Ep.03 – Dr Morgan Langille
Episode three of Inside Matters
Novel bioinformatic tools and technologies, microbiome characterisation, and the evolution of the field of microbiome.
Bioinformatics is the application of computer science and technology to biological data. It is an interdisciplinary field that integrates other areas of science and medicine.
There are a variety of approaches to study the microbiome. These include traditional approaches, such as culture, and more novel approaches that are culture independent, such as next generation sequencing. Some culture independent approaches to profiling the microbiome generate massive amounts of data. Bioinformatics enables researchers to interpret and make sense of the data, which in turn catalyses advances in scientific understanding.
There is no perfect bioinformatic tool or technology. Each has strengths and weaknesses. Some are better suited than others for specific purposes. Researchers such as Dr Langille as working to improve the current state-of-the-art to enable better microbiome research that is increasingly generating greater amounts of data.
Dr Langille is confident that as the cost of sequencing decreases and the quality of bioinformatic tools and technology improves, the field will develop novel microbiome-based diagnostics and therapeutics that will improve the lives of patients.
Key takeaways from this episode:
The gut microbiome is fundamental to human health. There are a variety of tools and techniques available to study the microbiome. These include traditional methods, such as culture, in which microorganisms reproduce and replicate on a predetermined growth medium (media) that has been selected to suit the target microorganism. Other more recently invented methods include those that involve next generation sequencing technology. The two most commonly used methods that leverage sequencing are marker gene surveys, which profile a specific gene (most commonly 16SrRNA gene) and shotgun metagenomics, which profiles all of the DNA in a sample. Each technique has strengths and weaknesses. For example, 16SrRNA sequencing can be conducted at relatively lower cost than shotgun metagenomics, but delivers less taxonomic resolution – typically to the genus level, sometimes species. Function can also be inferred by shotgun metagenomics. Both techniques require bioinformatics for biological interpretation of the data.
Dr Langille’s group have recently undertaken research that compared the performance of commonly used bioinformatic tools on 16SrRNA gene survey datasets. Such tools are used interchangeably in the microbiome literature. Dr Langille’s group showed that the tools produced substantially different results from the same datasets. Dr Langille recommends that researchers use several methods and focus on significant features of the data identified by most tools, as well as describing the potential limitations in each manuscript. To learn more, see here: https://www.nature.com/articles/s41467-022-28034-z#Sec7
Dr Langille’s group have developed a number of bioinformatic tools to catalyse research into the microbiome. Two examples discussed in the podcast were PICRUSt and JARRVIS, for more information see here: http://morganlangille.com