Molecular monitoring and characterization of the faecal microbiota of healthy dogs during fructan supplementation

Gut microbiome dysbiosis is associated with host genetics in the Norwegian Lundehund

A group of diseases have been shown to correlate with a phenomenon called microbiome dysbiosis, where the bacterial species composition of the gut becomes abnormal. The gut microbiome of an animal is influenced by many factors including diet, exposures to bacteria during post-gestational growth, lifestyle, and disease status. Studies also show that host genetics can affect microbiome composition. We sought to test whether host genetic background is associated with gut microbiome composition in the Norwegian Lundehund dog, a highly inbred breed with an effective population size of 13 individuals. The Lundehund has a high rate of a protein-losing enteropathy in the small intestine that is often reported as Lundehund syndrome, which negatively affects longevity and life-quality. An outcrossing project with the Buhund, Norrbottenspets, and Icelandic sheepdog was recently established to reintroduce genetic diversity to the Lundehund and improve its health. To assess whether there was an association between host genetic diversity and the microbiome composition, we sampled the fecal microbiomes of 75 dogs of the parental (Lundehund), F1 (Lundehund x Buhund), and F2 (F1 x Lundehund) generations. We found significant variation in microbiome composition from the parental Lundehund generation compared to the outcross progeny. The variation observed in purebred Lundehunds corresponded to dysbiosis as seen by a highly variable microbiome composition with an elevated Firmicutes to Bacteroidetes ratio and an increase in the prevalence of Streptococcus bovis/Streptococcus equinus complex, a known pathobiont that can cause several diseases. We tracked several other environmental factors including diet, the presence of a cat in the household, living in a farm and the use of probiotics, but we did not find evidence of an effect of these on microbiome composition and alpha diversity. In conclusion, we found an association between host genetics and gut microbiome composition, which in turn may be associated with the high incidence of Lundehund syndrome in the purebred parental dogs.

Diet-induced changes in fecal microbiota composition and diversity in dogs (Canis lupus familiaris): A comparative study of BARF-type and commercial diets

BACKGROUND

Diet is known to strongly modulate the composition of the gut microbiota, thereby affecting health conditions and disease. Natural BARF-type and commercial diets have been used for feeding pets (e.g. dogs and cats) promoting changes in the canine microbiota in terms of abundance, richness, and diversity that may favor certain metabolic processes and resistance to certain infectious agents. Therefore, the present study sought to identify microbiota changes in dogs fed with a BARF-type diet versus dogs fed with a commercial diet by sequencing the V4 region of the 16S rRNA gene.

METHODS

The microbiota of dogs fed with the BARF-diet (n = 20) and commercial-diet (n = 26) was studied using fecal samples. A metabarcoding strategy was employed by sequencing the V4 hypervariable region of the 16S rRNA gene using the Illumina HiSeq platform. DADA2 was used to assess the quality profile of the reads and to determine the core sample inference algorithm of the reads to infer amplicon sequence variants (ASVs). The taxonomic assignment was performed using sequences from the Silva v138 formatted reference database. The microbial diversity analysis was performed using the R package Phyloseq, which was used to calculate diversity and abundance indices and construct the respective graphs. Linear discriminant analysis (LDA) effect size analysis (LEfSe) was used to identify the differentially abundant taxa in the BARF group versus the commercial-diet group.

RESULTS

The diet causes changes in fecal microbiota composition and diversity, with richness and diversity being higher in BARF-fed dogs. Beta diversity analyses confirmed that diet is directly related to microbiota composition regardless of breed or sex. Differentially enriched taxa were identified in each of the diets as Fusobacterium, Bacteroides, and Clostridium perfringens in BARF-fed dogs and Prevotella, Turicibacter, Faecalibacterium, and Peptacetobacter (Clostridium) hiranonis, mostly relevant in carbohydrate metabolism, in commercial-fed dogs.

CONCLUSIONS

This study is the first one carried out in dogs from Colombia that seeks to identify changes in the intestinal microbiota concerning natural BARF type diet and commercial diet using a metabarcoding approach. Important differences were identified in terms of richness, diversity, and differentially enriched bacteria in each of the diets. The microbiota of dogs fed the BARF diet was characterized by higher richness and diversity compared to the commercial diet. However, it was identified that BARF-fed dogs can potentially acquire more opportunistic infections by pathogens of importance such as C. perfringens. Most of the taxa enriched in commercial diet-fed dogs are linked to carbohydrate metabolism, which may be directly related to diet composition.

