Deep Illumina-based shotgun sequencing reveals dietary effects on the structure and function of the fecal microbiome of growing kittens

Effects of a Nutraceutical Treatment on the Intestinal Microbiota of Sled Dogs

Dog sledding is the main discipline of working dogs on snow, consisting of a team of dogs pulling a sled under the guidance of the owner. To carry out this sport, dogs must have adequate nutrition and vitamin and antioxidant supplementation to ensure that the physical effort is optimal. The present study evaluated the effect that sporting activity and stress have on the canine intestinal microbiota by dividing the dogs into two groups: a control group that did not take any nutraceutical products and the treated group to which a nutraceutical product was administered. The nutraceutical administered in this study is used in all cases of canine intestinal dysbiosis in which it is essential to quickly restore a balanced intestinal microbiota. The results obtained show that in dogs not taking the nutraceutical, there is an increase in bacteria, such as Streptococcus spp. and E. coli, considered enteropathogenic to the detriment of beneficial bacterial species such as Faecalibacterium spp., Turicibacter spp., Blautia spp., Fusobacterium spp., and Clostridium hiranonis. Instead, the group of dogs treated with nutraceutical displays a lower amount of enteropathogenic bacteria and a great increase in the other bacterial species considered beneficial for the animal's health. The results obtained in the present study show that Microbiotal cane® can be used in dogs subject to intense sporting activity by preventing severe alterations at intestinal ecosystem levels by maintaining intestinal bacterial composition as balanced as possible.

Effects of Heat-Treated Bifidobacterium longum CECT-7384 Combined with Fibersol-2 on the Intestinal Health of Cats Submitted to an Abrupt Dietary Change: A Randomized Controlled Study

Abrupt dietary change can disrupt the intestinal balance in felines. This study aimed to assess the impact of heat-treated Bifidobacterium longum CECT-7384 combined with Fibersol-2 on the intestinal health of adult cats before and after dietary change. We selected 24 British shorthair cats, dividing them into two groups. From day 1 to day 14, the control group received a lower protein (33%) concentration (LPF) diet, while the treated group received the same LPF diet supplemented with 0.16% functional additives, consisting of Bifidobacterium longum CECT-7384 combined with Fibersol-2. Subsequently, from day 15 to day 28, the control group transitioned to a higher protein (40%) concentration (HPF) diet, while the treated group received the same HPF diet supplemented with 0.16% functional additives. Blood and fresh feces were collected on day 0, 14, 17, 21, and 28 of the experiment. The results suggest that the use of heat-treated Bifidobacterium longum CECT-7384 combined with Fibersol-2 may improve gastrointestinal function in cats by reducing serum LPS levels and fecal pH, while increasing fecal sIgA levels. In addition, the functional additive regulates the fecal microbiota and its function, promoting intestinal homeostasis and colonization with beneficial bacteria such as Blautia. Furthermore, on day 28, there was a significant difference in fecal microbiota beta diversity between the two groups. In summary, the addition of heat-treated Bifidobacterium longum CECT-7384 combined with Fibersol-2 contributes to improving the intestinal health of adult cats affected by abrupt dietary change.

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.

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.

Effects of antimicrobials on the gastrointestinal microbiota of dogs and cats

Among several environmental factors, exposure to antimicrobials has been in the spotlight as a cause of profound and long-term disturbance of the intestinal microbiota. Antimicrobial-induced dysbiosis is a general term and includes decreases in microbial richness and diversity, loss of beneficial bacterial groups, blooms of intestinal pathogens and alterations in the metabolic functions and end-products of the microbiota. Mounting evidence from human and experimental animal studies suggest an association between antimicrobial-induced dysbiosis and susceptibility to gastrointestinal, metabolic, endocrine, immune and neuropsychiatric diseases. These associations are commonly stronger after early life exposure to antimicrobials, a period during which maturation of the microbiota and immune system take place in parallel. In addition, these associations commonly become stronger as the number of antimicrobial courses increases. The repeatability of these findings among different studies as well as the presence of a dose-dependent relationship between antimicrobial exposure and disease development collectively require careful consideration of the need for antimicrobial use. There are limited studies are available in dogs and cats regarding the long-term effects of antimicrobials on the microbiota and subsequent susceptibility to diseases. This review discusses the effects of antimicrobials on the gastrointestinal microbiota and the most important associations between antimicrobial-induced dysbiosis and diseases in humans, dogs, and cats.

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.

Dietary enrichment of resistant starches or fibers differentially alter the feline fecal microbiome and metabolite profile

BACKGROUND

Cats are strict carnivores but possess a complex gastrointestinal (GI) microbial community that actively ferments dietary substrates that are not digested and reach the colon. The GI microbiota responses to dietary inclusion of resistant starches versus fibers have not been tested in cats. Thus, our objective was to evaluate the effects of diets enriched in resistant starch or fibers on the fecal characteristics, microbiome, and metabolite profiles of cats. Twelve healthy adult domestic shorthair cats (age = 9.6 ± 4.0 year; body weight = 3.9 ± 1.0 kg) were used in a replicated 3 × 3 Latin square design to test diets that were enriched with: (1) resistant starch (ERS), (2) a fiber-prebiotic-probiotic blend (FPPB), or (3) a fiber-prebiotic-probiotic blend + immune-modulating ingredients (iFPPB). In each 28-day period, 22 days of diet adaptation was followed by fecal and blood sample collection. Fecal samples were used for shotgun metagenomic sequencing. In addition, fecal and blood metabolite measurements and white blood cell stimulation was performed to assess immune function.

