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

Gut Microbiota Comparison in Rectal Swabs Versus Stool Samples in Cats with Kidney Stones

To investigate the role of the intestinal bacterial microbiota in the pathogenesis of calcium oxalate nephrolithiasis in cats, a condition characterized by the formation of kidney stones, it is desirable to identify a sample collection method that accurately reflects the microbiota's composition. The objective of this study was to evaluate the impact of fecal sample collection methods on the intestinal microbiota composition in two cat populations: healthy cats and kidney stone-diseased cats. The study included eighteen cats from the same colony, comprising nine healthy cats and nine cats with spontaneously occurring presumed calcium oxalate kidney stones. Three fecal collection methods were compared: rectal swabs, the collection of fresh stool, and the collection of stool exposed to ambient air for 24 h. The bacterial microbiota was analyzed through the high-resolution sequencing of the V3-V4 region of the 16S rRNA gene. For all cats, within the same individual, a one-way PERMANOVA analysis showed a significant difference between the rectal swabs and fresh stool (p = 0.0003), as well as between the rectal swabs and stool exposed to ambient air for 24 h (p = 0.0003), but no significant difference was identified between the fresh stool and non-fresh stool (p = 0.0651). When comparing the two populations of cats, this study provides seemingly conflicting results. (1) A principal component analysis (PCA) comparison revealed a significant difference in the bacterial composition between the healthy cats and the cats with kidney stones only when the sample was a fresh fecal sample (p = 0.0037). This finding suggests that the intestinal bacteria involved in the pathogenesis of kidney stones in cats are luminal and strictly anaerobic bacteria. Consequently, exposure to ambient air results in a loss of information, preventing the identification of dysbiosis. For clinical studies, non-fresh stool samples provided by owners does not appear suitable for studying the gut microbiota of cats with kidney stones; fresh stool should be favored. (2) Interestingly, the rectal swabs alone highlighted significant differences in the proportion of major phyla between the two populations. These findings highlight the critical importance of carefully selecting fecal collection methods when studying feline gut microbiota. Combining rectal swabs and fresh stool sampling provides complementary insights, offering the most accurate understanding of the gut microbiota composition in the context of feline kidney stone pathogenesis.

Fecal microbiota and concentrations of long-chain fatty acids, sterols, and unconjugated bile acids in cats with chronic enteropathy

Feline chronic enteropathies (FCE) are common causes of chronic gastrointestinal signs in cats and include different diseases such as food-responsive enteropathy (FRE), inflammatory bowel diseases (IBD), and low-grade intestinal T-cell lymphoma (LGITL). Although changes in intestinal microbiota and fecal metabolites have been reported in dogs and humans with chronic enteropathy, research in cats has been limited. Therefore, this study aimed to evaluate the fecal microbiota and lipid-related fecal metabolites in cats with FCE to a clinically healthy comparison group (CG). A total of 34 cats with FCE (13 FRE, 15 IBD, and 6 LGITL) and 27 cats in the CG were enrolled in this study. The fecal microbiota was evaluated by the qPCR-based feline Dysbiosis Index (DI). The feline DI in cats with CE (median: 1.3, range: -2.4 to 3.8) was significantly higher (p < 0.0001) compared to CG (median: - 2.3, Range: -4.3 to 2.3), with no difference found among the FCE subgroups. The fecal abundances of Faecalibacterium (p < 0.0001), Bacteroides (p < 0.0001), Fusobacterium (p = 0.0398), Bifidobacterium (p = 0.0004), and total bacteria (p = 0.0337) significantly decreased in cats with FCE. Twenty-seven targeted metabolites were measured by gas chromatography-mass spectrometry, including long-chain fatty acids (LCFAs), sterols, and bile acids (BAs). Fecal concentrations of 5 of 12 LCFAs were significantly increased in cats with FCE compared to CG. Fecal concentrations of zoosterol (p = 0.0109), such as cholesterol (p < 0.001) were also significantly increased in cats with FCE, but those of phytosterols were significantly decreased in this group. No differences in fecal BAs were found between the groups. Although no differences were found between the four groups, the fecal metabolomic pattern of cats with FRE was more similar to that of the CG than to those with IBD or LGITL. This could be explained by the mild changes associated with FRE compared to IBD and LGITL. The study showed changes in intestinal microbiota and alteration of fecal metabolites in FCE cats compared to the CG. Changes in fecal lipids metabolites suggest a dysmetabolism of lipids, including LCFAs, sterols, and unconjugated BAs in cats with CE.

Evaluation of fecal sample collection methods for feline gut microbiome profiling: fecal loop vs. litter box

Introduction

Microbial population structures within fecal samples are vital for disease screening, diagnosis, and gut microbiome research. The two primary methods for collecting feline fecal samples are: (1) using a fecal loop, which retrieves a rectal sample using a small, looped instrument, and (2) using the litter box, which collects stool directly from the litter. Each method has its own advantages and disadvantages and is suitable for different research objectives.