Association of gut microbiota and SCFAs with finishing weight of Diannan small ear pigs

Finishing weight is a key economic trait in the domestic pig industry. Evidence has linked the gut microbiota and SCFAs to health and production performance in pigs. Nevertheless, for Diannan small ear (DSE) pigs, a specific pig breed in China, the potential effect of gut microbiota and SCFAs on their finishing weight remains unclear. Herein, based on the data of the 16S ribosomal RNA gene and metagenomic sequencing analysis, we found that 13 OTUs could be potential biomarkers and 19 microbial species were associated with finishing weight. Among these, carbohydrate-decomposing bacteria of the families Streptococcaceae, Lactobacillaceae, and Prevotellaceae were positively related to finishing weight, whereas the microbial taxa associated with intestinal inflammation and damage exhibited opposite effects. In addition, interactions of these microbial species were found to be linked with finishing weight for the first time. Gut microbial functional annotation analysis indicated that CAZymes, such as glucosidase and glucanase could significantly affect finishing weight, given their roles in increasing nutrient absorption efficiency. Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthologies (KOs) and KEGG pathways analysis indicated that glycolysis/gluconeogenesis, phosphotransferase system (PTS), secondary bile acid biosynthesis, ABC transporters, sulfur metabolism, and one carbon pool by folate could act as key factors in regulating finishing weight. Additionally, SCFA levels, especially acetate and butyrate, had pivotal impacts on finishing weight. Finishing weight-associated species Prevotella sp. RS2, Ruminococcus sp. AF31-14BH and Lactobacillus pontis showed positive associations with butyrate concentration, and Paraprevotella xylaniphila and Bacteroides sp. OF04-15BH were positively related to acetate level. Taken together, our study provides essential knowledge for manipulating gut microbiomes to improve finishing weight. The underlying mechanisms of how gut microbiome and SCFAs modulate pigs' finishing weight required further elucidation.

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

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

Feeding Fiber-Bound Polyphenol Ingredients at Different Levels Modulates Colonic Postbiotics to Improve Gut Health in Dogs

Simple Summary

Microbes present in the large intestine of humans and companion animals produce bioactive metabolites from host-ingested food. These bioactive metabolites can influence host health. A prior study in dogs that were healthy or had chronic enteritis/gastroenteritis showed that stool quality improved when they ate food containing a fiber bundle made from fibers of pecan shells, flax seed, cranberry, citrus, and beet. In addition, eating food containing the fiber bundle resulted in the gut bacteria shifting from digesting mainly protein to digesting mainly carbohydrates. The present study tested the impact of the fiber bundle at a lower range of concentrations in dogs. Fecal levels of several bioactive metabolites with beneficial antioxidant or anti-inflammatory properties increased after dogs consumed food with the fiber bundle, though no changes in the bacteria or their functional pathways were observed. Stool quality remained in the acceptable range. These results suggest that the gut bacteria were able to digest the fiber bundle to produce beneficial bioactive metabolites to improve host health.

Abstract

This study assessed changes in canine fecal metabolites and microbiota with the consumption of foods with increasing concentrations of a fiber bundle including pecan shells, flax seed, and powders of cranberry, citrus, and beet that was previously shown (at 14% w/w) to improve stool quality, shift fecal bacterial metabolism from proteolysis to saccharolysis, increase abundance of saccharolytic bacteria, and decrease abundance of proteolytic bacteria. In this study, 48 healthy adult dogs were split evenly to consume different inclusion levels (0%, 1%, 2%, and 4%) of the fiber bundle for a 31-day period following a 28-day pre-feed period. Increases from baseline in the fecal short-chain fatty acids butyric acid, valeric acid, and hexanoic acid were observed only in the dogs that consumed the food with the 4% fiber bundle. With addition of any level of the fiber bundle, increases were seen in the polyphenols hesperidin, hesperetin, ponciretin, secoisolariciresinol diglucoside, secoisolariciresinol, and enterodiol. However, fecal microbiota and their metabolism, and stool scores were largely unaffected by the fiber bundle. Overall, addition of the fiber bundle appeared to increase bioactive metabolites of increased antioxidant and anti-inflammatory potency for beneficial to health and, at levels ≥4%, shifted gut bacterial metabolism toward saccharolysis.