RESULTS

A total of 1690 bacterial species were identified, with 259 species differing between fiber-rich and ERS treatments. In comparison with fiber-rich treatments that increased diversity and promoted Firmicutes and Bacteroidetes populations, resistant starch reduced microbial diversity and fecal pH, led to a bloom in Actinobacteria, and modified Kyoto Encyclopedia of Genes and Genomes orthology (KO) terms pertaining to starch and sucrose metabolism, fatty acid biosynthesis and metabolism, epithelial cell signaling, among others. Resistant starch also differentially modified fecal metabolite concentrations with relevance to GI and overall host health (increased butyrate; decreased propionate and protein catabolites - branched-chain fatty acids; phenols and indoles; ammonia) and reduced blood cholesterol, which correlated strongly with microbial taxa and KO terms, and allowed for a high predictive efficiency of diet groups by random forest analysis.

CONCLUSION

Even though domestic cats and other carnivores evolved by eating low-carbohydrate diets rich in protein and fat, our results demonstrate that the feline microbiome and metabolite profiles are highly responsive to dietary change and in directions that are predictable.

A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments

Metagenomic binning is the step in building metagenome-assembled genomes (MAGs) when sequences predicted to originate from the same genome are automatically grouped together. The most widely-used methods for binning are reference-independent, operating de novo and enable the recovery of genomes from previously unsampled clades. However, they do not leverage the knowledge in existing databases. Here, we introduce SemiBin, an open source tool that uses deep siamese neural networks to implement a semi-supervised approach, i.e. SemiBin exploits the information in reference genomes, while retaining the capability of reconstructing high-quality bins that are outside the reference dataset. Using simulated and real microbiome datasets from several different habitats from GMGCv1 (Global Microbial Gene Catalog), including the human gut, non-human guts, and environmental habitats (ocean and soil), we show that SemiBin outperforms existing state-of-the-art binning methods. In particular, compared to other methods, SemiBin returns more high-quality bins with larger taxonomic diversity, including more distinct genera and species.

Whole-Genome Shotgun Metagenomic Sequencing Reveals Distinct Gut Microbiome Signatures of Obese Cats

Overweight and obesity are growing health problems in domestic cats, increasing the risks of insulin resistance, lipid dyscrasias, neoplasia, cardiovascular disease, and decreasing longevity. The signature of obesity in the feline gut microbiota has not been studied at the whole-genome metagenomic level. We performed whole-genome shotgun metagenomic sequencing in the fecal samples of eight overweight/obese and eight normal cats housed in the same research environment. We obtained 271 Gbp of sequences and generated a 961-Mbp de novo reference contig assembly, with 1.14 million annotated microbial genes. In the obese cat microbiome, we discovered a significant reduction in microbial diversity (P < 0.01) and Firmicutes abundance (P = 0.005), as well as decreased Firmicutes/Bacteroidetes ratios (P = 0.02), which is the inverse of obese human/mouse microbiota. Linear discriminant analysis and quantitative PCR (qPCR) validation revealed significant increases of Bifidobacterium sp., Olsenella provencensis, Dialister sp.CAG:486, and Campylobacter upsaliensis as the hallmark of obese microbiota among 400 enriched species, whereas 1,525 bacterial species have decreased abundance in the obese microbiome. Phascolarctobacterium succinatutens and an uncharacterized Erysipelotrichaceae bacterium are highly abundant (>0.05%) in the normal gut with over 400-fold depletion in the obese microbiome. Fatty acid synthesis-related pathways are significantly overrepresented in the obese compared with the normal cat microbiome. In conclusion, we discovered dramatically decreased microbial diversity in obese cat gut microbiota, suggesting potential dysbiosis. A panel of seven significantly altered, highly abundant species can serve as a microbiome indicator of obesity. Our findings in the obese cat microbiome composition, abundance, and functional capacities provide new insights into feline obesity.

IMPORTANCE Obesity affects around 45% of domestic cats, and licensed drugs for treating feline obesity are lacking. Physical exercise and calorie restrictions are commonly used for weight loss but with limited efficacy. Through comprehensive analyses of normal and obese cat gut bacteria flora, we identified dramatic shifts in the obese gut microbiome, including four bacterial species significantly enriched and two species depleted in the obese cats. The key bacterial community and functional capacity alterations discovered from this study will inform new weight management strategies for obese cats, such as evaluations of specific diet formulas that alter the microbiome composition, and the development of prebiotics and probiotics that promote the increase of beneficial species and the depletion of obesity-associated species. Interestingly, these bacteria identified in our study were also reported to affect the weight loss success in human patients, suggesting translational potential in human obesity.

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.

Dietary Protein and Carbohydrate Levels Affect the Gut Microbiota and Clinical Assessment in Healthy Adult Cats

BACKGROUND

Relative levels of dietary protein and carbohydrate intake influence microbiota and their functional capabilities, but the effect has not been well documented in cats.

OBJECTIVES

The impact of 3 foods with different protein:carbohydrate ratios on the gut microbiota and functional attributes in healthy adult cats was evaluated.

