What is fungal barcoding?

08/24/2014 8:00 PM

08/19/2014 3:40 PM

Soo Chan Lee is senior research associate in molecular genetics and microbiology at Duke University. Here he explains how scientists are uncovering entirely new species of fungi and dissecting their roles in human health and disease. Questions and answers have been edited.

Q. How many different species of fungi are there? What is their function?

A. A study in 1990 estimated there are 1.5 million fungal species on Earth. A more recent study used the latest in DNA sequencing technology and upped that estimate to 5.1 million species and possibly even 13.5 million. However, fewer than 100,000 of these species have been studied.

Fungi play key roles in the ecosystem as a natural decomposer of waste and in the production of cheese, wine, bread and many fermented foods. Anyone who has enjoyed a mushroom pizza knows that fungi can be a food in and of themselves. Fungi are valuable industrially, as they help to produce biofuels such as biodiesel and ethanol. They can also produce life-saving medicines such as antibiotics.

Q. Why would you want to identify the exact species of a particular specimen?

A. Despite their many positive contributions, there are also negative aspects of fungi. Plant pathogenic fungi can cause serious economic losses to agriculture. Grains rust, potato wilt, rice blast, powdery mildews, apple scab and rye ergot are just a few of the plant diseases caused by fungi. Some researchers believe that rye ergot caused the gangrene that its victims misinterpreted as the result of witchcraft during the Salem witch trials.

Human fungal infections such as candidiasis, aspergillosis, mucormycosis, and cryptococcosis can be fatal to people with weak immune systems. The treatment will vary depending on which fungi caused an infection, but unfortunately we can’t figure out what particular species of fungus we are dealing with by looking under a microscope.

Fungal barcoding provides a molecular method for identifying the species and deciding which type of medicine is most likely to work.

Q. What is fungal barcoding?

A. The fungal barcode is basically short sections of DNA sequence that can be used to identify fungal species. This barcode area is shared across the majority of fungi, but also has enough small changes between different species that it can be used to distinguish one from another.

Q. Could you give specific examples of situations where you have used fungal DNA barcoding?

A. There have been a number of human outbreaks associated with fungi. Our group worked on the outbreak of a fungus called Cryptococcus gattii in the Pacific Northwest. More recently, we used this fungal barcode method to find that recalled Chobani yogurt contained a pathogenic form of the Mucor circinelloides fungi.

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