Methods and results

Whole-genome shotgun metagenomic sequencing were performed on the gut microbiomes of fecal samples collected using these two methods from 10 adult cats housed in the same research facility. We evaluated the influence of collection methods on feline microbiome analysis, particularly their impact on DNA extraction, metagenomic sequencing yield, microbial composition, and diversity in subsequent gut microbiome analyses. Interestingly, fecal sample collection using a fecal loop resulted in a lower yield of microbial DNA compared to the litterbox method (p = 0.004). However, there were no significant differences between the two groups in the proportion of host contamination (p = 0.106), virus contamination (p = 0.232), relative taxonomy abundance of top five phyla (Padj > 0.638), or the number of microbial genes covered (p = 0.770). Furthermore, no significant differences were observed in alpha-diversity, beta-diversity, the number of taxa identified at each taxonomic level, and the relative abundance of taxonomic units.

Discussion

These two sample collection methods do not affect microbial population structures within fecal samples and collecting fecal samples directly from the litterbox within 6 hours after defecation can be considered a reliable approach for microbiome research.

Impact of fecal sample preservation and handling techniques on the canine fecal microbiota profile

Canine fecal microbiota profiling provides insight into host health and disease. Standardization of methods for fecal sample storage for microbiomics is currently inconclusive, however. This study investigated the effects of homogenization, the preservative RNAlater, room temperature exposure duration, and short-term storage in the fridge prior to freezing on the canine fecal microbiota profile. Within 15 minutes after voiding, samples were left non-homogenized or homogenized and aliquoted, then kept at room temperature (20-22°C) for 0.5, 4, 8, or 24 hours. Homogenized aliquots then had RNAlater added or not. Following room temperature exposure, all aliquots were stored in the fridge (4°C) for 24 hours prior to storing in the freezer (-20°C), or stored directly in the freezer. DNA extraction, PCR amplification, then sequencing were completed on all samples. Alpha diversity (diversity, evenness, and richness), and beta diversity (community membership and structure), and relative abundances of bacterial genera were compared between treatments. Homogenization and RNAlater minimized changes in the microbial communities over time, although minor changes in relative abundances occurred. Non-homogenized samples had more inter-sample variability and greater changes in beta diversity than homogenized samples. Storage of canine fecal samples in the fridge for 24 h prior to storage in the freezer had little effect on the fecal microbiota profile. Our findings suggest that if immediate analysis of fecal samples is not possible, samples should at least be homogenized to preserve the existing microbiota profile.

Temporal Variability of the Dominant Fecal Microbiota in Healthy Adult Cats

While shifts in gut microbiota have been studied in diseased states, the temporal variability of the microbiome in cats has not been widely studied. This study investigated the temporal variability of the feline dysbiosis index (DI) and the abundance of core bacterial groups in healthy adult cats. The secondary aim was to evaluate the relationship between the fecal abundance of Clostridium hiranonis and the fecal concentrations of unconjugated bile acids. A total of 142 fecal samples collected from 17 healthy cats were prospectively included: nine cats with weekly collection over 3 weeks (at least four time points), five cats with monthly collection over 2 months (three time points), and three cats with additional collections for up to 10 months. The DI remained stable within the reference intervals over two months for all cats (Friedman test, p > 0.2), and 100% of the DI values (n = 142) collected throughout the study period remained within the RI. While some temporal individual variation was observed for individual taxa, the magnitude was minimal compared to cats with chronic enteropathy and antibiotic exposure. Additionally, the abundance of Clostridium hiranonis was significantly correlated with the percentage of fecal primary bile acids, supporting its role as a bile acid converter in cats.

The effects of torula yeast as a protein source on apparent total tract digestibility, inflammatory markers, and fecal microbiota dysbiosis index in Labrador Retrievers with chronically poor stool quality