METHODS

Male and female cats (n = 30; mean age: 5.1 y; mean body weight: 5.26 kg) were fed 1 of 3 foods [P28 (28.3% protein, dry matter basis), P35 (35.1%), and P55 (54.8%)] for 90 d in a Williams Latin Square design. Each food had a 1:1 ratio of animal (dried chicken) to plant (pea) protein; protein replaced carbohydrate as protein level increased. Fecal microbiota and their functional capability were assessed with 16S sequencing and the Kyoto Encyclopedia of Genes and Genomes database, respectively.

RESULTS

Fecal pH, ammonia, and branched-chain fatty acids (BCFAs) were higher when cats consumed P55 food than when they consumed P28 and P35. Clear separation of samples between P28 and P55 based on bacterial genera was observed, with partitioning into saccharolytic and proteolytic functions, respectively. Significantly higher α diversity was seen with P55 than with P28 and P35. Amino acid metabolism, mucin foraging pathways, and urea metabolism were higher with P55 than with P28, whereas feces from cats fed P28 had higher concentrations of carbohydrate-active enzymes and enzymes involved in SCFA pathways than with P55. Bacterial genera that showed positive associations with amino acid catabolism also showed positive associations with mucin degradation.

CONCLUSIONS

Despite higher protein digestibility and less protein arriving to the colon, when healthy adult cats consumed the highest level of protein (P55), their gut microbiota exhibited higher mucin glycan foraging and amino acid metabolism, leading to higher fecal pH, ammonia, and BCFAs. This is likely due to lower availability of carbohydrate substrates and dietary fiber as protein replaced carbohydrate in the food.

Fecal pollution mediates the dominance of stochastic assembly of antibiotic resistome in an urban lagoon (Yundang lagoon), China

Sewage and fecal pollution cause antibiotic resistance genes (ARGs) pollution in urban lagoons. Seasonality also affects ARG dynamics. However, knowledge of factors controlling ARG community assembly across seasons is still limited. Here, we revealed the seasonal variation of ARGs and depict the underlying assembly processes and drivers via high-throughput quantitative PCR in an urban lagoon, China. A higher richness and abundance of ARGs were observed in summer and winter compared to spring and fall (Kruskal-Wallis test, P < 0.05). Both ARG and prokaryotic communities were mainly governed by stochastic processes, however, these processes drove ARGs and prokaryotes differently across seasons. Stochastic processes played a more dominant role in shaping ARG communities in summer (average stochasticity: 83%) and winter (75%), resulting in a stable antibiotic resistome. However, no such seasonal pattern of stochastic processes was determined for prokaryotes, indicating a decoupling of the assembly process of ARGs and prokaryotes. Moreover, fecal microorganisms (e.g., Bacteroidetes and Faecalibacterium) mediated the stochastic processes of ARG profiles, via enhancement of prokaryotic biomass and mobile genetic element abundances. The tnpA-07 transposase was the key for the horizontal gene transfer. These findings will enhance our understanding of how fecal pollution shapes ARG community assembly in urban lagoons.

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.

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

The gut microbiome is a functional organ, and responds metabolically to the nutrient composition within the diet. Fiber, starch, and protein content have strong effects on the microbiome composition, and changes in these nutrient profiles can induce rapid shifts. Due to functional redundancy of bacteria within microbial communities, important metabolites for health can be produced by different bacteria. Microbiome alterations associated with disease are of greater magnitude than those seen in healthy dogs on different diets. Dietary changes, addition of prebiotics, and probiotics, can be beneficial to improve microbial diversity and to normalize metabolite production in diseased dogs.

Metagenomic analysis revealed a wide distribution of antibiotic resistance genes and biosynthesis of antibiotics in the gut of giant pandas

BACKGROUND

The gut microbiome is essential for the host's health and serves as an essential reservoir of antibiotic resistance genes (ARGs). We investigated the effects of different factors, including the dietary shifts and age, on the functional characteristics of the giant panda's gut microbiome (GPs) through shotgun metagenome sequencing. We explored the association between gut bacterial genera and ARGs within the gut based on network analysis.

RESULTS

Fecal samples (n=60) from captive juvenile, adult, and geriatric GPs were processed, and variations were identified in the gut microbiome according to different ages, the abundance of novel ARGs and the biosynthesis of antibiotics. Among 667 ARGs identified, nine from the top ten ARGs had a higher abundance in juveniles. For 102 ARGs against bacteria, a co-occurrence pattern revealed a positive association for predominant ARGs with Streptococcus. A comparative KEGG pathways analysis revealed an abundant biosynthesis of antibiotics among three different groups of GPs, where it was more significantly observed in the juvenile group. A co-occurrence pattern further revealed a positive association for the top ten ARGs, biosynthesis of antibiotics, and metabolic pathways.

CONCLUSION

Gut of GPs serve as a reservoir for novel ARGs and biosynthesis of antibiotics. Dietary changes and age may influence the gut microbiome's functional characteristics; however, it needs further studies to ascertain the study outcomes.

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.

Antibiotic resistance gene sharing networks and the effect of dietary nutritional content on the canine and feline gut resistome

BACKGROUND

As one of the most densely populated microbial communities on Earth, the gut microbiota serves as an important reservoir of antibiotic resistance genes (ARGs), referred to as the gut resistome. Here, we investigated the association of dietary nutritional content with gut ARG diversity and composition, using publicly available shotgun metagenomic sequence data generated from canine and feline fecal samples. Also, based on network theory, we explored ARG-sharing patterns between gut bacterial genera by identifying the linkage structure between metagenomic assemblies and their functional genes obtained from the same data.

