The top 4 challenges for microbiome companies

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The top 4 challenges for microbiome companies

Microbiome research is abundant and profoundly inspiring. Whether focusing on cancer drug response, or the more classical field of gut discomfort solutions, we are clearly on the brink of some long-anticipated breakthroughs. But despite the promise, companies in the field face challenges.
This blog focuses on four of these challenges. I believe we can actively work together to ensure these will not become problematic for the industry.

Why companies are investing in the microbiome domain

Microbiome research is highly interesting. On the one hand, this is because of therapy response to orally administered drugs and, on the other, because of the impact of dysbiosis of the microbiome ‘organ’ on the host. This research might well enable us to develop prophylactic products and therapeutics that are as profitable as antibiotics but cause no side effects or are more efficacious.

Hence, since 2010 investments in the microbiome space have increased every year and now amount to EUR 1.5 Billion, according to Global Engage.

2018 saw an even more active engagement of strategic investors with microbiome start-ups. Partnership deals with Rebiotix, 4D Pharma and Microbiotica are first examples of these. This development seems to indicate that the pharmaceutical sector is beginning to believe in and understand the role of the microbiome in therapeutics.

Whereas many companies focus on IBD, metabolic disease and oncology, others carefully choose a niche to operate from, such as Parkinson’s, psoriasis and a number of rare diseases. If they succeed in establishing a position, they are looking at great business potential. But the stakes are high. Only a handful of companies will thrive.

Below are four major challenges that microbiome companies, especially start-ups, face and that are specifically related to the way we work in this science-based field. We might be able to counter these.

Read more on the page of Global Engage.

Replacing dairy with plant protein in cheese

In recent years, interest in plant proteins has grown as they are sustainable and cost effective. However, replacing dairy proteins by dairy proteins, often gives issues. One of the food products where proteins can be replaced by plant proteins is cheese. As NIZO has more than 70 years’ experience in dairy and cheese technology and more than 15 years’ experience with functionalizing plant proteins for uses as alternative to animal proteins, NIZO started a consortium together with HAS Den Bosch, Bel Leerdammer, FujiOil and Daiya Foods.

The coming three years, the researchers will investigate and develop strategies that allow to fully or partially replace dairy protein for plant protein in new products having the characteristics of traditional cheese. To do so, the research team has to overcome intrinsic shortcomings of plant proteins: low solubility, inferior consistency/texture and flavour defects. Eventually, the developed strategies should allow partners to produce palatable new products based on plant proteins; with lower carbon footprint, comparable functionality and nutritional value matching traditional dairy cheeses.

To achieve these goals, NIZO will explore research directions like fermentation and enzymatic and physical protein modification. The researchers aim to replace typical dairy protein’s roles in cheese: network formation and gelation, emulsification and flavour generation in a physically and microbially stable and safe product. HAS University of Applied Sciences will be focussing on consumer acceptance and positioning of new plant based cheese alternative. Bel Leerdammer, FujiOil and Daiya Foods contribute to the knowledge platform by sharing specific expertise and pilot facilities in their respective market field.

This project is financially supported by the Dutch Topsector Agri & Food. Within the Topsector, private industry, knowledge institutes and the government are working together on innovations for safe and healthy food for 9 billion people in a resilient world.

For more information, please contact Dr. Eva Düsterhöft,, T: +31 318 659 635.


Recently published: Rational strain selection for protein transition

NIZO scientist have recently published a paper on the genome comparison of Lactococci originating from dairy and plant environments. The work demonstrates how advanced statistical and bioinformatic analysis allows to condense a huge amount of data into informative figures and tables for sensible data interpretation. One example is the Figure below where you can see at a glance which strains is most applicable for a specific functionality (in red).

As we are very busy with new fermentative strategies to support the protein transition movement an important point of this study is that it demonstrates how genomic information can be exploited for rational strain selection used to ferment novel substrates” according to our Expertise Group Leader Fermentation, Herwig Bachmann. “It allows us to group strains based on full genome sequences while zooming in on specific functionalities. We can more reliably address questions on e.g. what plant isolates are predicted to have a flavor formation profile most similar to that of strains isolated from dairy environment”, says Jos Boekhorst, our Scientist Microbiomics.

The work was carried out in collaboration with a project of the Top Institute Food and Nutrition.



NIZO is now partnering member of the Pharmabiotic Research Institute

The microbiome and its role in human health represents a paradigm shift in how medicines will be developed. The Pharmabiotic Research Institute (PRI) was founded to make Microbiotic Medicinal Products a therapeutic reality in Europe. The PRI, as a neutral and financially independent non-profit association, applies a unique collaborative approach to improve market access and provide technical and regulatory intelligence for its members. PRI members have a  stake in regulatory, technical and collaboration efforts of the microbiome & human health space.

