Using marine sponges, Flinders University researchers have developed a new technique to read complex microbial populations – a technique that could also be applied to improve analysis of the human microbiome.
To better understand the complexity of microbiomes, researchers from the Centre for Marine Bio-products Development at Flinders University chose to examine sea sponges – believed to be the oldest existing animals, from about 750 million years. Sponge tissue consists of up to 60% bacteria, making them ideal creatures to examine microbial diversity.
The researchers developed a multi-primer approach to uncover taxonomic “blind spots”, which led to dramatically improved results. For example, compared to a maximum of 41 microbial phyla reported by the global sponge microbiome survey of 81 sponge species, the Flinders University team revealed 57 phyla from only four local sponge species.
“This breakthrough marks a significant improvement in our ability to expand our knowledge of microbiomes,” says Professor Wei Zhang, who is lead author of the research.
Flinders colleague Professor Chris Franco uses the well-known “blindfolded men and an elephant” analogy to explain the effectiveness of the new multi-primer gene reading technique.
“Previously, using the current single primer method, researchers only described different parts of the microbiome, while we are now able to see the whole ‘elephant’,” says Professor Franco.
According to Dr Qi Yang, a postdoc researcher who commenced this research during her PhD candidature, “We were able to obtain sequence coverage of all the variable regions of the 16S rRNA ‘signature gene’ to analyse the amplicon-based microbiomes.
“From this initial examination of marine sponges, we are now confident that it can be applied across all microbiomes – including human microbiome studies.
“This will have many possible implications. For example, to better understand the human gut, we will now be able to identify many more types of bacteria, to obtain a more complete picture of the human microbiome.”
The findings have been published in the paper “Uncovering the hidden marine sponge microbiome by applying a multi-primer approach”, by Qi Yang, Chris Franco and Wie Zhang, published online in Scientific Reports, a nature research journal (DOI 10.1038/s41598-019-42694-w).
The publication of this paper rewards the persistence of two dogged years of research by Professor Zhang, Dr Qi Yang and Professor Chris Franco for this new multi-primer approach to earn recognition.