RESULTS

In both canine and feline gut microbiota, an increase in protein and a reduction in carbohydrate in the diet were associated with increased ARG diversity. ARG diversity of the canine gut microbiota also increased, but less strongly, after a reduction in protein and an increase in carbohydrate in the diet. The association between ARG and taxonomic composition suggests that diet-induced changes in the gut microbiota may be responsible for changes in ARG composition, supporting the links between protein metabolism and antibiotic resistance in gut microbes. In the analysis of the ARG-sharing patterns, 22 ARGs were shared among 46 genera in the canine gut microbiota, and 11 ARGs among 28 genera in the feline gut microbiota. Of these ARGs, the tetracycline resistance gene tet(W) was shared among the largest number of genera, predominantly among Firmicutes genera. Bifidobacterium, a genus extensively used in the fermentation of dairy products and as probiotics, shared tet(W) with a wide variety of other genera. Finally, genera from the same phylum were more likely to share ARGs than with those from different phyla.

CONCLUSIONS

Our findings show that dietary nutritional content, especially protein content, is associated with the gut resistome and suggest future research to explore the impact of dietary intervention on the development of antibiotic resistance in clinically-relevant gut microbes. Our network analysis also reveals that the genetic composition of bacteria acts as an important barrier to the horizontal transfer of ARGs. By capturing the underlying gene-sharing relationships between different bacterial taxa from metagenomes, our network approach improves our understanding of horizontal gene transfer dynamics.

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.

Diabetic cats have decreased gut microbial diversity and a lack of butyrate producing bacteria

Obesity and inactivity are major risk factors of feline diabetes mellitus (FDM) and human type II diabetes mellitus (T2DM). In recent years, changes in the gut microbiota have been suggested as a contributing factor to T2DM. Whether the gut microbiota (GM) composition plays a role in FDM remains unknown. The aim of the current study was firstly a cross-sectional comparison of the GM of diabetic cats, to that of lean, and of obese/overweight non-diabetic cats of a similar age. Specifically, fecal samples from 82 privately-owned cats from Denmark and Switzerland were sequenced using 16S rRNA gene amplicon metabarcoding. Secondly dietary intervention data was generated, by obtaining additional samples from a subset of cats after placing them on a high-protein diet for four weeks. The GM diversity of diabetic cats was lower than that of lean cats in the cross-sectional study, and lower compared to lean and to overweight/obese cats after diet intervention. Diabetic cats also exhibited fewer Anaerotruncus, Dialister, and unknown Ruminococcaceae than lean cats. Serum fructosamine levels correlated negatively with Prevotellaceae abundance and positively with Enterobacteriaceae abundance. In summary the intestinal microbiota of diabetic cats was characterized by decreased GM diversity and loss of butyrate producing bacterial genera.

PANCOSMA COMPARATIVE GUT PHYSIOLOGY SYMPOSIUM: ALL ABOUT APPETITE REGULATION: Effects of diet and gonadal steroids on appetite regulation and food intake of companion animals

The prominent incidence of overweight and obese pet animals not only results in higher morbidity and mortality, but also poses a threat for the quality of life, longevity, and well-being of dogs and cats. To date, strategies to prevent BW gain or to induce weight loss have had modest success in the pet population. In part, due to the complexity and the multifactorial nature of this disease, which involves pet-human interaction, environmental and dietary factors, and an intertwined metabolic process that still is not fully understood. As such, research methods to investigate the role of physiological hormones and dietary management on mechanisms related to the control of feelings of satiety and hunger in pet animals is warranted. Increasing interest exists in exploring gut chemosensing mechanisms, the crosstalk between metabolic-active tissues, and the interface between the gut microbiota and the nervous system (gut-brain axis). The noninvasive nature of research conducted in companion animals focuses on systemic approaches to develop environmental, nutritional, or therapeutic interventions that can be translated from research settings to pet-owned households. Because the majority of the pet population is spayed or neutered, it is important to determine the effect that sex hormones might have on appetite regulation and fasting metabolic rate of these animals. In general, studies have revealed that gonadectomy may establish a new "set point" characterized by increased food intake and BW, accompanied by physiological and behavioral changes. Some studies have also shown associations between gonadectomy and alterations in appetite-related hormones (e.g., ghrelin, leptin, adiponectin, glucagon-like peptide-1). Manipulation of macronutrients in diets of dogs and cats have also been investigated as a mean to improve satiety. Most of the research in this area has focused on high-protein diets, predominantly, for cats, and the use of dietary fiber sources of contrasting fermentability and viscosity profiles. Dietary fibers may affect the production of fermentative end products and gut microbiome, digestive and absorptive processes, appetite-related hormones, and promote "gut fill" and satiety. More recent studies have reported profound effects of dietary manipulation on the phylogeny and functional capacity of gut microbial communities of dogs and cats.