This study examined the effects of varying protein sources on apparent total tract digestibility, inflammatory markers, and fecal microbiota in Labrador Retrievers with historically poor stool quality. Thirty dogs (15 male, 15 female; aged 0.93 to 11.7 yr) with stool quality scores ≤2.5 on a 5-point scale (1 representing liquid stool and 5 representing firm stool) were randomly assigned to 1 of 3 nutritionally complete diets with differing protein sources and similar macronutrient profiles: 1) chicken meal (n = 10); 2) 10% brewer's yeast (n = 10); or 3) 10% torula yeast (n = 10). Another 10 dogs (five male, five female) with normal stool quality (scores ranging from 3 to 4) received diet 1 and served as negative control (NC). All dogs were fed diet 1 for 7 days, then provided their assigned treatment diets from days 7 to 37. Daily stool scores and weekly body weights were recorded. On days 7, 21, and 36, blood serum was analyzed for c-reactive protein (CRP), and feces for calgranulin C (S100A12), α1-proteinase inhibitor (α1-PI), calprotectin, and microbiota dysbiosis index. Apparent total tract digestibility was assessed using the indicator method with 2 g titanium dioxide administered via oral capsules. Stool scores were greater in NC (P < 0.01) as designed but not affected by treatment × time interaction (P = 0.64). Body weight was greater (P = 0.01) and CRP lower (P < 0.01) in NC dogs. Dry matter and nitrogen-free extract digestibility did not differ among groups (P ≥ 0.14). Negative controls had greater fat digestibility compared to BY (94.64 ± 1.33% vs. 91.65 ± 1.25%; P = 0.02). The overall effect of treatment was significant for protein digestibility (P = 0.03), but there were no differences in individual post hoc comparisons (P ≥ 0.07). Treatment did not affect S100A12 or α1-PI (P ≥ 0.44). Calprotectin decreased at a greater rate over time in TY (P < 0.01). The dysbiosis index score for BY and TY fluctuated less over time (P = 0.01). Blautia (P = 0.03) and Clostridium hiranonis (P = 0.05) abundances were reduced in BY and TY. Dogs with chronically poor stool quality experienced reduced body weights and increased serum CRP, but TY numerically increased protein digestibility, altered the microbiome, and reduced fecal calprotectin. Torula yeast is a suitable alternative protein source in extruded canine diets, but further research is needed to understand the long-term potential for improving the plane of nutrition and modulating gut health.

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.

Identification of a Sub-Clinical Salmonella spp. Infection in a Dairy Cow Using a Commercially Available Stool Storage Kit

Stool sampling is a useful tool for diagnosing gastrointestinal disease in veterinary medicine. The sub-clinical disease burden of Salmonella spp. in cattle can become significant for farmers. However, current methods of faecal sampling in a rural setting for diagnosis are not consistently sufficient for the preservation of Salmonella spp. in faeces. This study evaluated the use of a commercial stool storage kit for bacterial preservation in cow faecal samples compared to unpreserved stools placed into refrigeration at different time-points. A stool sample was collected per-rectum from one apparently healthy Holstein-Freisen cow. The sample was weighed and aliquoted into two sterile Falcon tubes and into two commercial kit tubes. The aliquots were then placed into refrigeration at 4 °C at 0, 24, and 96 h after processing. One commercial kit tube was not aliquoted and remained at ambient temperature. After 2 weeks, DNA was extracted from the samples and analysed using endpoint PCR, revealing a sub-clinical infection with Salmonella spp. The bacterium was best preserved when the stool was stored in the commercial kit at ambient temperature and re-homogenised immediately prior to DNA extraction. The unpreserved stool did not maintain obvious levels of Salmonella spp. after 24 h at ambient temperature. This commercial kit should be considered for use in the diagnosis of salmonellosis in cattle.

Effects of whole-grain cereals on fecal microbiota and short-chain fatty acids in dogs: a comparison of rye, oats and wheat

Dietary fiber in dog food is reported to promote healthy gut microbiota, but few studies have investigated the effects of whole-grain cereals, which contain a variety of fiber types and other bioactive compounds. The aim of the present study was to compare the effects of diets containing whole-grain rye (RYE), oats (OAT) and wheat (WHE) on fecal microbiota and short-chain fatty acid production. Eighteen dogs were fed three experimental diets, each for four weeks, in a cross-over design. Fecal samples were collected at the end of each diet period. Analysis of 16S rRNA gene amplicons showed that family Lachnospiraceae and genus Bacteroides were the gut microbial groups most affected by diet, with lowest relative abundance following consumption of RYE and a trend for a corresponding increase in genus Prevotella_9. Fecal acetate and propionate concentrations were higher after consumption of RYE compared with OAT. In conclusion, rye had the strongest effect on gut microbiota and short-chain fatty acids, although the implications for dog gut health are not yet elucidated.

The effects of ambient temperature exposure on feline fecal metabolome

Introduction

The fecal metabolome provides insight into overall gastrointestinal and microbial health. Methods for fecal sample storage in metabolomics research vary, however, making comparisons within current literature difficult. This study investigated the effect of ambient temperature exposure on microbial-derived metabolites of feline fecal samples.

Methods

Fecal samples were collected from 11 healthy cats from a local boarding facility. Samples were manually homogenized and aliquoted. The first aliquot was frozen at -80°C within 1 hour of defecation, and remaining samples were exposed to ambient temperature for 2, 4, 6, 8, 12, and 24 h prior to freezing at -80°C. Fecal metabolites were quantified using ¹H NMR spectroscopy. Fifty metabolites were grouped into six categories (27 amino acids, 8 fatty acids, 5 sugars, 3 alcohols, 2 nitrogenous bases, 5 miscellaneous).

