypothesized that the long-term feeding of specific diet formats would (a) lead to microbial composition changes due to aging, (b) impact body composition, and (c) affect insulin sensitivity in the aging cat. We observed that both diet and age affected fecal microbial composition, and while age correlated with changes in body composition, diet had no effect on body composition. Similarly insulin sensitivity was not affected by age nor diet. 16S rRNA sequencing found unclassified Peptostreptococcaceae were prominent across all ages averaging 21.3% of gene sequence reads and were higher in cats fed canned diets (average of 25.7% of gene sequence reads, vs. 17.0% for kibble-fed cats). Age-related effects on body composition and insulin sensitivity may become apparent as the cats grow older; this study will continue to assess these parameters.

Metagenomic insights into the roles of Proteobacteria in the gastrointestinal microbiomes of healthy dogs and cats

Interests in the impact of the gastrointestinal microbiota on health and wellbeing have extended from humans to that of companion animals. While relatively fewer studies to date have examined canine and feline gut microbiomes, analysis of the metagenomic DNA from fecal communities using next‐generation sequencing technologies have provided insights into the microbes that are present, their function, and potential to contribute to overall host nutrition and health. As carnivores, healthy dogs and cats possess fecal microbiomes that reflect the generally higher concentrations of protein and fat in their diets, relative to omnivores and herbivores. The phyla Firmicutes and Bacteroidetes are highly abundant, and Fusobacteria, Actinobacteria, and Proteobacteria also feature prominently. Proteobacteria is the most diverse bacterial phylum and commonly features in the fecal microbiota of healthy dogs and cats, although its reputation is often sullied as its members include a number of well‐known opportunistic pathogens, such as Escherichia coli, Salmonella, and Campylobacter, which may impact the health of the host and its owner. Furthermore, in other host species, high abundances of Proteobacteria have been associated with dysbiosis in hosts with metabolic or inflammatory disorders. In this review, we seek to gain further insight into the prevalence and roles of the Proteobacteria within the gastrointestinal microbiomes of healthy dogs and cats. We draw upon the growing number of metagenomic DNA sequence‐based studies which now allow us take a culture‐independent approach to examine the functions that this more minor, yet important, group contribute to normal microbiome function.

The fecal microbiomes of healthy dogs and cats often include Proteobacteria at varying abundances. This phylum can have a sullied reputation as it contains a number of well‐known pathogenic members. We explored the functions of the Proteobacteria in fecal shotgun metagenome datasets from healthy dogs and cats. The Proteobacteria appeared to be enriched for functions that are consistent with a role in helping to maintain the anaerobic environment of the gut for normal microbiome function.

Molecular diversity of the faecal microbiota of Toy Poodles in Japan

The intestinal microbiota was revealed with the recent advances in molecular techniques, such as high-throughput sequencing analysis. As a result, the microbial changes are thought to influence the health of humans and animals and such changes are affected by several factors including diet, genetics, age, sex, and diseases. Similar studies are being conducted in dogs, and the knowledge of intestinal microbiota in dogs is expanding. Nonetheless, basic information on intestinal microbiota in dogs is less than that of humans. Our aim was to study toy poodles (n=21), a popular companion dog, in terms of basic characteristics of the faecal microbiota by 16S rRNA gene barcoding analysis. In the faecal microbiota, Firmicutes, Bacteroidetes, Proteobacteria, and Fusobacteria were the dominant phyla (over 93.4% of faecal microbiota) regardless of the attributes of the dogs. In family level, Enterobacteriaceae, Bacteroidaceae, and Lachnospiraceae were most prevalent. In case of a dog with protein-losing enteropathy, the diversity of faecal microbiota was different between before and after treatment. This study provides basic information for studying on faecal microbiota in toy poodles.

