inBiome: Developing new tech for bacterial diagnostics

Microbial diseases kill 11 million people every year and bacterial infections remain public health's biggest challenge. Now the good news: Amsterdam scale-up inBiome has developed a new DNA-based diagnostics tool for identifying bacteria that radically outperforms traditional methods. In a clean lab at Amsterdam Science Park, I amsterdam spoke to inBiome's CEO and COO to discover why its tech is such a gamechanger.

“It blows my mind that with treating microbial infection, we are still relying on a technology that’s been around since the Wright Brothers,” exclaims Matt Clancy, inBiome’s chief operations officer.

“When diagnosing with traditional culture, you’re basically feeding bacteria, letting it grow and saying ‘oh, it looks like X’. And this takes days! Meanwhile, one in five deaths globally are from bacterial infection – 11 million people a year, more than AIDS and cancer combined! And, while you are waiting for the results, you throw a wide range of antibiotics at it. Isn’t this a crazy way to operate? It’s like giving someone chemotherapy and then wondering if they have cancer or not?”

inBiome wins the audience award at the Amsterdam ZorgInnovatie Awards in 2020

Dries Budding accepts the audience award at the Amsterdam ZorgInnovatie Awards in 2020

Clancy came on board at inBiome in December 2019 after a background in bringing financial innovations to market in the UK. He has all the zeal of the freshly converted – and inBiome’s founder and CEO, Dr Dries Budding, obviously enjoys his colleague’s enthusiasm.

 “And, of course,” adds Budding, “this carpet-bombing approach brings along a whole host of other problems by also killing off beneficial bacteria and increasing the chances of anti-resistance genes developing.”

How inBiome’s tech can help save more lives

inBiome is providing an alternative to this method. Its diagnostic platform Molecular Culture™ uses standard hospital equipment to characterise complex communities of bacteria, quickly detecting the DNA signature of nearly all bacterial species in a single assay. It not only confirms the presence of a specific pathogen but can give a full profile of given human microbiome – whether it’s intestinal, oral or vaginal.

Once the data is uploaded to the platform, the results are available within four hours – compared to the two or three days needed for a traditional culture diagnosis. It’s also much more precise and, by reducing the time to correct treatment, will significantly reduce healthcare costs. As a bonus, the individual results can be compared to other data coming in from different departments, hospitals, regions or socio-economic zones, allowing for automatic infection outbreak detection.

Why inBiome is ready to scale

After 12 years of hard work, inBiome is now ready to scale from the seven Dutch hospitals where Molecular Culture™ is already being used. With CE IVD approval already granted, the company can now start spreading – like a happy fungus – across Europe. And it is keen to expand to the US by applyig for FDA approval – something that the firm hopes to have by the end of 2021. “What do we still need? More money!” smiles Budding. “FDA approval in the US is a very expensive process. We need extra money to push this out as fast as possible.”


The faster the technology is in place, the faster the firm can widen their range of applications, providing even more diagnostics that can suggest personalised treatments, predict successful outcomes and even track potential pandemics.

We are talking to Clancy and Budding in inBiome’s clean lab at Amsterdam Science Park. Rows of freezers are filled with faecal samples – including a particularly prized wisp of millennia-old mammoth poop. “With the current heatwave, we’ve been a bit worried about one of the freezers going on the blink. You don’t want this stuff to defrost,” says Clancy.

Bad guys, good guys, Dutch guys

With bacteria, humans have tended to focus on the bad guys. This makes sense: bacteria and not viruses caused the great historical pandemics, including cholera and typhus. These disease names also happen to be common Dutch swear words – and that is not a coincidence. Not only has this tiny country experienced these outbreaks first-hand, but it has been at the forefront of microbiology since Antonie van Leeuwenhoek became the first person to see bacteria through his self-invented microscope.

“The Netherlands has one of the lowest rates of antimicrobial resistance in the world,” notes Budding. “And that’s because microbiology is being applied at the very highest level.”

Aerial photo Centraal Station and centre Amsterdam Peter Elenbaas

“Amsterdam has a huge global reputation for the life sciences,” says Clancy, “and we benefit from that.”

“I was in discussion with an American company,” recalls Budding. “They were planning to move to Germany but then during a big microbiology convention in Amsterdam, the CEO told me he completely changed his mind: they were coming to Amsterdam. Of course, he saw benefits such as the strong academic and research tradition, the infrastructure, the English language skills, the talent pool. But it was also because of the lifestyle,” chuckles Budding. "The CEO said he wanted to ride his bike to work.”

