Research and business opportunities in clinical microbiomics
Posted 6th July 2018 by Jane Williams
This article was originally published in Health Europa Quarterly on 3 May 2018, and is published here with permission.
Exploring areas of research and development related to the microbiome – the collective name for the micro-organisms living in the human body – is the central topic of the annual Microbiome R&D Business Collaboration Forum. This year’s focus at the event was on business collaboration and private investment into research and development projects in the microbiome.
The 5th Microbiome R&D Business Collaboration Forum: Europe featured a number of key speakers from across the sector, including representatives from public and private institutions, as well as international companies. Speakers at this year’s event included:
- Wouter De Jonge, Professor of Neurogastroenterology, AMC Amsterdam, the Netherlands;
- Cathryn Nagler, Bunning Food Allergy Professor, University of Chicago, USA, and Co-Founder and President of ClostraBio;
- Johan van Hylckama Vlieg, Vice President of Microbiome and Human Health Innovation;
- As well as Angela Horvath, Post-Doctoral Researcher at the University of Graz, Austria.
These speakers detailed cutting edge research, the investment opportunities that are afforded by this research, and the potential impact on health that better understanding of the microbiome could yield.
Clinical Microbiomics and human health
The skin microbiome plays an important role to not only skin health, but also wellbeing. Furthermore, low biomass of the skin microbiome can become a challenge for whole-genome metagenomics. Clinical Microbiomics provides end-to-end microbiome research services for both clinical and pre-clinical research, this includes:
- DNA extraction;
- Library preparation;
- Sequencing and bioinformatics.
Their bioinformatics platform provides partners with the advanced capabilities required in order to analyse and interpret microbiome metagenomics data. Clinical Microbiomics extensive collection of deep-sequenced adult, infant and mouse gut samples captures an estimated 80% of the diversity of the microbiome, far vaster than traditional reference-based methods. At the forum, director of scientific operations at Clinical Microbiomics, Jacob Bak Holm, Health Europa Quarterly saw Holm discuss metagenomic species of the skin.
The complications of sampling
Sampling can be complicated by a range of factors at several stages, Holm outlined, one of these being the use of soap and cosmetics prior to collection of the sample, obscuring the work conducted in the laboratory. Moreover, he added: “A low biomass sample is very sensitive towards contamination”, whether this be through cross contamination or contamination of the DNA from the environment of the lab.
Clinical Microbiomics have been advancing towards optimising the process, considering these challenges and, as a result, guiding clients on how to standardise sampling within any given study. “We have optimised our extraction profiles so that, now, they also fit very well to slow input, low input skin samples.”
Increasing the variety of skin sampling methods
In the laboratory, there are many different ways to sample skin and, moreover, these approaches are a lot standardised when working with the gut microbiome. Holm added: “When working with skin, you have the choice of many different types of swabs.” As a result, Clinical Microbiomics have tested these and are currently trialling a wax solution. Once applied, the wax solution can be taken off, yet, the majority of the bacteria from the skin will stay on the wax; “it turns out to be quite efficient,” Holm said.
“All in all, I think using the swabs, or this wax, are two quite efficient ways of sampling.” However, Holm furthered that this is often seen in guaranteed DNA-free products, and that as such should always be tested, due to the effects of these low biomass, low DNA products, on the sample. Once the client has decided on what type of sample is to be used, a specific protocol must be implemented, regardless of where the sample is being extracted from –either wax, or from a swab: “we have optimised that and are quite flexible.”
The bioinformatics platform
Following successful sampling of the skin and, subsequently, sequencing of the sample, is the identification of all the microbial genes. Moreover, this process is conducted using as many samples as possible. In one instance, Clinical Microbiomics used 1,942 samples, whereby they then proceeded to identify the genes and create a gene catalogue. “In this case, since we used that many samples, we can actually, on average, [identify] 82% of all the non-host genes in a given skin sample.” These genes have already been identified, previously, from the many samples previously collected and tested.
As a result, the genes can be studied, those genes which follow the same abundance across multiple samples can be isolated and, therefore, nutrigenomics pieces can be identified. The bioinformatics platform enables users to establish information about the nutrigenomics pieces, and of genes. From 1.972 samples, Clinical Microbiomics have identified 4.4 million genes, and a further 260 nutrigenomics pieces.
We have a dedicated skin microbiome track at the 6th Microbiome R&D and Business Collaboration Forum: USA. View the agenda here to find out more.
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