Brice Le Françios, R&D Scientist At DNA Genotek

On July 6-7, Microbiome Connect brought together 250 industry experts, innovative researchers and clinical leaders in Amsterdam for the eighth annual Microbiome Connect: Europe. Across the two days, a key area of discussion focussed on gaining a more detailed picture of complex microbial communities. We sat down with Brice Le Francois, Senior R&D Manager, DNA Genotek to shed some light on the critical role of metatranscriptomics to characterise microbiome functionality.

Over the past decade, a wealth of data has been generated on the human microbiome through metagenomic sequencing, with a combination of 16S and whole genome sequencing helping elucidate the composition and function of bacteria present. However, challenges remain in determining the bacterial activity in a microbiome sample. As Le Francois points out: “One thing to keep in mind is a relative abundance based on the DNA profile doesn’t necessarily suggest that a particular species is highly active – and vice versa, a low relative abundance species based on DNA profile might actually be highly active.”

Metatranscriptomic profiling directly identifies the bacterial activity in a sample, completely independent of relative abundance – exciting researchers looking to characterise these complex communities. Crucially, “it can give you a sense of what the bacterial species are doing, opening up a new avenue to confidently target specific species” enabling more personalised treatments. Current disease research predominantly focusses on differences in community structure through metagenomic sequencing, finding “there are more and more examples of disease where you look at the microbial community composition and you end up finding that it varies very, very little, if at all.” A key example of this is acne, where it’s now widely accepted that the disease is driven by a particular species, c. acnes. “If you look at the DNA profile and relative abundance of c. acnes there is no striking difference between an individual that’s suffering from the disease and a matching health control” – meaning that the answer relies on the specific strain and its function.

Lying within metatranscriptomic profiling is a host of untapped data and insights that can help us gain actionable insights on treating microbiome-associated diseases – and it’s also more accessible that ever, with the introduction of new tools & technologies and lowered sequencing costs. The benefits are clear, with metatranscriptomic profiling providing a missing link between metagenomics and metabolomics that “has the advantage of looking at gene expression, but can also help tie the taxonomy with those function pathways. That’s going to provide an extra layer that neither metagenomic sequencing nor metabolomics can provide.”

That’s not to say that metatranscriptomics comes without its challenges, despite technological advancements over the past three to five years. “Optimal sample collection and processing is going to be a major consideration for anyone that’s interested in doing metatranscriptomic profiling,” explained Le Francois, expanding that “RNA is very different from DNA: it’s much more unstable and very prone to degradation. This is something that we’ve learned the hard way. We really struggled to come up with a stabilisation chemistry able to preserve RNA – it took many new iterations and over three years.”

Moreover “bacteria are, by design, able to change their gene expression profile within seconds to respond to stressors from the environment. If you want to capture something that’s as close as possible to the in vivo state of the sample, you want to make sure that the collection process is going to have as little impact as possible on that gene expression.” The DNA Genotek team deal with this by ensuring the stabilisation chemistry interacts with the entire sample very rapidly, preventing any of these changes to gene expression. “You need to select a high-performance extraction kit in order to recover the highest quality RNA possible” because some of them are unable to prevent activity leading to RNA degradation, leading to poor quality RNA regardless of the quality of the input material. The more complex the sample, the more challenging this is.

Despite these challenges, Le Francois is optimistic about advancements in microbial analysis and the role metatranscriptomics can play in this research. “With metagenomic sequencing we lack actionable targets to treat diseases. In some cases, this may have led us to incorrect conclusions, like maybe selecting the wrong cohort for clinical testing.” After all, people may have shared microbial profiles through metagenomic sequencing – but that doesn’t mean they have shared microbial function, or metabolic activity. Metatranscriptomics will help fill some of the remaining gaps in our understanding “by identifying metabolic pathways and specific genes that drive that imbalance in the system.”

Metatranscriptomics offers a new and innovative way to analyse the microbiome, but that’s just one part of a wider shift in how we must study the microbiome moving forward – where we must start looking “at several analytes at once, so the multiomic angle: DNA, RNA and metabolites all at once… Each analyte is going to provide a unique perspective on the microbiome, and a layer that’s going to help unveil the interesting ties that the microbiome shares with a human host. I think there’s still lots to learn, but multiomics is going to play a big role in that learning process.”

The Microbiome Connect team is excited to see how this continues to impact the field of microbiome research over the coming months. If you’re interested to find out more about DNA Genotek’s metatranscriptomic services can streamline your microbial analysis and drug development contact Yas Hanee, EU Account Manager, [email protected] and Heloise Breton, MB Product Manager, [email protected].