Fecal microbiota transplantation effect on clinical severity and fecal microbial communities in dogs with chronic inflammatory enteropathies
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ABSTRACT:
PROVIDER: PRJEB71959 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR12756400_1.fastq.gz | Fastqsanger.gz | |||
| ERR12756400_2.fastq.gz | Fastqsanger.gz | |||
| ERR12756401_1.fastq.gz | Fastqsanger.gz | |||
| ERR12756401_2.fastq.gz | Fastqsanger.gz | |||
| ERR12756402_1.fastq.gz | Fastqsanger.gz |
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Project description:BackgroundFecal microbiota transplantation (FMT) has been advocated as a treatment for chronic enteropathy (CE) in dogs. However, so far only short-term clinical effects have been reported whereas the effect on the microbiota remains unexplored.Hypothesis/objectivesAssess if a single FMT enema can lead to clinical improvement in dogs with CE when accompanied by presumed favorable microbiota changes. The effect of glycerol as a cryopreservative when storing FMT preparations also was assessed.AnimalsSeven dogs with CE that received FMTs from 2 healthy donor dogs.Materials and methodsSix dogs received a single FMT, 1 dog received 3 consecutive FMTs. Canine chronic enteropathy clinical activity index (CCECAI) and fecal samples were obtained before (Day 0), and 7, 30 and 90 days after FMT. Samples were stored with and without 10% glycerol. Sequencing of microbiota (16S rRNA, Illumina) was performed and compared by accepted analysis pipelines.ResultsMedian CCECAI before FMT was 8 (range, 5-14), decreased to a median of 3 (range, 1-12) within 1 week and a median of 1 (range, 0-12) by Day 30 (P < .01), with an average duration of response of approximately 10 weeks. Significant variation in the donors' microbiota composition was observed across different donations. Recipient microbiota composition or diversity did not change over time. Glycerol addition was associated with a difference in microbiota composition (P ≤ .001).Conclusions and clinical importanceA single FMT can be considered an appropriate treatment in dogs with CE, but consistent microbiota changes were not observed.
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2015-11-19 | GSE69040 | GEO
Project description:Chronic inflammatory enteropathies (CIEs) in dogs involve the infiltration of gastrointestinal tissue with inflammatory cells. This study aimed to assess the sensitivity of serum and fecal 3-bromotyrosine (3-BrY) concentrations in dogs with CIE. The difference in 3-BrY concentrations in dogs with different gastrointestinal (GI) pathological changes was also assessed. In total, 68 dogs with CIE were enrolled in the study. The median serum 3-BrY concentration was 3.3 µmol/L, while the median 3-day mean and maximum fecal 3-BrY concentrations were 38.9 and 63.2 mmol/g of feces, respectively. The median serum C-reactive protein concentration was 45.0 mg/L. The median 3-day mean and maximum fecal α1-proteinase inhibitor concentrations were 6.1 and 9 µg/g of feces, respectively. Increased 3-BrY concentrations were observed in 90.9% of CIE dogs based on serum concentrations, 75.8% based on mean fecal concentrations, and 69.4% based on maximum fecal concentrations. A weak correlation (ρ = 0.31, p < 0.0118) was found between serum CRP and serum 3-BrY concentrations. There was no correlation between the canine chronic enteropathy clinical activity index and serum or fecal 3-BrY concentrations (p > 0.05). Additionally, no significant difference in serum or fecal 3-BrY concentrations was found among CIE dogs with different GI pathological changes (p > 0.05). In conclusion, dogs with CIE have increased 3-BrY concentrations in serum and fecal samples. However, 3-BrY concentrations may not accurately indicate the severity of gastrointestinal inflammation.