The Gastrointestinal Microbiome: A Review

The gastrointestinal microbiome is a diverse consortium of bacteria, archaea, fungi, protozoa, and viruses that inhabit the gut of all mammals. Studies in humans and other mammals have implicated the microbiome in a range of physiologic processes that are vital to host health including energy homeostasis, metabolism, gut epithelial health, immunologic activity, and neurobehavioral development. The microbial genome confers metabolic capabilities exceeding those of the host organism alone, making the gut microbiome an active participant in host physiology. Recent advances in DNA sequencing technology and computational biology have revolutionized the field of microbiomics, permitting mechanistic evaluation of the relationships between an animal and its microbial symbionts. Changes in the gastrointestinal microbiome are associated with diseases in humans and animals including inflammatory bowel disease, asthma, obesity, metabolic syndrome, cardiovascular disease, immune-mediated conditions, and neurodevelopmental conditions such as autism spectrum disorder. While there remains a paucity of data regarding the intestinal microbiome in small animals, recent studies have helped to characterize its role in host animal health and associated disease states. This review is intended to familiarize small animal veterinarians with recent advances in the field of microbiomics and to prime them for a future in which diagnostic tests and therapies will incorporate these developments into clinical practice.

Effects of obesity, energy restriction and neutering on the faecal microbiota of cats

Surveys report that 25-57 % of cats are overweight or obese. The most evinced cause is neutering. Weight loss often fails; thus, new strategies are needed. Obesity has been associated with altered gut bacterial populations and increases in microbial dietary energy extraction, body weight and adiposity. This study aimed to determine whether alterations in intestinal bacteria were associated with obesity, energy restriction and neutering by characterising faecal microbiota using 16S rRNA gene sequencing in eight lean intact, eight lean neutered and eight obese neutered cats before and after 6 weeks of energy restriction. Lean neutered cats had a bacterial profile similar to obese rodents and humans, with a greater abundance (P<0·05) of Firmicutes and lower abundance (P<0·05) of Bacteroidetes compared with the other groups. The greater abundance of Firmicutes in lean neutered cats was due to a bloom in Peptostreptococcaceae. Obese cats had an 18 % reduction in fat mass after energy restriction (P<0·05). Energy reduction was concurrent with significant shifts in two low-abundance bacterial genera and trends in four additional genera. The greatest change was a reduction in the Firmicutes genus, Sarcina, from 4·54 to 0·65 % abundance after energy restriction. The short duration of energy restriction may explain why few bacterial changes were observed in the obese cats. Additional work is needed to understand how neutering, obesity and weight loss are related to changes in feline microbiota and how these microbial shifts affect host physiology.

Transition of the intestinal microbiota of cats with age

The transition of intestinal microbiota with age has been well described in humans. However, the age-related changes in intestinal microbiota of cats have not been well studied. In the present study, we investigated the composition of intestinal microbiota of cats in 5 different age groups (pre-weanling, weanling, young, aged, senile) with a culture-based method. For lactobacilli and bifidobacteria, we also quantified with molecular-based method, real-time PCR. The results suggested that the composition of the feline intestinal microbiota changes with age, while the changes were different from those of humans and dogs. Bifidobacteria which are predominant in human intestine or lactobacilli which are predominant in dog intestine, did not appear to be important in cat intestines. Enterococci, instead, seem to be major lactic acid producing bacteria in cats. We also identified lactobacilli and bifidobacteria at the species level based on 16S rRNA gene sequences and found that the species composition of Lactobacillus also changed with age.

Bacterial microbiome in the nose of healthy cats and in cats with nasal disease

Background

Traditionally, changes in the microbial population of the nose have been assessed using conventional culture techniques. Sequencing of bacterial 16S rRNA genes demonstrated that the human nose is inhabited by a rich and diverse bacterial microbiome that cannot be detected using culture-based methods. The goal of this study was to describe the nasal microbiome of healthy cats, cats with nasal neoplasia, and cats with feline upper respiratory tract disease (FURTD).