Amsterdam’s rising reputation in AI

Budding and Clancy have also noticed that Amsterdam’s reputation for artificial intelligence is also on the rise. “We use it at every level of our work from raw data processing to the actual diagnostics. And it is also part of our long-term personalising and predicting goals,” says Budding. “We’ve had a constant flow of graduate students from Max Welling’s machine learning department at the University of Amsterdam, which has given us incredible value.”

“Smart Health is very interesting for us. Once we’re operational in thousands of hospitals and all the results enter our cloud-based storage this can work as a real-time encyclopaedia of infectious diseases. Previously hospital labs used to be separate entities that could not, or barely, communicate. Now, we’ll be able to tell if the same bug has shown up in two hospitals 100 miles apart – and if necessary, act on it,” says Budding.

inBiome's tech uses hospital equipment to characterise complex communities of bacteria

inBiome's tech uses standard hospital equipment to characterise complex communities of bacteria

“Then there’s the fact that everybody has a completely unique microbiome. So, if you want to model a microbiome’s profile and find those signals or triggers that discriminate between health and disease, that involves mass data. That means you need highly advanced algorithms. And, thanks to Welling and his students, we already know what models work best for our particular data.”

Let’s salute our microscopic friends

Microbiome is enjoying a moment up there with other trending terms such as circular economy and cryptocurrency. “We now know bacteria, and their symbiotic interactions with us and each other, have a huge role in our health,” says Budding. “They’ve been part of us since we emerged from the ocean. They provided us with functionalities we simply don’t have, and they’ve trained our immune systems to do all these things for us.”

“But over a century ago when the plague was still fresh on everyone’s mind, bacteria were indeed terrible. So, the whole medical focus was on killing anything and everything. But now we recognise this has a profound effect on our health since it also disturbs our normal, necessary bacteria.”

Science Amsterdam

Budding says the eureka moment that helped him launch inBiome was completely down to luck. As a graduate student at VUMC, he entered the world of DNA amplification technology. “We could search for that segment of DNA present in every bacterium. So, we could now detect a bacterium, but how could we identify it specifically? And that’s when discovered our ground-breaking technique. It was totally a chance event.”

Then Budding had a second lucky break after identifying two distinct vaginal microbiome profiles during his research. “It turned out one profile was of those women who got pregnant from IVF treatment and the other was of those women who didn’t. Now, that was interesting! From there, after we actually built chance into our company’s strategy: we’re focused on launching our Molecular Culture platform, but we make sure we expose ourselves to a wide variety of smaller left-field projects to maximise the chance of making those lucky discoveries.”  

How the challenges of the coronavirus pandemic helped inBiome

At the start of 2020, all looked rosy and the company was being recognised for its efforts. InBiome won the regional public prize of the Nationale Zorginnovatieprijs – the Dutch prize for the most innovative scale-up in healthcare. But then COVID-19 happened.

With universities shutting down and hospitals distracted, inBiome’s research-related income dried up. With no travelling or events on the horizon, networking opportunities to secure further funding also disappeared.

“But it also gave us focus,” says Clancy. “We planned out scenarios, looked at ways to adapt, and strengthened our network. The crisis also reinforced what we already knew: Amsterdam as a city of resilience. It showed the local sector at its best: competitors started helping each other; private companies turned their effort and expertise to support something so important, even without clear commercial gain; and local support organisations, like the Amsterdam Economic Board and Smart Health Amsterdam, provided advice and connections – if they didn’t know the answers themselves, they knew someone who did.”

inBiome's long-term vision

Meanwhile, inBiome pivoted to set up a COVID-19 test station in their building and contributed to an international study that found a potential link between susceptibility to COVID-19 and the make-up of a person’s throat microbiome.

Six months later, Budding and Clancy sense a shift back to relative normalcy. “Before COVID-19, the local life science sector was going from strength to strength, and now continues down the same path. In a strange way, I think the crisis highlighted the value of our technology,” says Clancy.

“We are interested in finding an investor with a long-term vision that can see the potential of our business and its ground-breaking technology,” says Budding. “One that is not purely concerned with hitting a specific financial goal at a specific quarter. More people are recognising infectious disease is very important from both a health and economic perspective. Just imagine if we had rapid diagnostics in place when COVID-19 first broke out. It would have been a whole different story.”

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