Effect of sequentially fed high protein, hydrolyzed protein, and high fiber diets on the fecal microbiota of healthy dogs: a cross-over study

Background

Dietary content and environmental factors can shape the gut microbiota, and consequently, the way the gut microbiota metabolizes fats, carbohydrates, and proteins, affecting overall health of the host. We evaluated the impact of 3 diets (all meat [raw], high-insoluble fiber dry extruded diet and hydrolyzed protein dry extruded diet) on the gut microbiota of healthy dogs in a cross-over sequential study.

Results

We showed that diet can have an effect on the gut microbiome in dogs, which was influenced by the order of feeding. High-protein (all meat) diets were characterized by an increase in bacteria belonging to the Fusobacteria and Bacteroidetes phyla, whereas a high-insoluble fiber commercial diet correlated with increases in Firmicutes and Actinobacteria phyla. However, the individual dog’s baseline microbiota had the most impact on the magnitude and nature of the changes in response to dietary intervention.

Conclusion

Our results suggest that the dog fecal microbiota is driven by protein and fiber composition to different degrees in individual animals, and targeted modification of these patterns could be useful in the modulation of the gut microbiota in different diseases.

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-021-00101-8.

High-Fat Diets Led to OTU-Level Shifts in Fecal Samples of Healthy Adult Dogs

High fat diets have been reported to negatively affect the microbiota in both mice and humans. However, there is a lack of studies in canine models. The variation among the gastrointestinal (GI) tract anatomy/physiology and typical diet compositions of these animal species may lead to vastly different results. Due to the large inclusion rate of dietary fat in pet food, it is critical to understand its effects in a canine model. Therefore, the study objective was to report the effects of high fat, low carbohydrate diets on the fecal microbiota in healthy adult dogs. Eight adult beagles were randomly assigned to one of four dietary treatments within each 15-day period of a replicated 4x4 Latin Square design. Diets contained 32% (T1), 37% (T2), 42% (T3), and 47% (T4) fat. T2, T3, and T4 were created by adding increasing levels of canola oil to T1, a commercially manufactured canned canine diet, which served as the control diet. Fresh fecal samples were collected during the last 5 days of each period for microbial analysis. DNA was extracted from fecal samples and paired-end 16S rRNA gene amplicon sequencing was performed using the Illumina MiSeq platform. When comparing whole microbial communities using PERMANOVA, no significant differences were observed among treatments (P = 0.735). Individual OTUs were analyzed using the GLIMMIX procedure of SAS with fixed effects of diet and room, and the random effects of period and animal. Out of the 100 most abundant individual OTUs, 36 showed significant differences in abundance based on treatment (q < 0.05). Overall, OTUs assigned to genera related to fat digestion increased while OTUs assigned to genera involved in carbohydrate digestion decreased. In conclusion, the microbial community adapted to dietary intervention without jeopardizing the health of the animals, evaluated by body condition score, fecal characteristics, and blood parameters.

First description of Streptococcus lutetiensis from a diseased cat

This paper describes for the first time the isolation of Streptococcus lutetiensis in a cat with intestinal lymphoma. The Streptococcus bovis group has undergone significant taxonomic changes over the past two decades and, in 2002, Poyart et al. described two distinct novel species within the genus Streptococcus: Streptococcus lutetiensis and Streptococcus pasteurianus. The bovis group streptococci include commensal species and subspecies or opportunistic pathogens of humans and animals. The cat was referred to the Veterinary Teaching Hospital, University of Bologna for chronic diarrhoea associated with fresh blood. A diagnosis of intestinal lymphoma was advanced. S. lutetiensis was accidentally isolated from the faeces of the cat and identified through MALDI-TOF and 16s rRNA sequencing. The Kirby-Bauer test revealed that the isolate was resistant to enrofloxacin, erythromycin, clindamycin, marbofloxacin and tetracycline. The detection of S. lutetiensis in cat faeces might suggest that it could be a normal inhabitant of cat intestinal tract or that it could be involved in the manifestation of intestinal diseases. Since bacteria belonging to the S. bovis group are considered emerging pathogens, additional research is required to evaluate the role of S. lutetiensis in cats and its role in the transmission of antimicrobial resistance. SIGNIFICANCE AND IMPACT OF THE STUDY: In this study the isolation of Streptococcus lutetiensis from a cat with intestinal lymphoma was described for the first time. An antimicrobial susceptibility test performed by means of the disc diffusion method revealed that the isolate was resistant to enrofloxacin, erythromycin, clindamycin, marbofloxacin and tetracycline. Nowadays the ecological or pathogenetic role of S. lutetiensis in the gut of animals remains unclear but, even if its role as commensal bacterium was confirmed, the presence of multi-resistant S. lutetiensis in cat gut could favour the transmission of antimicrobial resistance to other bacteria.