Results

Concentrations of 20 out of 50 metabolites significantly differed due to ambient temperature exposure (7 amino acids, 6 fatty acids, 2 alcohols, 1 nitrogenous base, 4 miscellaneous). The earliest detected changes occurred 6 h post-defecation for cadaverine and fumaric acid.

Discussion

This study shows ambient temperature exposure alters the composition of the feline fecal metabolome, but short-term (up to 4 h) exposure prior to storage in the freezer seems to be acceptable.

Fecal identification markers impact the feline fecal microbiota

Fecal diagnostics are a mainstay of feline medicine, and fecal identification markers help to distinguish individuals in a multi-cat environment. However, the impact of identification markers on the fecal microbiota are unknown. Given the increased interest in using microbiota endpoints to inform diagnosis and treatment, the objective of this study was to examine the effects of orally supplemented glitter and crayon shavings on the feline fecal microbiota (amplicon sequencing of 16S rRNA gene V4 region). Fecal samples were collected daily from six adult cats that were randomized to receive oral supplementation with either glitter or crayon for two weeks, with a two-week washout before receiving the second marker. No adverse effects in response to marker supplementation were seen for any cat, and both markers were readily identifiable in the feces. Microbiota analysis revealed idiosyncratic responses to fecal markers, where changes in community structure in response to glitter or crayon could not be readily discerned. Given these findings, it is not recommended to administered glitter or crayon shavings as a fecal marker when microbiome endpoints are used, however their clinical use with other diagnostics should still be considered.

Recovery of Fecal Microbiome and Bile Acids in Healthy Dogs after Tylosin Administration with and without Fecal Microbiota Transplantation

Antibiotics cause gut dysbiosis and bile acid dysmetabolism in dogs. The effect of fecal microbiota transplantation (FMT) on microbiome and metabolome recovery is unknown. This prospective, randomized, placebo-controlled study included sixteen healthy purpose-bred dogs. All dogs received tylosin 20 mg/kg PO once daily (days 1–7) and were randomly assigned to either receive one FMT via enema (day 8), daily oral FMT capsules (days 8–21), or daily placebo capsules (days 8–21). Fecal samples were frozen at regular intervals until day 42. Quantitative PCR for 8 bacterial taxa was performed to calculate the fecal dysbiosis index (FDI) and fecal concentrations of unconjugated bile acids (UBA) were measured using gas chromatography-mass spectrometry. Tylosin altered the abundance of most evaluated bacteria and induced a significant decrease in secondary bile acid concentrations at day 7 in all dogs. However, most parameters returned to their baseline by day 14 in all dogs. In conclusion, tylosin markedly impacted fecal microbiota and bile acid concentrations, although return to baseline values was quick after the antibiotic was discontinued. Overall, FMT did not accelerate recovery of measured parameters. Further studies are warranted to confirm the value of FMT in accelerating microbiota recovery in antibiotic-associated dysbiosis in dogs.

Dysbiosis index to evaluate the fecal microbiota in healthy cats and cats with chronic enteropathies

OBJECTIVES

Previous studies have identified various bacterial taxa that are altered in cats with chronic enteropathies (CE) vs healthy cats. Therefore, the aim of this study was to develop a targeted quantitative molecular method to evaluate the fecal microbiota of cats.

METHODS

Fecal samples from 80 client-owned healthy cats and 68 cats with CE were retrospectively evaluated. A panel of quantitative PCR (qPCR) assays was used to measure the fecal abundance of total bacteria and seven bacterial taxa: Bacteroides, Bifidobacterium, Clostridium hiranonis, Escherichia coli, Faecalibacterium, Streptococcus and Turicibacter. The nearest centroid classifier algorithm was used to calculate a dysbiosis index (DI) based on these qPCR abundances.

RESULTS

The abundances of total bacteria, Bacteroides, Bifidobacterium, C hiranonis, Faecalibacterium and Turicibacter were significantly decreased, while those of E coli and Streptococcus were significantly increased in cats with CE (P <0.027 for all). The DI in cats with CE was significantly higher compared with healthy cats (P <0.001). When the cut-off value of the DI was set at 0, it provided 77% (95% confidence interval [CI] 66-85) sensitivity and 96% (95% CI 89-99) specificity to differentiate the microbiota of cats with CE from those of healthy cats. Fifty-two of 68 cats with CE had a DI >0.

CONCLUSIONS AND RELEVANCE

A qPCR-based DI for assessing the fecal microbiota of cats was established. The results showed that a large proportion of cats with CE had an altered fecal microbiota as evidenced by an increased DI. Prospective studies are warranted to evaluate the utility of this assay for clinical assessment of feline CE.

Preliminary evaluation of probiotic effects on gastrointestinal signs in dogs with multicentric lymphoma undergoing multi-agent chemotherapy: A randomised, placebo-controlled study

BACKGROUND

Gastrointestinal (GI) toxicity is a major dose-limiting factor in dogs undergoing chemotherapy. A proposed mechanism of GI toxicity includes chemotherapy-driven GI dysbiosis. This study was designed to determine the effects of probiotic administration on GI side-effects in dogs receiving multi-agent chemotherapy.

