Microbiomes, Clinician Guidelines and Relative Quantification – The SBT Episode 16 with Phylo Bioscience.

Our ‘Science Behind the Technology’ series gives us the chance to speak to our members about what they are working on, their plans for the future and why you should care about their work.

Phylo Bioscience is a CQC registered company that provides microbiome analysis from their laboratory at Unit DX. They offer analysis for gut, immune and oral health (amongst others), working with clinicians to aid diagnosis and informing their decision making.

This month, Laboratory Director Dr Jaspal Patil joined Anna Fleming to discuss the importance of microbiomes, and the field’s vital need for transparency and accuracy.

Jaspal of Phylo Bioscience putting their new PCR machine to use.

Jaspal of Phylo Bioscience putting their new PCR machine to use.

Microbiome Analysis

In September 2018, the Stroud-based Invivo Clinical provided seed investment into Phylo and they set up a two laboratory spaces at Unit DX. Their focus is on offering high-quality analysis for areas that cannot currently be addressed, or improving on existing services offered by competitors.

As Jaspal explains:

“We’re providing a service, working with clinicians to investigate patients’ microbiomes. Microbiomes are populations of microbes that live within the human body. Our bodies have billions of cells, but our microbiome makes up even more, and while we have identified around 20,000 human genes, the human microbiome has millions of genes. These organisms live inside our bodies and produce and release their own proteins, so you can imagine how much influence they can have on our health.

“At Phylo we test different microbiomes – usually oral, gut, or vaginal. We receive a sample from a patient – say a saliva sample – we extract the DNA and protein, and then we test for a wide range of pathogens using real-time PCR (polymerase chain reaction) – a technique to detect microbial genes. We also check for some non-pathogenic bacteria, because sometimes your ‘good’ bacteria levels drop during an infection. Then we look at the protein levels which show if there’s inflammation present.

“Interestingly, if you have inflammation in another part of the body, we can often tell by analysing the saliva. Recent research, for example, has shown a link between the saliva microbiome and neurodegenerative diseases like Alzheimer’s, so it’s indicative of much more than just oral health. The gut microbiome is also connected to other conditions – cancer, diabetes, cardiovascular diseases, mental health and neurodegenerative diseases, to name a few.”

Anna – So do you diagnose these conditions?

“The results we produce gives clinicians a guideline, but it’s not an absolute diagnosis. The clinician should consider lots of other factors too; it’s not black and white, it’s about considering everything and making an informed decision. That’s something the clinician needs to do rather than us. So we’re not just about screening; our results are part of a bigger picture.

Are there other labs that provide this kind of service? 

“We’re the only company working on some of these microbiomes; there is only one other company that does the oral microbiome and they’re based in the US, and no one else is currently working commercially on the vaginal microbiome. So in those areas, there isn’t much competition, however, there are a few other labs doing gut microbiome screening.

Jaspal and Leon hard at work in the lab.

Jaspal and Leon hard at work in the lab.

New techniques

“Most of the companies out there use absolute quantification of microbes in a given sample. The results of microbial abundance are often reported as per gram or per milliliter of the sample. On the other hand, at Phylo we do a relative quantification of microbial gene expression and we report the microbial abundance results relative to endogenous control which is individual to each sample. As per our understanding, we realised that quantification of microbial gene expression relative to endogenous control was more precise, consistent and scientific”.

“In relative quantification, the results are always normalised to an endogenous control, which is essentially a conserved microbial region. That’s something that isn’t expected to change because of an infection, and it acts as a platform from which you can measure the changes in your microbiome. The good thing about this technique is that each time a patient provides a sample (often before and after treatment), you take the same amount of DNA and use the same endogenous control gene and normalise it, and then you can very confidently say how the load of your microbiome has changed. No one else we know of in the market is doing it this way. We’re confident in our results and proud of what we’re bringing to the market.”

“We’re also very careful to use only the best equipment on the market, and we’re developing our own laboratory management system which minimises human error and allows us to produce really customisable reports for clinicians. It also means we have a maximum turnaround time of about 10 working days, which gives us a competitive edge over the industry standard of 3-4 weeks.”

Anna – Can you tell me about how Phylo started?

“Phylo started through seed investment from Invivo Clinical, a company based out of Stroud that has been working to provide EU clinicians with microbiome diagnostics for the last ten years. They had become frustrated with many commercial operations not embracing the role of multiple microbiomes and their impact on health and disease. Then, we worked together to create a team that would focus on scientific transparency, reproducibility, and flexibility.  Invivo will be commercialising the science and results we produce. All clinicians will also have access to the scientific team at Phylo, which includes an expanding advisory board that has decades of experience in human microbiome research.”

Next steps

“Next month we’ll be launching our new lab management system fully, and we’re branching out into the nasal and urinary microbiomes. In the less immediate future, we’re also hoping to develop screens and work on cancer. Our main goal is to provide precise, transparent and highly specific reports to clinicians.

To find out more about Phylo Bioscience, follow their LinkedIn page for updates on publications and progress.

By | 2020-01-06T16:01:28+00:00 September 4th, 2019|The Science Behind the Technology|