Balance of saccharolysis and proteolysis underpins improvements in stool quality induced by adding a fiber bundle containing bound polyphenols to either hydrolyzed meat or grain-rich foods

Dietary fiber is a key component in gastrointestinal health maintenance partly due to its fermentation by the gut microbiome. The food-dependent effects of a novel fiber bundle added to hydrolyzed meat (HM) or grain-rich (GR) foods in healthy dogs (n = 16) or those with chronic enteritis/gastroenteritis (n = 16) were examined. Addition of fiber to either food improved stool quality in dogs regardless of health status; microbiome diversity of dogs with chronic enteritis/gastroenteritis became more similar to healthy dogs. The abundance of bacteria mediating beneficial saccharolytic processes (eg, Lachnospiraceae) significantly increased on addition of fiber to the GR food, while those mediating detrimental proteolytic catabolism (eg, Desulfovibrionaceae) significantly decreased. Fiber addition to the HM food led to significant changes in saccharolytic/proteolytic bacteria. Higher levels of free saccharides in feces upon fiber addition to either food indicated increased saccharolysis. Fiber addition to the GR food decreased levels of fecal free amino acids, indicating decreased proteolysis. Addition of fiber decreased fecal pH for both foods but likely by different mechanisms: addition of fiber to the HM food led to increased straight-chain short-chain fatty acids (SCFAs) and no significant change in proteolytic branched-chain SFCAs, while in the GR food, fiber mainly led to decreased proteolytic branched-chain SFCAs. Other postbiotics related to intestinal health were consistently altered when fiber was added to either food. Plant-derived bioactive molecules were enriched in feces from dogs fed either food with added fiber, which could account for the observed modulation of the canine gut microbiome and shifts in metabolic capacity.

Inulin with different degrees of polymerization modulates composition of intestinal microbiota in mice

The study aimed to analyze the global influences of dietary inulin with different degrees of polymerization (DP) on intestinal microbial communities. Six-week-old male C57BL/6J mice were treated with fructo-oligosaccharides and inulin for 6 weeks. Fecal samples were obtained at time point 0 and 6th week. 16S rRNA sequence analysis was used to measure intestinal microbiota performed on the Illumina MiSeq platform. Influences of dietary inulin on intestinal microbiota were more complex effects than bifidogenic effects, relative abundance of butyrate-producing bacteria increased after interventions. Akkermansia muciniphila, belonging to mucin-degrading species, became a dominant species in Verrucomicrobia phylum after treatment with fructo-oligosaccharides and inulin. Modulation effects of intestinal microbiota were positively correlated with DP. Lower DP interventions exhibited better effects than higher DP treatment on stimulation of probiotics. We hypothesized that Akkermansia muciniphila played an important role on maintaining balance between mucin and short chain fatty acids.

A diet change from dry food to beef induces reversible changes on the faecal microbiota in healthy, adult client-owned dogs

BACKGROUND

Diet has a major influence on the composition of the gut microbiota, whose importance for gut health and overall well-being is increasingly recognized. Knowledge is limited regarding health implications, including effects on the faecal microbiota, of feeding a diet with high content of red meat to dogs, despite some owners' apparent preference to do so. The aim of this study was to evaluate how a diet change from commercial dry food to one with a high content of boiled minced beef and vice versa influenced the faecal microbiota, and short chain fatty acid profile in healthy, adult, client-owned dogs.

RESULTS

The diet change influenced the faecal microbiota composition and diversity (Shannon diversity index). The most abundant OTUs in samples of dogs fed the dry food and high minced beef were affiliated with the species Faecalibacterium prausnitzii and Clostridia hiranonis respectively. The high minced beef diet apparently also influenced the short chain fatty acid profile, with increased isovaleric acid, as well as an increase in faecal pH. These effects were reversed when the commercial dry food was reintroduced in weeks 6 and 7.

CONCLUSIONS

Results of this study can aid in the understanding of how diet changes influence the faecal microbiota and metabolite content on a short-term basis. Long-term studies are required to investigate potential implications for canine gut and general health.

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.

