New UCC spinout SeqBiome makes microbiome and nutrition research the focus

Its launch as the university’s most recent spin-out company now counts Nestlé Group as a newly signed-up client offering services that also includes biostatistical and bioinformatic analysis counting and sample processing.

Through our work at the APC we noticed an increasing interest from food and pharma industry to be able to access high-quality microbiome analysis,” ​comments Dr Marcus Claesson, SeqBiome founder and CEO.

"For instance, companies might want to know if their existing or new functional foods or therapeutic agents have desirable or undesirable effects on the gut microbiome. ​

"This is not always possible to do through traditional academic collaborations, especially when there is a need for rapid analysis, which is why we took the opportunity to create a spin-out that could solely focus on this.​

“After a short few months our existing clients and partners already include Nestle, MARS Petcare, Atlantia, Alpinia Institute, Microbion and the PrecisionBiotics Group.”​

UCC and the APC​

SeqBiome is currently based in several locations across county Cork with much of the sequencing capacity leased from the Moorepark Teagasc Food Research Centre in North Cork.

The team of six have access to a number of Illumina, Ion and NanoPore instruments with data analysis mostly carried out on high-end computers and in the cloud.

SeqBiome joins a number of initiatives started by the UCC and the APC Microbiome Ireland, another institute founded by the university back in 2003.

Other new firms spun associated with the APC include Atlantia Food Clinical Trials, Artugen Therapeutics, 4D Pharma Cork, and PrecisionBiotics. 

“Academics are no longer the only ones interested in conducting high quality microbiome research,”​ says Dr Claesson.

“Indeed, APC Microbiome Ireland and Teagasc, from which SeqBiome spun out, has lots of great examples of successful industry-academia collaborations. ​

“However, many industry microbiome projects are more suitable for a CRO company like SeqBiome, due to considerations of timelines, IP or particular project content,”​ he adds.

“Given the increased appreciations of the importance of the microbiome, and the impact that food and pharma can have on microbiomes, it is not surprising that these two sectors have coalesced around this area.”​

Microbiome research areas​

Dr Claesson highlights particular areas of microbiome research that are garnering more attention than others with personalised and animal nutrition two examples of where industry are focusing their efforts.

In addition, Dr Claesson also sees a mix of both pro- and pre-biotics studies, often with fibre as one of the components, as well as a growing interest in fermented foods.

“There are often changes in many bacteria, and not a single species. In other words, it’s important to also analyse these in co-abundant groups with cross-feeding and ecological driver/passenger dynamics.​

“Genome characterisation of particular strains of interest is also important as these will be part of functional foods products and might need compliance with regulations.​

“The skin microbiome is also receiving a lot of attention from cosmetic companies whose products should either promote healthy bacteria, or make sure that they don’t cause any undesirable perturbations.​

“The pharmaceutical sector has started to investigate the microbiome for drug metabolism, stability and mode of action contributions. I would not be surprised if ruling out hazardous microbiome effects became a regulatory requirement before long,”​ says Dr Claesson.

“There is potential for the health sector to leverage developments in artificial intelligence to develop microbiome-based diagnostic/prognostic tools and clinically relevant patient stratifications where patient with a particular microbiome profile are more or less responsive to a certain treatment. ​

“In addition to DNA sequencing being of relevance to microbiome studies, it continues to be important for studying individual strains of bacteria, yeasts and viruses. ​

"Indeed, Paul Cotter (SeqBiome CTO) is also leading a team of researchers who make up the Irish Coronavirus Sequencing Consortium.”​

Dr Claesson profile​

Dr Claesson is principal investigator at APC Microbiome Ireland and Chair of the EU COST Action ML4Microbiome that is aiming to optimise the use of Machine Learning in microbiome science.

With close to 20 years’ microbiome experience, his research interest includes the role of the microbiome in inflammatory bowel disease and associated methods development.

Dr Claesson recently published two large microbiome studies​​ on inflammatory bowel disease described by the researchers as "two of the most important and largest microbiome studies ever undertaken in patients with chronic Inflammatory Bowel Disease (IBD)"​.​

The findings may lead to ways to predict IBD relapse in patients based on their microbiome markers.

While the condition can be controlled with drugs, the unpredictability of relapses is a challenge for patients and is a reason why the microbiome is so important in providing markers to predict relapse.

“SeqBiome is a great example of the APC’s ambition to translate high-quality research and state-of-the-art capability into commercial reality with the creation of increased critical mass, hi-tech jobs and economic success – centred around microbiome science,”​ adds APC director Paul Ross.

“This is perfectly aligned with SFI objectives and government strategy to deliver economic impact built on a world-class scientific knowledge base.”​