METHODS

Ten client-owned dogs with multicentric lymphoma were enrolled in a prospective, randomised, placebo-controlled single-blinded study. On the first day of the cyclophosphamide doxorubicin vincristine prednisone (CHOP)-based chemotherapy protocol, dogs were randomised to receive either daily oral probiotic at a dose of 200 × 109 cfu/10 kg (n = 5) or daily oral placebo (n = 5). Complete blood count, faecal score (FS), faecal microbiome analysis (qPCR) and adverse events scores were performed at baseline and on the day of each subsequent chemotherapy dose, as well as 3 days after doxorubicin (days 0, 7, 14, 21, 24 and 28).

RESULTS

Overall, 40% of dogs had an abnormal GI microbiome at baseline, specifically decreased faecal C. hiranonis and Fusobacterium abundances. Dogs receiving probiotics had increased faecal Streptococcus (p = 0.02) and E. coli. (p = 0.01). No dogs receiving probiotics experienced diarrhoea (FS ≥ 3.5) compared to four of five receiving placebo. (F 2.895; p = 0.13).

CONCLUSION

GI microbiome dysbiosis was common in this group of dogs with multicentric lymphoma. Probiotics were well-tolerated, with no negative side effects. Further studies are needed to explore broader microbiome and metabolome changes, as well as clinical benefit.

Impact of oral amoxicillin and amoxicillin/clavulanic acid treatment on bacterial diversity and β-lactam resistance in the canine faecal microbiota

BACKGROUND

Aminopenicillins with or without a β-lactamase inhibitor are widely used in both human and veterinary medicine. However, little is known about their differential impact on the gut microbiota and development of antimicrobial resistance.

OBJECTIVES

To investigate changes in the faecal microbiota of dogs treated with amoxicillin or amoxicillin/clavulanic acid.

METHODS

Faeces collected from 42 dogs (21 per treatment group) immediately before, during and 1 week after termination of oral treatment with amoxicillin or amoxicillin/clavulanic acid were analysed by culture and 16S rRNA gene sequence analysis.

RESULTS

In both groups, bacterial counts on ampicillin selective agar revealed an increase in the proportion of ampicillin-resistant Escherichia coli during treatment, and an increased occurrence and proportion of ampicillin-resistant enterococci during and after treatment. 16S rRNA gene analysis showed reductions in microbial richness and diversity during treatment followed by a return to pre-treatment conditions approximately 1 week after cessation of amoxicillin or amoxicillin/clavulanic acid treatment. While no significant differences were observed between the effects of amoxicillin and amoxicillin/clavulanic acid on microbial richness and diversity, treatment with amoxicillin/clavulanic acid reduced the abundance of taxa that are considered part of the beneficial microbiota (such as Roseburia, Dialister and Lachnospiraceae) and enriched Escherichia, although the latter result was not corroborated by phenotypic counts.

CONCLUSIONS

Our results suggest a limited effect of clavulanic acid on selection of antimicrobial resistance and microbial richness when administered orally in combination with amoxicillin. However, combination with this β-lactamase inhibitor appears to broaden the spectrum of amoxicillin, with potential negative consequences on gut health.

Low fermentable oligosaccharides, disaccharides, monosaccharides, and polyols diet compared with traditional dietary advice for diarrhea-predominant irritable bowel syndrome: a parallel-group, randomized controlled trial with analysis of clinical and microbiological factors associated with patient outcomes

BACKGROUND

The efficacy and factors associated with patient outcomes for a diet low in fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (LFD) compared with traditional dietary advice (TDA) based on modified National Institute for Clinical Excellence guidelines for irritable bowel syndrome with diarrhea (IBS-D) in regions consuming a non-Western diet are unclear.

OBJECTIVES

We aimed to determine the efficacy of an LFD compared with TDA for the treatment of IBS-D in Chinese patients and to investigate the factors associated with favorable outcomes.

METHODS

One hundred and eight Chinese IBS-D patients (Rome III criteria) were randomly assigned to an LFD or TDA. The primary endpoint was a ≥50-point reduction in the IBS Severity Scoring System at 3 wk. Fecal samples collected before and after the dietary intervention were assessed for changes in SCFAs and microbiota profiles. A logistic regression model was used to identify predictors of outcomes.

RESULTS

Among the 100 patients who completed the study, the primary endpoint was met in a similar number of LFD (30 of 51, 59%) and TDA (26 of 49, 53%) patients (∆6%; 95% CI: -13%, 24%). Patients in the LFD group achieved earlier symptomatic improvement in stool frequency and excessive wind than those following TDA. LFD reduced carbohydrate-fermenting bacteria such as Bifidobacterium and Bacteroides, and decreased saccharolytic fermentation activity. This was associated with symptomatic improvement in the responders. High saccharolytic fermentation activity at baseline was associated with a higher symptom burden (P = 0.01) and a favorable therapeutic response to the LFD (log OR: 4.9; 95% CI: -0.1, 9.9; P = 0.05).

