Quadram pushes best practice microbiome study with web resource launch
The resource aims to address the lack of reproducibility amongst the majority of studies the Institute says hampers the translation of microbiome research to the clinic.
“The application of different methodologies and techniques to different microbiome studies limits their usefulness and validation, and the ability to compare data across different studies,” says the Institute, based in Norwich in the UK.
“Few widely accepted standards or reference reagents exist for conducting gut microbiome research.
“Establishing standard operating procedures (SOPs) for sample collection and analysis is a prerequisite for the establishment of biospecimen repositories and large databases, and for validating and comparing results from different studies,” they add.
Along with freely accessible protocols developed and optimised for microbiome studies, the Institute is also committing to updating these rules to keep pace with the speed of microbiome research.
These protocols look to cover study design considerations, sample size for a microbiome experiment, sample collection and initial processing of faecal samples as well as recommendations for optimum DNA extraction and quality control.
The protocols extend to 16S and shotgun metagenomic Illumina library preparation, microbiome informatics, statistical analysis of microbiome data, virome-specific and mycobiome-specific protocols.
“Quadram is providing protocols that have been developed, optimised and applied to microbiome studies across the Institute,” comments the team.
“It is to be noted that some protocols, particularly those involving automation and informatics, are constantly evolving and being improved.
“Nevertheless, these protocols highlight critical concepts and key features, and so serve as a valuable benchmark.
“While it is our intention to keep these protocols up to date, users are reminded that this is a rapidly evolving field and they should monitor the latest literature.”
The launch of Quadram’s resource coincides with a recent paper published in Frontiers in Veterinary Science, that review best practices for conducting clinical trials that study the effects of an intervention on the microbiota.
The paper, published in April this year, aims to address common mistakes made, such as cost-cutting decisions that reduce the study’s value and ultimately prevent brands from making product claims.
Like Quardram’s recommendations, the paper also covers experimental design, dietary considerations, recruitment, and microbiota sampling choices.
The review, authored by US-based biotech firm AnimalBiome, also looks at basic and commonly used designs in intervention trials and microbiome studies, with general recommendations and caveats for each.
“Limiting study costs poses a substantial risk of conducting an underpowered or fundamentally flawed study with inconclusive results,” the paper concludes.
“Conversely, a larger expenditure for a well-designed study of adequate size may be more expensive up front, but can pay dividends in credible, well-supported product claims and more successful products.”