Methodology/Principal findings

DNA was extracted from nasal swabs of healthy cats (n = 28), cats with nasal neoplasia (n = 16), and cats with FURTD (n = 15), and 16S rRNA genes were sequenced. High species richness was observed in all samples. Rarefaction analysis revealed that healthy cats living indoors had greater species richness (observed species p = 0.042) and Shannon diversity (p = 0.003) compared with healthy cats living outdoors. Higher species richness (observed species p = 0.001) and Shannon diversity (p<0.001) were found in middle-aged cats in comparison to healthy cats in different age groups. Principal coordinate analysis revealed separate clustering based on similarities in bacterial molecular phylogenetic trees of 16S rRNA genes for indoor and outdoor cats. In all groups examined, the most abundant phyla identified were Proteobacteria, Firmicutes, and Bacteroidetes. At the genus level, 375 operational taxonomic units (OTUs) were identified. In healthy cats and cats with FURTD, Moraxella spp. was the most common genus, while it was unclassified Bradyrhizobiaceae in cats with nasal neoplasia. High individual variability was observed.

Conclusion

This study demonstrates that the nose of cats is inhabited by much more variable and diverse microbial communities than previously shown. Future research in this field might help to develop new diagnostic tools to easily identify nasal microbial changes, relate them to certain disease processes, and help clinicians in the decision process of antibiotic selection for individual patients.

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

Prebiotics are selectively fermentable dietary compounds that result in changes in the composition and/or activity of the intestinal microbiota, thus conferring benefits upon host health. In veterinary medicine, commercially available products containing prebiotics have not been well studied with regard to the changes they trigger on the composition of the gut microbiota. This study evaluated the effect of a commercially available nutraceutical containing fructo-oligosaccharides (FOS) and inulin on the fecal microbiota of healthy cats and dogs when administered for 16 days. Fecal samples were collected at two time points before and at two time points during prebiotic administration. Total genomic DNA was obtained from fecal samples and 454-pyrosequencing was used for 16S rRNA gene bacterial profiling. The linear discriminant analysis (LDA) effect size (LEfSe) method was used for detecting bacterial taxa that may respond (i.e., increase or decrease in its relative abundance) to prebiotic administration. Prebiotic administration was associated with a good acceptance and no side effects (e.g., diarrhea) were reported by the owners. A low dose of prebiotics (50 mL total regardless of body weight with the end product containing 0.45% of prebiotics) revealed a lower abundance of Gammaproteobacteria and a higher abundance of Veillonellaceae during prebiotic administration in cats, while Staphylococcaceae showed a higher abundance during prebiotic administration in dogs. These differences were not sufficient to separate bacterial communities as shown by analysis of weighted UniFrac distance metrics. A predictive approach of the fecal bacterial metagenome using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) also did not reveal differences between the period before and during prebiotic administration. A second trial using a higher dose of prebiotics (3.2 mL/kg body weight with the end product containing 3.1% of prebiotics) was tested in dogs and revealed a lower abundance of Dorea (family Clostridiaceae) and a higher abundance of Megamonas and other (unknown) members of Veillonellaceae during prebiotic administration. Again, these changes were not sufficient to separate bacterial communities or predicted metabolic profiles according to treatment. A closer analysis of bacterial communities at all time-points revealed highly individualized patterns of variation. This study shows a high interindividual variation of fecal bacterial communities from pet cats and dogs, that these communities are relatively stable over time, and that some of this variation can be attributable to prebiotic administration, a phenomenon that may be affected by the amount of the prebiotic administered in the formulation. This study also provides insights into the response of gut bacterial communities in pet cats and dogs during administration of commercially available products containing prebiotics. More studies are needed to explore potentially beneficial effects on host health beyond changes in bacterial communities.