In vitro influence of dietary protein and fructooligosaccharides on metabolism of canine fecal microbiota

Background

The present in vitro study investigated whether the utilization of fructooligosaccharides (FOS) may influence canine fecal microbial population in presence of diets differing in their protein content and digestibility. Fresh fecal samples were collected from five adult dogs, pooled, and incubated for 24 h with the undigested residue of three diets: 1, Low protein high digestibility diet (LP HD, crude protein (CP) 229 g/kg); 2, High protein high digestibility diet (HP HD, CP 304 g/kg); 3, High protein low digestibility diet (HP LD, CP 303 g/kg) that had been previously subjected to enzymatic digestion. In the in vitro fermentation study, there were six treatments: 1) LP HD; 2) HP HD 3) HP LD; 4) LP HD + FOS; 5) HP HD + FOS; 6) HP LD + FOS. Fructooligosaccharides were added at the final concentration of 1.5 g/L. Samples of fermentation fluid were collected at 6 and 24 h of incubation.

Results

Values of pH were reduced by FOS at 6 and 24 h (P < 0.001); conversely, low protein digestibility and high dietary protein level resulted in higher pH at both sampling times (P < 0.001). At 24 h, FOS lowered ammonia (−10 %; P < 0.001) and resulted (P < 0.05) in higher concentrations of total volatile fatty acids (VFA) (+43 %), acetic acid (+14 %), propionic acid (+75 %) and n-butyric acid (+372 %). Conversely, at 24 h, low protein digestibility resulted (P < 0.01) in lower concentrations of acetic acid (−26 %), propionic acid (−37 %) and total VFA (−21 %). Putrescine concentrations were increased at 6 and 24 h of fermentation by low protein digestibility (+21 and 22 %, respectively; P < 0.05) and FOS (+18 and 24 %, respectively; P < 0.01). After 24 h of fermentation, high dietary protein level resulted in lower counts of lactobacilli and enterococci (−0.5 and −0.7 log cells/mL, respectively; P < 0.05) whereas low protein digestibility tended to increase counts of C. perfringens (+0.2 log cells/mL; P = 0.07).

Conclusions

Results from the present study showed that diets rich in protein may exert negative influences on the canine intestinal ecosystem, slightly increasing the presence of ammonia and reducing counts of lactobacilli and enterococci. Moreover, the presence of poorly digestible protein resulted in lower concentrations of VFA. Conversely, administration of FOS may improve metabolism of canine intestinal microbiota, reducing ammonia concentrations and enhancing VFA production.

Genomics, evolution, and molecular epidemiology of the Streptococcus bovis/Streptococcus equinus complex (SBSEC)

The Streptococcus bovis/Streptococcus equinus complex (SBSEC) is a group of human and animal derived streptococci that are commensals (rumen and gastrointestinal tract), opportunistic pathogens or food fermentation associates. The classification of SBSEC has undergone massive changes and currently comprises 7 (sub)species grouped into four branches based on sequences identities: the Streptococcus gallolyticus, the Streptococcus equinus, the Streptococcus infantarius and the Streptococcus alactolyticus branch. In animals, SBSEC are causative agents for ruminal acidosis, potentially laminitis and infective endocarditis (IE). In humans, a strong association was established between bacteraemia, IE and colorectal cancer. Especially the SBSEC-species S. gallolyticus subsp. gallolyticus is an emerging pathogen for IE and prosthetic joint infections. S. gallolyticus subsp. pasteurianus and the S. infantarius branch are further associated with biliary and urinary tract infections. Knowledge on pathogenic mechanisms is so far limited to colonization factors such as pili and biofilm formation. Certain strain variants of S. gallolyticus subsp. macedonicus and S. infantarius subsp. infantarius are associated with traditional dairy and plant-based food fermentations and display traits suggesting safety. However, due to their close relationship to virulent strains, their use in food fermentation has to be critically assessed. Additionally, implementing accurate and up-to-date taxonomy is critical to enable appropriate treatment of patients and risk assessment of species and strains via recently developed multilocus sequence typing schemes to enable comparative global epidemiology. Comparative genomics revealed that SBSEC strains harbour genomics islands (GI) that seem acquired from other streptococci by horizontal gene transfer. In case of virulent strains these GI frequently encode putative virulence factors, in strains from food fermentation the GI encode functions that are pivotal for strain performance during fermentation. Comparative genomics is a powerful tool to identify acquired pathogenic functions, but there is still an urgent need for more physiological and epidemiological data to understand SBSEC-specific traits.