CONCLUSIONS

An LFD and TDA each reduced symptoms in Chinese IBS-D patients; however, the LFD achieved earlier symptomatic improvements in stool frequency and excessive wind. The therapeutic effect of the LFD was associated with changes in the fecal microbiota and the fecal fermentation index. At baseline, the presence of severe symptoms and microbial metabolic dysbiosis characterized by high saccharolytic capability predicted favorable outcomes to LFD intervention.This trial was registered at clinicaltrials.gov as NCT03304041.

Fecal Bacterial Microbiota of Healthy Free-Ranging, Healthy Corralled, and Chronic Diarrheic Corralled Rhesus Macaques (Macaca mulatta)

A clinical challenge to nearly every primate facility in North America is chronic idiopathic diarrhea (CID), the pathogenesis of which has yet to be fully elucidated. However, wild macaques appear resistant to CID, a trend that we observed in the free-ranging population of the Caribbean Primate Research Center. The gastrointestinal microbiota has been shown to have a significant role in the pathogenesis of disease and in maintaining normal health and development of the gut. In humans, chronic diarrhea is associated with alteration of the gut microbiota, which has lower bacterial diversity than does the microbiota of healthy humans. The current study was designed to describe and compare the fecal bacterial microbiota of healthy corralled, CID corralled, and healthy, free-ranging macaques. Fresh fecal samples were collected from healthy corralled (HC; n = 30) and CID (n = 27) rhesus macaques and from healthy macaques from our free-ranging colony (HF; n = 43). We excluded macaques that had received antibiotics during the preceding 60 d (90 d for healthy animals). Bacterial DNA was extracted, and the V4 region of the 16S rRNA gene was sequenced and compared with known databases. The relative abundance of Proteobacteria was higher in CID animals than HC animals, but otherwise few differences were found between these 2 groups. HF macaques were differentially enriched with Christensenellaceae and Helicobacter, which are highly associated with a 'healthy' gut in humans, as compared to corralled animals, whereas CID animals were enriched with Proteobacteria, which are associated with dysbiosis in other species. These results indicate that environment has a greater influence than health status on the gut microbiota. Furthermore, the current data provided targets for future studies on potential clinical interventions, such as probiotics and fecal transplants.

Impact of Ambient Temperature Sample Storage on the Equine Fecal Microbiota

Sample storage conditions are an important factor in fecal microbiota analyses in general. The objective of this study was to investigate the effect of sample storage at room temperature on the equine fecal microbiota composition. Fecal samples were collected from 11 healthy horses. Each sample was divided into 7 sealed aliquots. One aliquot was immediately frozen at -80 °C; the remaining aliquots were stored at room temperature (21 to 22 °C) with one transferred to the freezer at each of the following time points: 6, 12, 24, 48, 72 and 96 h. The Illumina MiSeq sequencer was used for high-throughput sequencing of the V4 region of the 16S rRNA gene. Fibrobacteraceae (Fibrobacter) and Ruminococcaceae (Ruminococcus) were enriched in samples from 0 h and 6 h, whereas taxa from the families Bacillaceae, Planococcaceae, Enterobacteriaceae and Moraxellaceae were enriched in samples stored at room temperature for 24 h or greater. Samples frozen within the first 12 h after collection shared similar community membership. The community structure was similar for samples collected at 0 h and 6 h, but it was significantly different between samples frozen at 0 h and 12 h or greater. In conclusion, storage of equine fecal samples at ambient temperature for up to 6 h before freezing following sample collection had minimal effect on the microbial composition. Longer-term storage at ambient temperature resulted in alterations in alpha-diversity, community membership and structure and the enrichment of different taxa when compared to fecal samples immediately frozen at -80 °C.

The Fecal Bacterial Microbiota in Horses with Equine Recurrent Uveitis

The objective of this study was to describe and compare the fecal bacterial microbiota of horses with equine recurrent uveitis (ERU) and healthy horses using next-generation sequencing techniques. Fecal samples were collected from 15 client-owned horses previously diagnosed with ERU on complete ophthalmic examination. For each fecal sample obtained from a horse with ERU, a sample was collected from an environmentally matched healthy control with no evidence of ocular disease. The Illumina MiSeq sequencer was used for high-throughput sequencing of the V4 region of the 16S rRNA gene. The relative abundance of predominant taxa, and alpha and beta diversity indices were calculated and compared between groups. The phyla Firmicutes, Bacteroidetes, Verrucomicrobia, and Proteobacteria predominated in both ERU and control horses, accounting for greater than 60% of sequences. Based on linear discriminant analysis effect size (LEfSe), no taxa were found to be enriched in either group. No significant differences were observed in alpha and beta diversity indices between groups (p > 0.05 for all tests). Equine recurrent uveitis is not associated with alteration of the gastrointestinal bacterial microbiota when compared with healthy controls.