Apparent total-tract macronutrient digestibility, serum chemistry, urinalysis, and fecal characteristics, metabolites and microbiota of adult dogs fed extruded, mildly cooked, and raw diets1

Despite their popularity, little research has been performed on lightly cooked and raw diet formats for pets. Therefore, the objective of this study was to determine the apparent total-tract macronutrient digestibility (ATTD); fecal characteristics, metabolites, and microbiota; serum chemistry metabolites; urinalysis; and voluntary physical activity levels of adult dogs fed commercial diets differing in processing type. The diets included: 1) extruded dry kibble (EXT) diet; 2) high-moisture roasted refrigerated (RR) diet; 3) high-moisture grain-free roasted refrigerated (GFRR) diet; and 4) raw (RAW) diet. Eight dogs (mean age = 3.6; mean BW = 13.0 kg) were used in a replicated 4 × 4 Latin square design. Each period consisted of 28 d, with a 14-d adaptation phase followed by a 7-d phase for measuring voluntary physical activity, 1-d adaptation phase to metabolic cages, 5-d phase for fecal and urine collection, and 1 d for blood collection. Except for microbiota, all data were analyzed statistically by mixed models using SAS. Microbiota data were analyzed using Quantitative Insights Into Microbial Ecology (QIIME) and Statistical Analyses of Metagenomic Profiles (STAMP) software. Many differences in digestibility were observed, including greater (P < 0.05) ATTD of CP and fat in dogs fed GFRR and RR than dogs fed EXT. Dogs fed RAW had the lowest fecal pH and DM %, but fecal scores were not affected. Dogs fed RR had higher (P < 0.05) fecal indole and total phenol and indole concentrations than dogs fed the other diets. Dogs fed RAW had a higher (P < 0.05) fecal ammonia concentration than dogs fed the other diets. Fecal microbial diversity was altered by diet, with dogs fed GFRR and RAW having reduced species richness than dogs fed EXT. Dogs fed RR, GFRR, or RAW had lower (P < 0.05) Actinobacteria and higher (P < 0.05) Fusobacteria than dogs fed EXT. Dogs fed RAW or GFRR had higher (P < 0.05) Proteobacteria than dogs fed EXT or RR. Dogs fed RAW had higher (P < 0.05) Bacteroidetes and lower (P < 0.05) Firmicutes than dogs fed EXT. Serum triglycerides were within reference ranges, but greater (P < 0.05) in dogs fed EXT than dogs fed GFRR and RAW. All diets were well tolerated and dogs remained healthy throughout the study. In conclusion, the lightly cooked and raw diets tested were highly palatable, highly digestible, reduced blood triglycerides, maintained fecal quality and serum chemistry, and modified the fecal microbial community of healthy adult dogs.

Effects of dietary rapeseed meal supplementation on cecal microbiota in laying hens with different flavin-containing monooxygenase 3 genotypes

To evaluate the effect of dietary rapeseed meal (RM) supplementation on cecal trimethylamine and bacteria in laying hens with different flavin-containing monooxygenase 3 (FMO3) genotypes, a 3 × 2 2-factorial arrangement was employed using FMO3 genotypes (AA, AT, and TT) and dietary RM (0 and 14% of diet) as the main effects. At 50 wk of age, 36 hens of AT genotype and 36 hens of TT genotype were randomly allotted to one of the 2 dietary treatments, and each dietary treatment consisted of 3 replicates with 6 birds each. A total of 12 hens with AA genotype were allotted to one of the 2 dietary treatments that consisted of 3 replicates with 2 hens. Hens were fed 0% RM in a corn-soybean (SM) diet for one wk before the 6-week feeding trial period. Dietary RM supplementation increased trimethylamine (TMA) concentrations in both egg yolks (P < 0.0001) and cecal chyme (P < 0.0001). Dietary RM supplementation increased bacterial abundance and diversity (P < 0.0001). Weighted UniFrac, Nonmetric Multidimensional Scaling, and analysis of similarity (R-ANOSIM = 0.1516; P-value = 0.014) indicated distinct clustering was dependent on diets rather than FMO3 genotypes. Twenty-four phyla (most dominant, Bacteroides, Firmicutes, and Proteobacteria) and 229 genera were identified in the cecal samples. Compared with the SM diets, RM diets increased the proportion of Firmicutes (P = 0.004), Proteobacteria (P = 0.006), and Firmicutes:Bacteroides (P = 0.001), and some low-abundance phyla (P < 0.01), whereas the abundance of Bacteroides was lower (P = 0.0002). The abundance of 42 genera varied with dietary types. Six phyla and 35 genera were positively correlated with TMA concentration in the cecal chyme. In conclusion, the major TMA-producing bacteria in cecal were from Firmicutes and Proteobacteria phyla. The major TMA-producing bacterial genera could be from the genera that positively correlated with TMA concentration.

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.

Similarity of the dog and human gut microbiomes in gene content and response to diet

BACKGROUND

Gut microbes influence their hosts in many ways, in particular by modulating the impact of diet. These effects have been studied most extensively in humans and mice. In this work, we used whole genome metagenomics to investigate the relationship between the gut metagenomes of dogs, humans, mice, and pigs.

RESULTS

We present a dog gut microbiome gene catalog containing 1,247,405 genes (based on 129 metagenomes and a total of 1.9 terabasepairs of sequencing data). Based on this catalog and taxonomic abundance profiling, we show that the dog microbiome is closer to the human microbiome than the microbiome of either pigs or mice. To investigate this similarity in terms of response to dietary changes, we report on a randomized intervention with two diets (high-protein/low-carbohydrate vs. lower protein/higher carbohydrate). We show that diet has a large and reproducible effect on the dog microbiome, independent of breed or sex. Moreover, the responses were in agreement with those observed in previous human studies.