Development and genetic influence of the rectal bacterial flora of newborn calves

The aim of the study was to investigate a dynamic change in the rectal flora of calves as well as to study a genetic influence on the intestinal microflora of calves. The bacterial community of fecal samples from calves was examined by PCR single strand conformation polymorphism (PCR-SSCP) in two independent studies. In study one 14 newborn calves of the same farm were examined. Sampling was conducted directly after delivery (meconium) and after 6 h, 12 h, 24 h, 48 h, 3 d, 7 d, 14 d and 42 d of life. In study two 6 twin calves and their coresident of the same age and farm were analysed in order to study for the first time whether genetic predisposition of the host may influence the fecal microflora. All calves were weaned directly after delivery and received pumped colostrum without direct contact to other farm animals. After delivery and during the first 12h of life the SSCP profiles were simple, but became more complex since the bacterial diversity increased with time in all calves. It became obvious that the intra-individual band-pattern similarity decreased over time and inter-individual similarity was low. The analysis of fecal samples from twin calves revealed higher similarity in SSCP profiles for twins compared to their coresident indicating that the individual microflora might be genetically or epigenetically influenced. The insight that there are several conformities between intestinal microfloras of healthy calves and that there might be genetic influence on the fecal flora could help to prevent diarrhoeal diseases in the future.

Abrupt temporal fluctuations in the chicken fecal microbiota are explained by its gastrointestinal origin

One of the main challenges in understanding the composition of fecal microbiota is that it can consist of microbial mixtures originating from different gastrointestinal (GI) segments. Here, we addressed this challenge for broiler chicken feces using a direct 16S rRNA gene-sequencing approach combined with multivariate statistical analyses. Broiler feces were chosen because of easy sampling and the importance for pathogen transmission to the human food chain. Feces were sampled daily for 16 days from chickens with and without a feed structure-induced stimulation of the gastric barrier function. Overall, we found four dominant microbial phylogroups in the feces. Two of the phylogroups were related to clostridia, one to lactobacilli, and one to Escherichia/Shigella. The relative composition of these phylogroups showed apparent stochastic temporal fluctuations in feces. Analyses of dissected chickens at the end of the experiment, however, showed that the two clostridial phylogroups were correlated to the microbiota in the cecum/colon and the small intestine, while the upper gut (crop and gizzard) microbiota was correlated to the lactobacillus phylogroup. In addition, chickens with a stimulated gizzard also showed less of the proximate GI dominating bacterial group in the feces, supporting the importance of the gastric barrier function. In conclusion, our results suggest that GI origin is a main determinant for the chicken fecal microbiota composition. This knowledge will be important for future understanding of factors affecting shedding of both harmful and beneficial gastrointestinal bacteria through feces.

In vitro effects of synbiotic fermentation on the canine faecal microbiota

Stirred, pH-controlled anaerobic batch cultures were used to investigate the in vitro effects of galacto-oligosaccharides (GOS) alone or combined with the probiotic Bifidobacterium bifidum 02 450B on the canine faecal microbiota of three different donors. GOS supported the growth of B. bifidum 02 450B throughout the fermentation. Quantitative analysis of bacterial populations by FISH revealed significant increases in Bifidobacterium spp. counts (Bif164) and a concomitant decrease in Clostridium histolyticum counts (Chis150) in the synbiotic-containing vessels compared with the controls and GOS vessels. Vessels containing probiotic alone displayed a transient increase in Bifidobacterium spp. and a transient decrease in Bacteroides spp. Denaturing gradient gel electrophoresis analysis showed that GOS elicited similar alterations in the microbial profiles of the three in vitro runs. However, the synbiotic did not alter the microbial diversity of the three runs to the same extent as GOS alone. Nested PCR using universal primers, followed by bifidobacterial-specific primers illustrated low bifidobacterial diversity in dogs, which did not change drastically during the in vitro fermentation. This study illustrates that the canine faecal microbiota can be modulated in vitro by GOS supplementation and that GOS can sustain the growth of B. bifidum 02 450B in a synbiotic combination.

