Stabilization of swine faecal samples influences taxonomic and functional results in microbiome analyses

Monger, Xavier C.; Saucier, Linda; Gilbert, Alex-An; Vincent, Antony T.

doi:10.1016/j.mex.2022.101716

Cited by 5 publications

(5 citation statements)

References 38 publications

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“…However, a favorable-quality DNA sample is initially required to amplify the full-length gene for long-read sequencing; therefore, one limitation of this approach is the difficulty of achieving full-length gene amplification in low-quality DNA samples. In the present study, the DNA in PDE samples was degraded for several reasons, including being collected without nucleic acid preservation (NAP), RNA/DNA Stabilization Buffer, multiple freeze-thaw events, and being kept at -20˚C for a long period of time (29). Degraded samples may have insufficient quantities of DNA to amplify the full-length 16S rDNA gene.…”

Section: Discussionmentioning

confidence: 99%

Bacterial classification based on metagenomic analysis in peritoneal dialysis effluent of patients with chronic kidney disease

Visedthorn,

Klomkliew,

Sawaswong

et al. 2024

Biomed Rep

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End-stage kidney disease (ESKD) is the final stage of chronic kidney disease (CKD), in which long-term damage has been caused to the kidneys to the extent that they are no longer able to filter the blood of waste and extra fluid. Peritoneal dialysis (PD) is one of the treatments that remove waste products from the blood through the peritoneum which can improve the quality of life for patients with ESKD. However, PD-associated peritonitis is an important complication that contributes to the mortality of patients, and the detection of bacterial pathogens is associated with a high culture-negative rate. The present study aimed to apply a metagenomic approach for the bacterial identification in the PD effluent (PDE) of patients with CKD based on 16S ribosomal DNA sequencing. As a result of this investigation, five major bacteria species, namely Escherichia coli, Phyllobacterium myrsinacearum, Streptococcus gallolyticus, Staphylococcus epidermidis and Shewanella algae, were observed in PDE samples. Taken together, the findings of the present study have suggested that this metagenomic approach could provide a greater potential for bacterial taxonomic identification compared with traditional culture methods, suggesting that this is a practical and culture-independent alternative approach that will offer a novel preventative infectious strategy in patients with CDK.

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Section: Discussionmentioning

confidence: 99%

Bacterial classification based on metagenomic analysis in peritoneal dialysis effluent of patients with chronic kidney disease

Visedthorn,

Klomkliew,

Sawaswong

et al. 2024

Biomed Rep

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“…Animal housing conditions were described in a previously published paper ( Monger et al, 2022 ). The experimental design was approved by the Animal Protection Committee of Université Laval prior to the experiments (2019057–1).…”

Section: Methodsmentioning

confidence: 99%

“…The digesta from pig number two at the Ctl2 period could not be collected as there was no digesta at the time of sampling. All the samples were stabilized using the PERFORMAbiome•GUT | PB-200 sampling kit according to the manufacturer’s instructions (DNAgenotek, Ottawa, Ontario, Canada) and as suggested elsewhere ( Monger et al, 2022 ).…”

Section: Methodsmentioning

confidence: 99%

Effect of a probiotic and an antibiotic on the mobilome of the porcine microbiota

Monger,

Saucier,

Guay

et al. 2024

Front. Genet.

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Introduction: To consider the growing health issues caused by antibiotic resistance from a “one health” perspective, the contribution of meat production needs to be addressed. While antibiotic resistance is naturally present in microbial communities, the treatment of farm animals with antibiotics causes an increase in antibiotic resistance genes (ARG) in the gut microbiome. Pigs are among the most prevalent animals in agriculture; therefore, reducing the prevalence of antibiotic-resistant bacteria in the pig gut microbiome could reduce the spread of antibiotic resistance. Probiotics are often studied as a way to modulate the microbiome and are, therefore, an interesting way to potentially decrease antibiotic resistance.Methods: To assess the efficacy of a probiotic to reduce the prevalence of ARGs in the pig microbiome, six pigs received either treatment with antibiotics (tylvalosin), probiotics (Pediococcus acidilactici MA18/5M; Biopower® PA), or a combination of both. Their faeces and ileal digesta were collected and DNA was extracted for whole genome shotgun sequencing. The reads were compared with taxonomy and ARG databases to identify the taxa and resistance genes in the samples.Results: The results showed that the ARG profiles in the faeces of the antibiotic and combination treatments were similar, and both were different from the profiles of the probiotic treatment (p < 0.05). The effects of the treatments were different in the digesta and faeces. Many macrolide resistance genes were detected in a higher proportion in the microbiome of the pigs treated with antibiotics or the combination of probiotics and antibiotics. Resistance-carrying conjugative plasmids and horizontal transfer genes were also amplified in faeces samples for the antibiotic and combined treatments. There was no effect of treatment on the short chain fatty acid content in the digesta or the faeces.Conclusion: There is no positive effect of adding probiotics to an antibiotic treatment when these treatments are administered simultaneously.

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“…Different preservative methods have been proposed for stabilizing microbial community structures, especially for investigation of human fecal microbiota [29][30][31][32]. However, only a few published studies have investigated preservation methods using animal feces [33][34][35], and notably, these investigations did not include fecal samples from cattle. Additionally, little published research is available regarding impacts of preservatives on other important sample types such as respiratory secretions.…”

Section: Introductionmentioning

confidence: 99%

Effectiveness of stabilization methods for the immediate and short-term preservation of bovine fecal and upper respiratory tract genomic DNA

Pinnell,

Wolfe,

Castle

et al. 2024

PLoS ONE

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Previous research on stabilization methods for microbiome investigations has largely focused on human fecal samples. There are a few studies using feces from other species, but no published studies investigating preservation of samples collected from cattle. Given that microbial taxa are differentially impacted during storage it is warranted to study impacts of preservation methods on microbial communities found in samples outside of human fecal samples. Here we tested methods of preserving bovine fecal respiratory specimens for up to 2 weeks at four temperatures (room temperature, 4°C, -20°C, and -80°C) by comparing microbial diversity and community composition to samples extracted immediately after collection. Importantly, fecal specimens preserved and analyzed were technical replicates, providing a look at the effects of preservation method in the absence of biological variation. We found that preservation with the OMNIgene®•GUT kit resulted in community structure most like that of fresh samples extracted immediately, even when stored at room temperature (~20°C). Samples that were flash-frozen without added preservation solution were the next most representative of original communities, while samples preserved with ethanol were the least representative. These results contradict previous reports that ethanol is effective in preserving fecal communities and suggest for studies investigating cattle either flash-freezing of samples without preservative or preservation with OMNIgene®•GUT will yield more representative microbial communities.

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Stabilization of swine faecal samples influences taxonomic and functional results in microbiome analyses

Cited by 5 publications

References 38 publications

Bacterial classification based on metagenomic analysis in peritoneal dialysis effluent of patients with chronic kidney disease

Bacterial classification based on metagenomic analysis in peritoneal dialysis effluent of patients with chronic kidney disease

Effect of a probiotic and an antibiotic on the mobilome of the porcine microbiota

Effectiveness of stabilization methods for the immediate and short-term preservation of bovine fecal and upper respiratory tract genomic DNA

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