CONCLUSIONS

We conclude that findings in dogs may be predictive of human microbiome results. In particular, a novel finding is that overweight or obese dogs experience larger compositional shifts than lean dogs in response to a high-protein diet.

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.

Systematic review of the effects of the intestinal microbiota on selected nutrients and non-nutrients

PURPOSE

There is considerable interest in the effects of the intestinal microbiota (IM) composition, its activities in relation with the metabolism of dietary substrates and the impact these effects may have in the development and prevention of certain non-communicable diseases. It is acknowledged that a complex interdependence exists between the IM and the mammalian host and that the IM possesses a far greater diversity of genes and repertoire of metabolic and enzymatic capabilities than their hosts. However, full knowledge of the metabolic activities and interactions of the IM and the functional redundancy that may exist are lacking. Thus, the current review aims to assess recent literature relating to the role played by the IM in the absorption and metabolism of key nutrients and non-nutrients.

METHODS

A systematic review (PROSPERO registration: CRD42015019087) was carried out focussing on energy and the following candidate dietary substrates: protein, carbohydrate, fat, fibre, resistant starch (RS), and polyphenols to further understand the effect of the IM on the dietary substrates and the resulting by-products and host impacts. Particular attention was paid to the characterisation of the IM which are predominantly implicated in each case, changes in metabolites, and indirect markers and any potential impacts on the host.

RESULTS

Studies show that the IM plays a key role in the metabolism of the substrates studied. However, with the exception of studies focusing on fibre and polyphenols, there have been relatively few recent human studies specifically evaluating microbial metabolism. In addition, comparison of the effects of the IM across studies was difficult due to lack of specific analysis/description of the bacteria involved. Considerable animal-derived data exist, but experience suggests that care must be taken when extrapolating these results to humans. Nevertheless, it appears that the IM plays a role in energy homeostasis and that protein microbial breakdown and fermentation produced ammonia, amines, phenols and branch chain fatty acids, and a greater diversity in the microbes present. Few recent studies appear to have evaluated the effect of the IM composition and metabolism per se in relation with digestible dietary carbohydrate or fat in humans. Intakes of RS and prebiotics altered levels of specific taxa that selectively metabolised specific prebiotic/carbohydrate-type substances and levels of bifidobacteria and lactobacilli were observed to increase. In controlled human studies, consistent data exist that show a correlation between the intake of fibre and an increase in bifidobacteria and short-chain fatty acids, in particular butyrate, which leads to lower intestinal pH. Dietary polyphenols rely on modification either by host digestive enzymes or those derived from the IM for absorption to occur. In the polyphenol-related studies, a large amount of inter-individual variation was observed in the microbial metabolism and absorption of certain polyphenols.

CONCLUSIONS

The systematic review demonstrates that the IM plays a major role in the breakdown and transformation of the dietary substrates examined. However, recent human data are limited with the exception of data from studies examining fibres and polyphenols. Results observed in relation with dietary substrates were not always consistent or coherent across studies and methodological limitations and differences in IM analyses made comparisons difficult. Moreover, non-digestible components likely to reach the colon are often not well defined or characterised in studies making comparisons between studies difficult if not impossible. Going forward, further rigorously controlled randomised human trials with well-defined dietary substrates and utilizing omic-based technologies to characterise and measure the IM and their functional activities will advance the field. Current evidence suggests that more detailed knowledge of the metabolic activities and interactions of the IM hold considerable promise in relation with host health.

The effect of storage at ambient temperature on the feline fecal microbiota

BACKGROUND

Feline fecal microbiota analyses can potentially be impacted by a variety of factors such as sample preparation, sequencing method and bioinformatics analyses. Another potential influence is changes in the microbiota from storage of samples prior to processing. This study examined the effect of ambient temperature exposure on the feline fecal microbiota composition. Fecal samples were collected from 12 healthy cats, within 15 min after defecation. Samples were aliquoted and the first aliquot was frozen at -80 °C within 1 hour of defecation. Remaining aliquots were maintained at ambient temperature (20 to 23 °C) and frozen at -80 °C at 6, 12, 24, 36, 48, 72 and 96 h after collection. DNA was extracted from all aliquots, and polymerase chain reaction (PCR). The PCR products were sequenced with next-generation sequencing (Illumina MiSeq).

RESULTS

No significant differences were observed in alpha and beta biodiversity indexes, as well as relative abundance of different taxa over time (P > 0.05 for all tests between time points). Principal coordinate analyses demonstrated that samples cluster mainly by cat, with no significant differences between time points (AMOVA, P > 0.05; HOMOVA, P > 0.05). Linear discriminant analysis effect size method was performed and failed to detect any enriched taxa, between time points. Random forest algorithm analysis indicated homogeneity across time points.

CONCLUSIONS

Although existing evidence from human fecal storage studies is contradictory, a recent study in companion animals agreed with the current study, demonstrating that maintenance of feline fecal samples at ambient temperature for up to 4 days has no effect on the bacterial membership and structure.