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.

Bighorn sheep gut microbiomes associate with genetic and spatial structure across a metapopulation

Studies in laboratory animals demonstrate important relationships between environment, host traits, and microbiome composition. However, host-microbiome relationships in natural systems are understudied. Here, we investigate metapopulation-scale microbiome variation in a wild mammalian host, the desert bighorn sheep (Ovis canadensis nelsoni). We sought to identify over-represented microbial clades and understand how landscape variables and host traits influence microbiome composition across the host metapopulation. To address these questions, we performed 16S sequencing on fecal DNA samples from thirty-nine bighorn sheep across seven loosely connected populations in the Mojave Desert and assessed relationships between microbiome composition, environmental variation, geographic distribution, and microsatellite-derived host population structure and heterozygosity. We first used a phylogenetically-informed algorithm to identify bacterial clades conserved across the metapopulation. Members of genus Ruminococcaceae, genus Lachnospiraceae, and family Christensenellaceae R7 group were among the clades over-represented across the metapopulation, consistent with their known roles as rumen symbionts in domestic livestock. Additionally, compositional variation among hosts correlated with individual-level geographic and genetic structure, and with population-level differences in genetic heterozygosity. This study identifies microbiome community variation across a mammalian metapopulation, potentially associated with genetic and geographic population structure. Our results imply that microbiome composition may diverge in accordance with landscape-scale environmental and host population characteristics.

Bacterial fecal microbiota is only minimally affected by a standardized weight loss plan in obese cats

Background

Research in humans and mice suggests that obesity influences the abundance and diversity of gastrointestinal (GI) microbiota, and that an “obese microbiome” influences energy metabolism and fat storage in the host. Microbiota membership and composition have been previously assessed in healthy cats. However, research investigating the effects of obesity and weight loss on the cat’s fecal microbiota is limited. Therefore, this study’s objective was to evaluate differences in fecal microbial abundance and biodiversity, as well as serum cobalamin and folate concentrations in obese cats, before and after weight loss, and compare to lean cats.

Fourteen lean and 17 obese healthy client-owned cats were fed a veterinary therapeutic weight loss food at maintenance energy requirement for 4 weeks. At the end of week 4, lean cats finished the study, whereas obese cats continued with a 10-week weight loss period on the same food, fed at individually-tailored weight loss energy requirements. Body weight and body condition score were recorded every 2 weeks throughout the study. At the end of each period, a fecal sample and food-consumption records were obtained from the owners, and serum cobalamin and folate concentrations were analysed. DNA was extracted from fecal samples, polymerase chain reaction (PCR) was performed, and products were sequenced using next-generation sequencing (Illumina MiSeq).

Results

No significant differences in the relative abundance of taxa and in biodiversity indices were observed between cats in either group (P > 0.05 for all tests). Nevertheless, some significantly enriched taxa, mainly belonging to Firmicutes, were noted in linear discriminant analysis effect size test in obese cats before weight loss compared to lean cats. Serum cobalamin concentrations were significantly higher in lean compared to obese cats both before and after weight loss. Serum folate concentrations were higher in obese cats before weight loss compared to after.

Conclusions

The association between feline obesity and the fecal bacterial microbiota was demonstrated in enriched taxa in obese cats compared to lean cats, which may be related to enhanced efficiency of energy-harvesting. However, in obese cats, the fecal microbial abundance and biodiversity were only minimally affected during the early phase of a standardized weight loss plan.

Evaluation of the effects of anthelmintic administration on the fecal microbiome of healthy dogs with and without subclinical Giardia spp. and Cryptosporidium canis infections

BACKGROUND

The gastrointestinal microbiome plays an important role in host health and there is increasing concern regarding the deleterious effects of pharmaceuticals on the fecal microbiome. The effect of anthelmintic therapy on the fecal microbiome in dogs has not yet been evaluated. The purpose of this study was to evaluate the effect of anthelmintic administration on the fecal microbiome of dogs with and without subclinical Giardia species and Cryptosporidium canis infections.

METHODOLOGY/PRINCIPAL FINDINGS

Part 1: 6 healthy adult research beagles with subclinical giardiasis and cryptosporidiosis were administered a commercially available preparation of febantel combined with pyrantel and praziquantel (FPP) orally daily for three days. Part 2: 19 healthy staff-owned dogs without giardiasis or cryptosporidiosis were divided into a treatment group (n = 9) that was administered fenbendazole orally daily for five days and an untreated control group (n = 10). For both parts of the study, feces were collected at multiple time points before and after anthelmintic (FPP or fenbendazole) administration. Fecal DNA was extracted for Illumina sequencing of the bacterial 16S rRNA gene and qPCR assays. Neither FPP nor fenbendazole treatment caused a significant change in alpha or beta diversity or the relative abundance of bacterial species. Upon univariate statistical analysis neither FPP or fenbendazole caused minimal changes in the fecal microbiota.