Metabolic Profiling Reveals Effects of Age, Sexual Development and Neutering in Plasma of Young Male Cats

Neutering is a significant risk factor for obesity in cats. The mechanisms that promote neuter-associated weight gain are not well understood but following neutering, acute changes in energy expenditure and energy consumption have been observed. Metabolic profiling (GC-MS and UHPLC-MS-MS) was used in a longitudinal study to identify changes associated with age, sexual development and neutering in male cats fed a nutritionally-complete dry diet to maintain an ideal body condition score. At eight time points, between 19 and 52 weeks of age, fasted blood samples were taken from kittens neutered at either 19 weeks of age (Early Neuter (EN), n = 8) or at 31 weeks of age (Conventional Neuter (CN), n = 7). Univariate and multivariate analyses were used to compare plasma metabolites (n = 370) from EN and CN cats. Age was the primary driver of variance in the plasma metabolome, including a developmental change independent of neuter group between 19 and 21 weeks in lysolipids and fatty acid amides. Changes associated with sexual development and its subsequent loss were also observed, with differences at some time points observed between EN and CN cats for 45 metabolites (FDR p<0.05). Pathway Enrichment Analysis also identified significant effects in 20 pathways, dominated by amino acid, sterol and fatty acid metabolism. Most changes were interpretable within the context of male sexual development, and changed following neutering in the CN group. Felinine metabolism in CN cats was the most significantly altered pathway, increasing during sexual development and decreasing acutely following neutering. Felinine is a testosterone-regulated, felid-specific glutathione derivative secreted in urine. Alterations in tryptophan, histidine and tocopherol metabolism observed in peripubertal cats may be to support physiological functions of glutathione following diversion of S-amino acids for urinary felinine secretion.

Pre- and post-weaning diet alters the faecal metagenome in the cat with differences in vitamin and carbohydrate metabolism gene abundances

Dietary format, and its role in pet nutrition, is of interest to pet food manufacturers and pet owners alike. The aim of the present study was to investigate the effects of pre- and post-weaning diets (kibbled or canned) on the composition and function of faecal microbiota in the domestic cat by shotgun metagenomic sequencing and gene taxonomic and functional assignment using MG-RAST. Post-weaning diet had a dramatic effect on community composition; 147 of the 195 bacterial species identified had significantly different mean relative abundances between kittens fed kibbled and canned diets. The kittens fed kibbled diets had relatively higher abundances of Lactobacillus (>100-fold), Bifidobacterium (>100-fold), and Collinsella (>9-fold) than kittens fed canned diets. There were relatively few differences in the predicted microbiome functions associated with the pre-weaning diet. Post-weaning diet affected the abundance of functional gene groups. Genes involved in vitamin biosynthesis, metabolism, and transport, were significantly enriched in the metagenomes of kittens fed the canned diet. The impact of post-weaning diet on the metagenome in terms of vitamin biosynthesis functions suggests that modulation of the microbiome function through diet may be an important avenue for improving the nutrition of companion animals.

The influence of weight and gender on intestinal bacterial community of wild largemouth bronze gudgeon (Coreius guichenoti, 1874)

Background

Largemouth bronze gudgeon (Coreius guichenoti) is of economic importance in China, distributed in upstream regions of the Yangtze River in China. But it has recently dramatically declined and is close to elimination. However, there is little knowing about the character of its intestinal microbiota. This study was conducted to elucidate the intestinal microbiota of wild largemouth bronze gudgeon with different body weight and gender.

Results

Thirty wild largemouth bronze gudgeon were measured for body length and body weight, and identified for male and female according to gonadal development, and thereafter the intestinal microbiota’s were assessed by MiSeq sequencing of 16S rRNA genes. The results revealed that phyla Proteobacteria and Tenericutes were dominant in wild largemouth bronze gudgeon intestine independent of the body weight. Shannon’s and Inverse Simpson’s diversity indexes were significant (P < 0.05) different between male and female fish. The phylum profile in the intestine of male fish revealed that phylum Proteobacteria was dominant, in contrast to female fish where five phyla Tenericutes, Proteobacteria, Firmicutes, Fusobacteria and Spirochaetes were dominant. The genus profile revealed that genera Shewanella and Unclassified bacteria were dominant in male fish, while genus Mycoplasma was dominant in female fish.

Conclusions

Our results revealed that the intestinal microbial community of wild largemouth bronze gudgeon was dominated by the phyla Proteobacteria and Tenericutes regardless of the different body weight, but the communities are significant different between male and female fish. These results provide a theoretical basis to understand the biological mechanisms relevant to the protection of the endangered fish species.