As one of the featured collaborative projects of the UQ Genomics Initiative, the cross-institutional project ‘Metagenome-enabled human and mouse microbiomics’ kicked off earlier in 2016. The project aims to build the microbiome equivalent of the human and mouse reference genomes by developing a low-cost high-throughput metagenomic pipeline to characterise the human and murine microbiomes of specific habitats, such as gut, skin and oral cavity; as well as capture more of this biodiversity as cultured isolates.
Currently, the team has successfully developed a cost-effective high throughput method for metagenomic sample processing. For the analysis of metagenomic data, they have designed a bioinformatic pipeline that efficiently processes data for genome-level identification and the classification of metabolic pathways. Finally, the team has also created a web portal for the collection of metadata from study participants.
In parallel, members of the “most wanted” taxa of microbes are being recovered using samples obtained from clinical and small animal studies by a variety of innovative techniques for microbe culture, empowered in part from the provision of the metagenomic data. In turn, these “new” isolates will enter our existing DNA sequencing pipelines, and further advance the depth, breadth and discriminative power of our reference genome database and bioinformatics pipelines.
Building on the pre-existing microbiome database, the research team has thus far collected over 520 gut and oral microbiome samples, including 160 samples from participants of the first beta test and 360 samples from UQ students undertaking microbiology subjects. From these data, the team has extracted 1178 high quality draft genomes of gut and oral microbial populations. The study is also incorporated into the undergraduate microbiology practical curriculum (MICR2000/3000/4000), where students have the opportunity to learn about the human microbiome firsthand by analysing their own microbiome genome data. In addition, the team has produced a collection of more than 100 microbe isolates representing all three domains of life (Bacteria, Archaea, Eukarya), which are being used by UQ collaborators for in vitro studies and planned small animal studies.
The team is currently working on further improving the analytical pipeline to include viromes and antibiotic resistance genes and growing the metagenomic databases for human and murine microbiome characterisation at the population genome level. This will form the basis for affordable and routine microbiome testing, replacing 16S amplicon profiling, and broadly enable genome-directed isolation of specific microbes that can be used for the preparation of rationally-designed microbial consortia for (pre-)clinical testing and development of microbe-based therapeutics. The methodologies and data outcomes resulting from this study have also led to a commercialisation opportunity in the form of a spin-off company called Microba. The company will offer comprehensive metagenomic microbiome profiles to clinicians and the general public.
For more information about the project and collaborative opportunities, please contact Prof. Hugenholtz at email@example.com.