In an article recently published in Genome Medicine, a group of UBC researchers discussed the implications of metagenomics for infectious disease surveillance, in public health. We sat down with Dr. David Patrick, Professor and Director at UBC’s School of Population and Public Health, and one of the authors of the article, for a quick Q&A.
Dr. David Patrick
In a few words, what is metagenomics?
Metagenomics is a way of describing the diversity of genetic material in a specimen. We use it to focus on the full range of microbes present in a sample. When the sample comes from human tissue, this is known as the microbiome.
We should consider this current genetic sequencing technology to be a new and powerful toolkit for studying the causes of health and illness; not unlike looking down a microscope for the first time.
What are the main metagenomic techniques for pathogen detection?
The main steps involve first preparing the specimen and deeply sequencing the genetic material it contains. Then, computers are used to subtract out the reads that represent human genetic material. Finally, the various remaining reads are compared against existing databases to identify the microbial species present or to point to newly discovered microbes.
What is the added value of metagenomic techniques compared to conventional laboratory techniques?
There are several advantages. Conventional laboratory techniques are sometimes limited to identifying organisms that can be grown. There are thousands and thousands of microbes of considerable importance to our health that we cannot grow. These can be detected through metagenomics.
Further, most traditional microbiological studies focus on identifying a fixed number of known microbes. This is much like playing the parlour game of 20 questions. Sooner or later, you run out of questions – or in research, you run out of money. Limits such as this are very much lifted by metagenomic techniques.
Source: BioMed Central
What are the challenges of using metagenomic techniques?
Experiments have to be very carefully conducted. Patient and control specimens need to be carefully selected. We need to exclude the possibility of contamination and false results. There can be a great deal of information in just one specimen so it is necessary to have a very rigorous approach to analysis to determine what findings may actually be important. Finally, if our initial studies find a new association between an illness and a microbe, follow-up studies are required to ensure that the finding is reproducible, real and causal.
What do you see as the future of metagenomics in public health?
In the short term, we’ll see pay-off from studies of the human gut microbiome – from a broader understanding of the total diversity of microbes in our gastrointestineal (GI) tract. Already, this field is pointing to better treatment of C. difficile infections and there is the very real possibility that manipulation of the gut microbiome could have influence in diseases ranging from inflammatory bowel disease through to obesity and asthma.
We want to see if we can marry new sequencing science (including metagenomics) with state of the art epidemiological study design. Bringing these areas of research together could shed light on several illnesses where the cause presently remains unknown.
At the tail end of the 19th century, experimental microbiology as introduced by Louis Pasteur and others shed light on the causes of dozens of diseases that had been mysteries throughout history: TB, leprosy, typhoid, cholera and the list goes on. It was an explosion of discovery because new tools were available to look at vexing old problems.
I believe we are in a parallel era right now. The next two decades will prove a fascinating time in the understanding of human health.
“Metagenomics for pathogen detection in public health” was written by Ruth R. Miller, Vincent Montoya, Jennifer L. Gardy, David M. Patrick and Patrick Tang, and published in Genome Medicine.