Investigation of the faecal microbiota associated with canine chronic diarrhoea

Diarrhoea is a common problem in dogs and can result in disturbance of the normal intestinal microbiota. However, little is known about the gastrointestinal microbiota of dogs with chronic diarrhoea and controlled canine studies of dietary management are scarce. The aims of this study were to investigate the predominant faecal microbiota of chronic diarrhoea dogs and to examine the effect(s) of a fibre blend on the canine faecal microbiota. A 3-week fibre supplementation feeding study was performed in nine chronic diarrhoea and eight control dogs. Atopobium cluster, Lactobacillus-Enterococcus group and Clostridium cluster XIV were the predominant bacterial groups in all dogs. Chronic diarrhoea dogs had significantly higher Bacteroides counts at baseline and significantly lower Atopobium cluster counts following fibre supplementation compared with control dogs. Atopobium cluster levels increased significantly in control dogs, while counts of sulphate-reducing bacteria decreased significantly and Clostridium clusters I and II counts increased significantly in chronic diarrhoea dogs during fibre supplementation. Microbial profiles (detected by denaturing gradient gel electrophoresis) demonstrated interindividual variation, with greater similarity seen between the chronic diarrhoea and control dogs' profiles after fibre supplementation compared with baseline. In conclusion, fibre supplementation induced changes in the canine faecal microbiota, with greater resemblance between the microbiota of chronic diarrhoea and control dogs after this dietary modulation.

Estimation of intestinal permeability in healthy dogs using the contrast medium iohexol

BACKGROUND

Iohexol is a nonradioactive marker that has been used successfully to test intestinal permeability in humans with inflammatory bowel disease. There is evidence in dogs that iohexol shares a similar permeability pathway as (51)chromium-EDTA, the gold standard marker.

OBJECTIVE

The objective of this study was to determine an optimal oral iohexol dosage for an intestinal permeability serum test (IPST) and to use the test to estimate intestinal permeability in healthy dogs.

METHODS

Eight clinically healthy dogs free of gastrointestinal, liver, and pancreatic disease were used in the study. Dosages of 0.25, 0.5, 1.0, 2.0, and 4.0 mL/kg of Omnipaque-350 (iohexol) were administered to 2 dogs at weekly intervals. Iohexol concentration was determined in serum samples obtained hourly for 6 hours after administration by high-performance liquid chromatography. Using the optimal dosage, iohexol was administered to 8 dogs twice, 6-36 days (mean 10 days) apart, and coefficients of variation (CVs) for iohexol concentration were calculated.

RESULTS

A dosage of 2.0 mL/kg was chosen as optimal for the IPST, based on ease of iohexol detection in serum, intestinal contrast, and clinical effects of iohexol. Following administration of this dose to healthy dogs, mean (+/-SD) serum iohexol concentrations were 8.74+/-4.38, 11.89+/-5.67, 12.40+/-5.47, 9.23+/-5.54, 7.61+/-5.13, and 5.27+/-2.67 microg/mL at 1, 2, 3, 4, 5, and 6 hours after iohexol administration, respectively. CVs between the 2 test days were 28-45%.

CONCLUSIONS

Using the iohexol dosage established in this study, the iohexol IPST was easy to perform as a marker for intestinal permeability in dogs. Further studies to establish reference intervals and evaluate the diagnostic value of the iohexol IPST in dogs with gastrointestinal disease are warranted.

Evaluation of (GTG)5-PCR for rapid identification of Streptococcus mutans

Repetitive sequence-based polymerase chain reaction (PCR) fingerprinting using the (GTG)(5) primer was applied for fast screening of bacterial strains isolated from dental plaque of early childhood caries (ECC)-affected children. A group of 29 Gram-positive bacteria was separated into a homogeneous cluster together with Streptococcus mutans reference strains and constituted an aberrant branch after the numerical analysis of (GTG)(5)-PCR fingerprints. Automated ribotyping with EcoRI restriction enzyme (RiboPrinter microbial characterization system) revealed high genetic heterogeneity among the tested group and proved to be a good tool for strain-typing purposes. Further characterization of the studied strains was achieved by extensive phenotyping and whole-cell protein fingerprinting and confirmed all the strains as S. mutans representatives. Obtained results showed rep-PCR fingerprinting with the (GTG)(5) primer to be a fast and reliable method for identification of S. mutans.