CONCLUSION

FPP administration was associated with minimal alterations of the fecal microbiome of healthy research beagles with subclinical giardiasis and cryptosporidiosis. Fenbendazole administration was associated with minimal alterations of the fecal microbiome of healthy staff owned dogs.

The impact of storage conditions on human stool 16S rRNA microbiome composition and diversity

Background

Multiple factors can influence stool sample integrity upon sample collection. Preservation of faecal samples for microbiome studies is therefore an important step, particularly in tropical regions where resources are limited and high temperatures may significantly influence microbiota profiles. Freezing is the accepted standard to preserve faecal samples however, cold chain methods are often unfeasible in fieldwork scenarios particularly in low and middle-income countries and alternatives are required. This study therefore aimed to address the impact of different preservative methods, time-to-freezing at ambient tropical temperatures, and stool heterogeneity on stool microbiome diversity and composition under real-life physical environments found in resource-limited fieldwork conditions.

Methods

Inner and outer stool samples collected from one specimen obtained from three children were stored using different storage preservation methods (raw, ethanol and RNAlater) in a Ugandan field setting. Mixed stool was also stored using these techniques and frozen at different time-to-freezing intervals post-collection from 0-32 h. Metataxonomic profiling was used to profile samples, targeting the V1-V2 regions of 16S rRNA with samples run on a MiSeq platform. Reads were trimmed, combined and aligned to the Greengenes database. Microbial diversity and composition data were generated and analysed using Quantitative Insights Into Microbial Ecology and R software.

Results

Child donor was the greatest predictor of microbiome variation between the stool samples, with all samples remaining identifiable to their child of origin despite the stool being stored under a variety of conditions. However, significant differences were observed in composition and diversity between preservation techniques, but intra-preservation technique variation was minimal for all preservation methods, and across the time-to-freezing range (0-32 h) used. Stool heterogeneity yielded no apparent microbiome differences.

Conclusions

Stool collected in a fieldwork setting for comparative microbiome analyses should ideally be stored as consistently as possible using the same preservation method throughout.

Omeprazole Minimally Alters the Fecal Microbial Community in Six Cats: A Pilot Study

Although they have historically been thought of as safe medications, proton pump inhibitors such as omeprazole have been associated with an increased risk of enteric, particularly Clostridium difficile, infections in people. In cats, omeprazole is often the first choice acid suppressant prescribed for the treatment of upper gastrointestinal (GI) ulceration and bleeding. Despite this, no studies to date have explored the effect of omeprazole on the feline fecal microbiome and metabolome. Therefore, the purpose of this pilot study was to evaluate the effect of prolonged omeprazole administration on the fecal microbiome and metabolome in healthy cats to identify targets for analysis in a larger subset of cats with GI disease. A within-subjects, before and after, pilot study was performed whereby six healthy adult cats received 60 days of placebo (250 mg lactose PO q 12 h) followed by 5 mg (0.83–1.6 mg/kg PO q 12 h) omeprazole. On days 0, 30, and 60 of placebo and omeprazole therapy, the fecal microbiome and metabolome were characterized utilizing 16S ribosomal RNA sequencing by Illumina and untargeted mass spectrometry-based methods, respectively. Omeprazole administration resulted in no significant changes in the global microbiome structure or richness. However, transient changes were noted in select bacterial groups with omeprazole administration resulting in an increased sequence percentage of Streptococcus, Lactobacillus, Clostridium, and Faecalibacterium spp. and a decreased sequence percentage of Bifidobacterium spp. Significance was lost for all of these bacterial groups after adjustment for multiple comparisons. The fecal concentration of O-acetylserine and aminomalonate decreased with omeprazole therapy, but significance was lost after adjustment for multiple comparisons. The results of this pilot study conclude that omeprazole has a mild and transient impact on the fecal microbiome and metabolome when orally administered to healthy cats for 60 days. Based on the findings of this pilot study, evaluation of the effect of omeprazole specifically on Streptococcus, Lactobacillus, Clostridium, Faecalibacterium, and Bifidobacterium spp. is warranted in cats with primary GI disease.

[The Microbiome - The Unscheduled Parameter for Future Therapies]

The microbiome is defined as the total of cellular microorganisms of baczerial, viral or e. g., parasite origin living on the surface of a body. Within the anatomical areas of otorhinolaryngology, a significant divergence and variance can be demonstrated. For ear, nose, throat, larynx and cutis different interactions of microbiome and common factors like age, diet and live style factors (e. g., smoking) have been detected in recent years. Besides, new insights hint at a passible pathognomic role of the microbiome towards diseases in the ENT area. This review article resumes the present findings of this rapidly devloping scientific area.