A study by a team of international researchers has led to the development of a bioinformatics tool to help more accurately identify species of microbes within complex microbial communities.
A study by a team of international researchers has led to the development of a bioinformatics tool to help more accurately identify species of microbes within complex microbial communities.
In a paper published this month in the prestigious journal Nature Communications, the research team, including an academic from UNSW Canberra, describes how taking into account where the microbes were located will improve classification accuracy rates.
Co-author Dr Ben Kaehler, a UNSW Canberra academic, said the technology that has stemmed from this research is expected to be used by scientists across a range of fields.
Microbes are the microscopic organisms with which we share nearly every environment on Earth, including our own bodies. To help understand microbes they are grouped or classified in much the same way as we taxonomically classify plants and animals. Most microbes are harmless, some are deadly, but it is the patterns in which they occur that can give us a much richer picture of human and environmental health.
“There is an incredible diversity of genetic information in microbes, it's as if we can open a window on a parallel universe that's all around us. Taxonomic classification is one way of looking at that information,” said Dr Kaehler.
“The outcome from this research is a tool called q2-clawback, that allows scientists to consider environment-specific taxonomic abundance information and classify more accurately to the species level.
“Best practice says to classify microbes to the species level, but current techniques for classifying short DNA sequences in microbiome studies have limited accuracy, so many scientists stop at the genus level.
“This research has shown that using this species abundance information improves the classification accuracy to the point where we're now doing as well or better at the species level than we used to be doing at the genus level,” he said.
To illustrate how the method works, under a popular experimental protocol, the genetic material retrieved from the species Lactobacillus helveticus is almost indistinguishable from that obtained from a different species in the same genus, Lactobacillus hamsteri. L. hamsteri was isolated from the gut of a hamster in 1987. L. helveticus makes up over 21% of the genetic material found in a database of 3,921 human vaginal microbiome samples, where L. hamsteri was not observed at all. So, if you observed a similar genetic sequence in a human vaginal microbiome sample, you could confidently call it L. helveticus. On the other hand, if you were analysing a hamster gut microbiome, you would have to be more careful.
“What we’ve done is improve the methods that will enable others in their field of work. And the thing that has made this successful is that all of this data exists because people have contributed it to databases because they're good science citizens. I’m proud that through this tool we can make life better for the people who have been contributing.”
In addition to UNSW Canberra, the team also comprised researchers from the University of California San Diego, Northern Arizona University, and the Australian National University.
Read the paper here:
https://www.nature.com/articles/s41467-019-12669-6