Effects of the Dietary Protein and Carbohydrate Ratio on Gut Microbiomes in Dogs of Different Body Conditions

Obesity has become a health epidemic in both humans and pets. A dysbiotic gut microbiota has been associated with obesity and other metabolic disorders. High-protein, low-carbohydrate (HPLC) diets have been recommended for body weight loss, but little is known about their effects on the canine gut microbiome. Sixty-three obese and lean Labrador retrievers and Beagles (mean age, 5.72 years) were fed a common baseline diet for 4 weeks in phase 1, followed by 4 weeks of a treatment diet, specifically, the HPLC diet (49.4% protein, 10.9% carbohydrate) or a low-protein, high-carbohydrate (LPHC) diet (25.5% protein, 38.8% carbohydrate) in phase 2. 16S rRNA gene profiling revealed that dietary protein and carbohydrate ratios have significant impacts on gut microbial compositions. This effect appeared to be more evident in obese dogs than in lean dogs but was independent of breed. Consumption of either diet increased the bacterial evenness, but not the richness, of the gut compared to that after consumption of the baseline diet. Macronutrient composition affected taxon abundances, mainly within the predominant phyla, Firmicutes and Bacteroidetes. The LPHC diet appeared to favor the growth of Bacteroides uniformis and Clostridium butyricum, while the HPLC diet increased the abundances of Clostridium hiranonis, Clostridium perfringens, and Ruminococcus gnavus and enriched microbial gene networks associated with weight maintenance. In addition, we observed a decrease in the Bacteroidetes to Firmicutes ratio and an increase in the Bacteroides to Prevotella ratio in the HPLC diet-fed dogs compared to these ratios in dogs fed other diets. Finally, analysis of the effect of diet on the predicted microbial gene network was performed using phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt).

More than 50% of dogs are either overweight or obese in the United States. A dysbiotic gut microbiota is associated with obesity and other metabolic problems in humans. HPLC diets have been promoted as an effective weight loss strategy for many years, and potential effects were reported for both humans and dogs. In this study, we explored the influence of the protein and carbohydrate ratio on the gut microbiome in dogs with different body conditions. We demonstrated significant dietary effects on the gut microbiome, with greater changes in obese dogs than in lean dogs. The HPLC diet-fed dogs showed greater abundances of Firmicutes but fewer numbers of Bacteroidetes than other dogs. This knowledge will enable us to use prebiotics, probiotics, and other nutritional interventions to modulate the gut microbiota and to provide an alternative therapy for canine obesity.

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.

Characterization of Microbial Mat Microbiomes in the Modern Thrombolite Ecosystem of Lake Clifton, Western Australia Using Shotgun Metagenomics

Microbialite-forming communities interact with the environment and influence the precipitation of calcium carbonate through their metabolic activity. The functional genes associated with these metabolic processes and their environmental interactions are therefore critical to microbialite formation. The microbiomes associated with microbialite-forming ecosystems are just now being elucidated and the extent of shared pathways and taxa across different environments is not fully known. In this study, we profiled the microbiome of microbial communities associated with lacustrine thrombolites located in Lake Clifton, Western Australia using metagenomic sequencing and compared it to the non-lithifying mats associated with surrounding sediments to determine whether differences in the mat microbiomes, particularly with respect to metabolic pathways and environmental interactions, may potentially contribute to thrombolite formation. Additionally, we used stable isotope biosignatures to delineate the dominant metabolism associated with calcium carbonate precipitation in the thrombolite build-ups. Results indicated that the microbial community associated with the Lake Clifton thrombolites was predominantly bacterial (98.4%) with Proteobacteria, Cyanobacteria, Bacteroidetes, and Actinobacteria comprising the majority of annotated reads. Thrombolite-associated mats were enriched in photoautotrophic taxa and functional genes associated with photosynthesis. Observed δ¹³C values of thrombolite CaCO₃ were enriched by at least 3.5‰ compared to theoretical values in equilibrium with lake water DIC, which is consistent with the occurrence of photoautotrophic activity in thrombolite-associated microbial mats. In contrast, the microbiomes of microbial communities found on the sandy non-lithifying sediments of Lake Clifton represented distinct microbial communities that varied in taxa and functional capability and were enriched in heterotrophic taxa compared to the thrombolite-associated mats. This study provides new insight into the taxa and functional capabilities that differentiate potentially lithifying mats from other non-lithifying types and suggests that thrombolites are actively accreting and growing in limited areas of Lake Clifton.

Innovations in Canine and Feline Nutrition: Technologies for Food and Nutrition Assessment

Pet owners have increasing concerns about the nutrition of their pets, and they desire foods and treats that are safe, traceable, and of high nutritive value. To meet these high expectations, detailed chemical composition characterization of ingredients well beyond that provided by proximate analysis will be required, as will information about host physiology and metabolism. Use of faster and more precise analytical methodology and novel technologies that have the potential to improve pet food safety and quality will be implemented. In vitro and in vivo assays will continue to be used as screening tools to evaluate nutrient quality and adequacy in novel ingredients prior to their use in animal diets. The use of molecular and high-throughput technologies allows implementation of noninvasive studies in dogs and cats to investigate the impact of dietary interventions by using systems biology approaches. These approaches may further improve the health and longevity of pets.

The Gut Microbiome in the NOD Mouse

The microbiome (or microbiota) are an ecological community of commensal, symbiotic, and pathogenic microorganisms that outnumber the cells of the human body tenfold. These microorganisms are most abundant in the gut where they play an important role in health and disease. Alteration of the homeostasis of the gut microbiota can have beneficial or harmful consequences to health. There has recently been a major increase in studies on the association of the gut microbiome composition with disease phenotypes.The nonobese diabetic (NOD) mouse is an excellent mouse model to study spontaneous type 1 diabetes development. We, and others, have reported that gut bacteria are critical modulators for type 1 diabetes development in genetically susceptible NOD mice.Here we present our standard protocol for gut microbiome analysis in NOD mice that has been routinely implemented in our research laboratory. This incorporates the following steps: (1) Isolation of total DNA from gut bacteria from mouse fecal samples or intestinal contents; (2) bacterial DNA sequencing, and (3) basic data analysis.