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Project description:Transcriptional profiling of dog muscle tissue comparing control dogs. tested, genomewide, for genes differentially expressed in muscle between the escapers and the affected dogs. Using Agilent mRNA SurePrint Canine arrays, we compared muscle gene expression of the two escapers, four affected, and four normal dogs at age 2 years. normal, affected DMD, and escapers
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2013-02-22 | E-GEOD-44545 | biostudies-arrayexpress
Project description:Canine chronic inflammatory enteropathy implicates multifactorial pathogenesis where immunological dysregulation and gut microbiota changes have a central role. Most sequencing-based taxonomic studies have been focused on the fecal microbiota. However, the analysis of these samples does not provide complete information regarding the composition of the small intestine affected by this canine disease. Therefore, in this study, we aimed to characterize the intestinal bacterial microbiota in dogs with inflammatory bowel disease (IBD) (n = 34) by means of duodenal biopsies and fecal samples collected at the time of the diagnosis and to compare those to a group of healthy dogs (n = 12) using the 16S ribosomal RNA (16S rRNA) gene-targeted sequencing (Illumina MiSeq platform). Our study showed that IBD dogs presented differences in the fecal bacterial communities when compared with healthy dogs, with a lower relative abundance of Prevotellaceae (p = 0.005), Prevotella (p = 0.002), and Prevotellaceae Ga6A1 group (0.006); Erysipelotrichales (p = 0.019), Candidatus Stoquefichus (p < 0.001), Erysipelotrichaceae (p = 0.011), and Allobaculum (p = 0.003); Lachnospiraceae NK4A136 group (p = 0.015), Sellimonas (p = 0.042), Oscillospirales (p = 0.037), Oscillospiraceae UCG-005 (p < 0.001), Faecalibacterium (p = 0.028), and Fournierella (p = 0.034); Acidaminococcales, Acidaminococcaceae, and Phascolarctobacterium (p = 0.001); Aeromonadales (p = 0.026), Succinivibrionaceae (p = 0.037), and Succinivibrio (p = 0.031). On the other hand, a higher relative abundance of Enterococcaceae (Enterococcus; p = 0.003), Streptococcaceae (Streptococcus, p = 0.021), Enterobacterales (p = 0.027), Enterobacteriaceae (p = 0.008), and Escherichia-Shigella (p = 0.011) was detected. Moreover, when evaluating α-diversity, the dogs with IBD showed lower diversity in terms of richness and abundance of species (observed species [p = 0.031] and Shannon index [p = 0.039]). Furthermore, fecal microbiota in dogs with IBD was significantly different from healthy dogs (p = 0.006). However, only a few taxa relative abundance shifts (lower Rubrobacteria, Rubrobacterales, Rubrobacteriaceae, and Rubrobacter [p = 0.002]; Cyanobacteria [p = 0.010], Vampirivibrionia, Obscuribacterales, and Obscuribacteraceae [p = 0.005]; Neisseriaceae [p = 0.004] and Conchiformibius [p = 0.003]) were observed when assessing duodenal-associated microbiota of dogs with IBD. Thus, even if the bowel inflammation mainly affects the small intestine in the IBD-affected dogs of the study, fecal specimens may constitute a better sample due not only to their easy availability but also in terms of searching for bacterial taxa as biomarkers for canine IBD. The use of different diets in the study can also have a partial influence on the microbiota composition. Future studies encompassing multi-omics approaches should evaluate the functionality in both levels to unravel the pathophysiology of canine IBD.
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Project description:BackgroundFecal microbiota transplantation (FMT) is a therapeutic intervention used to treat diseases associated with the gut microbiome. In the human gut microbiome, phages have been implicated in influencing human health, with successful engraftment of donor phages correlated with FMT treatment efficacy. The impact that gastrointestinal phages exert on human health has primarily been connected to their ability to modulate the bacterial communities in the gut. Nonetheless, how FMT affects recipients' phage populations, and in turn, how this influences the gut environment, is not yet fully understood. In this study, we investigated the effects of FMT on the phageome composition of participants within the Gut Bugs Trial (GBT), a double-blind, randomized, placebo-controlled trial that investigated the efficacy of FMT in treating obesity and comorbidities in adolescents. Stool samples collected from donors at the time of treatment and recipients at four time points (i.e., baseline and 6 weeks, 12 weeks, and 26 weeks post-intervention), underwent shotgun metagenomic sequencing. Phage sequences were identified and characterized in silico to examine evidence of phage engraftment and to assess the extent of FMT-induced alterations in the recipients' phageome composition.ResultsDonor phages engrafted stably in recipients following FMT, composing a significant proportion of their phageome for the entire course of the study (33.8 ± 1.2% in females and 33.9 ± 3.7% in males). Phage engraftment varied between donors and donor engraftment efficacy was positively correlated with their phageome alpha diversity. FMT caused a shift in recipients' phageome toward the donors' composition and increased phageome alpha diversity and variability over time.ConclusionsFMT significantly altered recipients' phage and, overall, microbial populations. The increase in microbial diversity and variability is consistent with a shift in microbial population dynamics. This proposes that phages play a critical role in modulating the gut environment and suggests novel approaches to understanding the efficacy of FMT in altering the recipient's microbiome.Trial registrationThe Gut Bugs Trial was registered with the Australian New Zealand Clinical Trials Registry (ACTR N12615001351505). Trial protocol: the trial protocol is available at https://bmjopen.bmj.com/content/9/4/e026174 . Video Abstract.
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