For NIZO this means an unique possibility to transfer knowledge and experience with other companies and research institutes in the microbiome and clinical area, like the Clinical Studies Task Group.


NIZO is gespecialiseerd in wetenschappelijk onderzoek op het gebied van voeding in relatie tot gezondheid. Voor voedingsmiddelen onderzoek zoekt NIZO regelmatig vrijwilligers in verschillende doelgroepen. Wanneer u mee doet aan een voedingsmiddelen onderzoek helpt u mee aan de vooruitgang van de wetenschap. Daarnaast krijgt u vaak een financiële vergoeding voor deelname. Deelname is altijd vrijwillig.

Om op de hoogte te blijven van onze onderzoeken kunt u ons volgen via deze website of via Facebook of Instagram

Via onderstaande links kunt u meer informatie krijgen over de onderzoeken die we bij NIZO uitvoeren en hoe u zich voor de verschillende onderzoeken kan aanmelden. Hierin staat ook vermeld aan welke criteria deelnemers moeten voldoen, dit verschilt per onderzoek. Nadat u zich heeft aanmeld voor een onderzoek krijgt u uitgebreide informatie over het onderzoek, daarna kunt u altijd nog bepalen of u wel of niet wilt deelnemen aan het onderzoek.

Lopende studies: 

Relation between spores in milk powders and predictability of spoilage of UHT milk products

Check out our most recent publication in the International Journal of Dairy Technology, which focusses on “Spores in Dairy – new insights in detection, enumeration and risk assessment”!

NIZO scientists Robyn Eijlander and Marjon Wells-Bennik, together with scientists from Abbott, bioMérieux, FrieslandCampina, Nestlé and U.S. Dairy Export Council, describe the evaluation of various methods that are used in the food industry to detect and enumerate heat-resistant spores in milk powders and offer practical solutions for standardization. The publication furthermore highlights new insights on modelling spore heat resistance of Geobacillus stearothermophilus.


Our Business Development Manager Food Beverage and Ingredients, Ben van der Deen, visited Alberta last February, meeting with potential business partners and laying out NIZO’s expertise in the plant-protein sector. As part of the Plant Protein Alliance of Alberta’s Global Business Network series of events, Ben van der Deen had a successful networking breakfast to an audience of industry players.

As we have to feed roughly 10 billion people in the near future, companies will need to make better use of their products and global supply chains will become very important. Besides, there’s an increasing demand for very high-value food applications. Developing these products may include researching how to produce better flavours and mouth feel, increase protein functionality, and create easier digestibility.

Owen Fieldberg, of Fieldberg Farms and Altiva Inc., near Medicine Hat, was at the breakfast session with Ben van der Deen and learned how NIZO might help propel forward his organic hemp business. “Opportunities to lean into institutions such as NIZO, with their depth of knowledge and historical experience, can only enhance our ability to create new products and lead the field,” Fieldberg said.

If you would like to know more about this subject, please do not hesitate to contact us.

Click here to read the article.

Launch of Quality control kit for miris human milk analyzer™

NIZO congratulates MIRIS on the launch of the Miris Calibration Control Kit™, quality control material for the Miris Human Milk Analyzer™!

At NIZO, we are proud to have supported MIRIS in the development of the standardized solutions found in the Miris Calibration Control Kit™.  With the Miris Calibration Control Kit™, Miris introduces standardization in the process of analyzing human milk for individual nutrition of preterm babies. Miris Calibration Control Kit™ contains standardized solutions with known concentrations of fat, protein and carbohydrates that correspond to those found in average human milk and to the high end of the Miris Human Milk Analyzer™ measuring range.

The Trade-Offs project, headed by Dr Herwig Bachmann

The TiFN Trade-Offs project, headed by Dr Herwig Bachmann, which studies the optimisation of dairy fermentations, scored 9 out of 10 at the mid-term evaluation of the project.The reviewers were very enthusiastic about the progress made in just 2 years. They noted the quality of the team. Finally they assessed the potential synergy within the project and the industrial relevance of the outcomes.

Should you wish to learn more about this project, please do not hesitate to connect with us.


Azitra’s Clinical Study of AZT-04 for Cosmetic Use Completes Enrollment

NIZO is proud to have contributed to this clinical study by assisting Azitra in development of the formulation used in this study focusing on microbiome-based cosmetics and therapeutics!

Please connect with our experts in case you would like to learn more about our capabilities in this field.

Click here to read the article