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

Companion animals provide an excellent model for studies of the gut microbiome because potential confounders such as diet and environment can be more readily controlled for than in humans. Additionally, domestic cats and dogs are typically neutered early in life, enabling an investigation into the potential effect of sex hormones on the microbiome. In a longitudinal study to investigate the potential effects of neutering, neutering age and gender on the gut microbiome during growth, the faeces of kittens (16 male, 14 female) were sampled at 18, 30 and 42 weeks of age. DNA was shotgun sequenced on the Illumina platform and sequence reads were annotated for taxonomy and function by comparison to a database of protein coding genes. In a statistical analysis of diversity, taxonomy and functional potential of the microbiomes, age was identified as the only factor with significant associations. No significant effects were detected for gender, neutering, or age when neutered (19 or 31 weeks). At 18 weeks of age the microbiome was dominated by the genera Lactobacillus and Bifidobacterium (35% and 20% average abundance). Structural and functional diversity was significantly increased by week 30 but there was no further significant increase. At 42 weeks of age the most abundant genera were Bacteroides (16%), Prevotella (14%) and Megasphaera (8%). Significant differences in functional potential included an enrichment for genes in energy metabolism (carbon metabolism and oxidative phosphorylation) and depletion in cell motility (flagella and chemotaxis). We conclude that the feline faecal microbiome is predominantly determined by age when diet and environment are controlled for. We suggest this finding may also be informative for studies of the human microbiome, where control over such factors is usually limited.

Gut microbiota of humans, dogs and cats: current knowledge and future opportunities and challenges

High-throughput DNA sequencing techniques allow for the identification and characterisation of microbes and their genes (microbiome). Using these new techniques, microbial populations in several niches of the human body, including the oral and nasal cavities, skin, urogenital tract and gastrointestinal tract, have been described recently. Very little data on the microbiome of companion animals exist, and most of the data have been derived from the analysis of the faeces of healthy laboratory animals. High-throughput assays provide opportunities to study the complex and dense populations of the gut microbiota, including bacteria, archaea, fungi, protozoa and viruses. Our laboratory and others have recently described the predominant microbial taxa and genes of healthy dogs and cats and how these respond to dietary interventions. In general, faecal microbial phylogeny (e.g. predominance of Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria) and functional capacity (e.g. major functional groups related to carbohydrate, protein, DNA and vitamin metabolism; virulence factors; and cell wall and capsule) of the canine and feline gut are similar to those of the human gut. Initial sequencing projects have provided a glimpse of the microbial super-organism that exists within the canine and feline gut, but leaves much to be explored and discovered. As DNA provides information only about potential functions, studies that focus on the microbial transcriptome, metabolite profiles, and how microbiome changes affect host physiology and health are clearly required. Future studies must determine how diet composition, antibiotics and other drug therapies, breed and disease affect or are affected by the gut microbiome and how this information may be used to improve diets, identify disease biomarkers and develop targeted disease therapies.

Functional gene arrays-based analysis of fecal microbiomes in patients with liver cirrhosis

Background

Human gut microbiota plays an important role in the pathogenesis of cirrhosis complications. Although the phylogenetic diversity of intestinal microbiota in patients with liver cirrhosis has been examined in several studies, little is known about their functional composition and structure.

Results

To characterize the functional gene diversity of the gut microbiome in cirrhotic patients, we recruited a total of 42 individuals, 12 alcoholic cirrhosis patients, 18 hepatitis B virus (HBV)-related cirrhosis patients, and 12 normal controls. We determined the functional structure of these samples using a specific functional gene array, which is a combination of GeoChip for monitoring biogeochemical processes and HuMiChip specifically designed for analyzing human microbiomes. Our experimental data showed that the microbial community functional composition and structure were dramatically distinctive in the alcoholic cirrhosis. Various microbial functional genes involved in organic remediation, stress response, antibiotic resistance, metal resistance, and virulence were highly enriched in the alcoholic cirrhosis group compared to the control group and HBV-related cirrhosis group. Cirrhosis may have distinct influences on metabolic potential of fecal microbial communities. The abundance of functional genes relevant to nutrient metabolism, including amino acid metabolism, lipid metabolism, nucleotide metabolism, and isoprenoid biosynthesis, were significantly decreased in both alcoholic cirrhosis group and HBV-related cirrhosis group. Significant correlations were observed between functional gene abundances and Child-Pugh scores, such as those encoding aspartate-ammonia ligase, transaldolase, adenylosuccinate synthetase and IMP dehydrogenase.

Conclusions

Functional gene array was utilized to study the gut microbiome in alcoholic and HBV-related cirrhosis patients and controls in this study. Our array data indicated that the functional composition of fecal microbiomes was heavily influenced by cirrhosis, especially by alcoholic cirrhosis. This study provides new insights into the functional potentials and activity of gut microbiota in cirrhotic patients with different etiologies.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-753) contains supplementary material, which is available to authorized users.