Detection and identification of bacteria intimately associated with fungi of the order Sebacinales

Because of their beneficial impact on plants, the highly diverse mycorrhizal fungi grouped in the order Sebacinales lay claim to high ecological and agricultural significance. Here, we describe for the first time associations of Sebacinoid members with bacteria. Using quantitative PCR, denaturating gradient gel electrophoresis and fluorescence in situ hybridization, we detected an intimate association between Piriformospora indica and Rhizobium radiobacter, an alpha-Proteobacterium. The stability of the association, vertical transmission of the bacteria during asexual fungal reproduction and fungal plant colonization was monitored using R. radiobacter-specific primers. Treatment of mycelium or fungal protoplasts with antibiotics highly efficient against the free bacteria failed to cure the fungus. Barley seedlings dip-inoculated with R. radiobacter showed growth promotion and systemic resistance to the powdery mildew fungus Blumeria graminis comparable to P. indica inoculation. By screening additional isolates of the Sebacina vermifera complex, three species-specific associations with bacteria from the genera Paenibacillus, Acinetobacter and Rhodococcus were found. These findings suggest that Sebacinales species regularly undergo complex interactions involving host plants and bacteria reminiscent of other ectomycorrhizal and endomycorrhizal associations.

Effects of dietary inulin on the intestinal short chain fatty acids and microbial ecology in broiler chickens as revealed by denaturing gradient gel electrophoresis

Inulin can stimulate the growth of the intestinal bacteria as well as alter the ratio among various short chain fatty acids (SCFA) produced. In the present study, we analyzed the effect of dietary inulin on the intestinal bacterial community as determined by denaturing gradient gel electrophoresis analysis of universal 16S rDNA after amplication with PCR and SCFA profile. Broilers were fed a diet primarily composed of corn-soybean meal or same diet with 1% inulin for 42 d. The relative weight of digesta-filled ceca of the inulin-fed group was higher (P<0.01) than in the control group. Amongst SCFA, only acetate could be detected in the jejunal digesta, which tended to be higher (P=0.09) in inulin-fed group compared with the control group. Inulin did not affect the total concentration of SCFA in the cecal digesta. The relative proportion of n-butyrate was elevated (P=0.05) with a concomitant decrease in the concentration of n-valerate (P<0.05) in the inulin-fed group compared with the control group. Dietary inulin did not affect the number of PCR-denaturing gradient gel electrophoresis bands nor their diversity in the jejunal and cecal digesta. Intragroup similarities were not different between the groups, nor were any differences between intra-and intergroup similarities in the jejunal and cecal samples. In conclusion, inulin altered the cecal microbial metabolic activity without any major impact on the composition of intestinal bacterial communities as measured by the present techniques.

Coamplification of eukaryotic DNA with 16S rRNA gene-based PCR primers: possible consequences for population fingerprinting of complex microbial communities

The main aim of this study was to evaluate the specificity of three commonly used 16S rRNA gene-based polymerase chain reaction (PCR) primer sets for bacterial community analysis of samples contaminated with eukaryotic DNA. The specificity of primer sets targeting the V3, V3-V5, and V6-V8 hypervariable regions of the 16S rRNA gene was investigated in silico and by community fingerprinting of human and fish intestinal samples. Both in silico and PCR-based analysis revealed cross-reactivity of the V3 and V3-V5 primers with the 18S rRNA gene of human and sturgeon. The consequences of this primer anomaly were illustrated by denaturing gradient gel electrophoresis (DGGE) profiling of microbial communities in human feces and mixed gut of Siberian sturgeon. DGGE profiling indicated that the cross-reactivity of 16S rRNA gene primers with nontarget eukaryotic DNA might lead to an overestimation of bacterial biodiversity. This study has confirmed previous sporadic indications in literature indicating that several commonly applied 16S rRNA gene primer sets lack specificity toward bacteria in the presence of eukaryotic DNA. The phenomenon of cross-reactivity is a potential source of systematic error in all biodiversity studies where no subsequent analysis of individual community amplicons by cloning and sequencing is performed.

Effects of dietary scFOS on immunoglobulins in colostrums and milk of bitches

Fructo-oligosaccharides (scFOS) are prebiotic ingredients that improve protection against pathogens probably through promoting the growth of gastrointestinal bacteria-like Bifidobacteria and Lactobacilli: this stimulation may lead to a better development of immune repertoire and/or stimulation of the local immune response. According to the existence of the immune entero-mammary link, we were wondering if the dietary supplementation with scFOS could enhance the mucosal immunoglobulin level in mammary secretions. Results in this study show that bitches supplemented with scFOS exhibit higher colostrum and milk IgM content without concomitant effect on IgG1, IgG2 and IgA. In addition, intranasally immunized puppies exhibited a trend to higher Bordetella bronchiseptica-specific IgM immune response. The dietary supplementation with scFOS increased the IgM level in colostrums and milk of bitches by mechanisms which remain to be elucidated.