New paper! 

On May 21, our paper in deciphering metabolic functions of Faecalibacterium prausnitzii (F. duncaniae A2-165) is now published in Microbiome Research Reports. In this paper, we leveraged the metabolomics technique and GuMI platform to identify novel metabolic function of Faecalibacterium bacteria under physiologically relevant microenvironment, i.e., oxygen gradient, flow, primary colonic epithelium cells. We found F. duncaniae A2-165 contribute to the nucleoside metabolism, production and consumption of certain amino acids. Additionally, the presence of bacteria changed the expression of many transcription factor genes related to viral infection and bacterial recognition. This study showcase the application of GuMI platform to discover new functions of gut microbes and their impact on the host.

Read more about GuMI 1.0, GuMI2.0, SynComs, or organoids and monolayer

New paper about GuMI 2.0! 

Our paper in advancing gut microphysiological systems with the introduction of GuMI 2.0 is now published in npj Biofilms and Microbiomes. This innovative fluidic platform allows for the co-culture of primary human colonic epithelium, antigen-presenting cells, CD4+ naïve T cells, and the highly oxygen-sensitive bacterium Faecalibacterium prausnitzii.

In a pivotal pilot experiment, we successfully cocultured colonic epithelium with a defined population of adult gut microbes, known as synthetic microbial communities or SynCom.

Through the utilization of GuMI 2.0, we found that dendritic cells and macrophages play essential roles in secreting cytokines and chemokines in both the apical and basolateral compartments of the epithelial monolayer. Furthermore, the presence of CD4+ T cells was found to alter immune responses to Faecalibacterium prausnitzii at both cytokine and transcriptional levels.

This milestone brings us one step closer to accurately mimicking the complexity of the host-microbiome interplay in both health and disease conditions. By offering more human-relevant models, GuMI 2.0 holds promise for advancing our understanding of various medical conditions and potentially informing future therapeutic interventions.

Read more about GuMI 1.0, GuMI2.0, SynComs, or organoids and monolayer

The coculture of human colonic epithelium, antigen-presenting cells, CD4+ naïve T cells, and the highly oxygen-sensitive bacterium Faecalibacterium prausnitzii.

New funding! The Dutch cabinet has allocated 200 million euros from the National Growth Fund to the Holomicrobiome Consortium to establish Holomicrobiome Institute in the next ten years. This consortium will conduct research into microbiomes in a holistic approach. The Molecular Biology and Microbial Food Safety Group  is part of the consortium. Congratulations to all consortium members and the partners!! See more here.


New member! Virginia Bruno is joining us on February 1  2024 as a PhD student jointly supervised by Molecular Biology and Microbial Food Safety Group at UvA and Gut Research Group at AUMC. She will work on establishing advanced multi-cellular in vitro models to study host-mycobiome interactions underlying the pathophysiology of IBD and IBS. Welcome Virginia!


New grant! On November 27th 2023, ZonMw announced that 7 new breakthrough projects receive the funding totaling € 2,100,000 for research into microplastics. Dr. Jianbo Zhang is involved in the project (Micro)2 corona, where a new collaboration will be established with the project coordinator Dr. Hans Bouwmeester at the Wageningen University & Research, and project partners Dr. Stefan van Leeuwen and Anna Undas at the Wageningen Food Safety Research (WFSR). In this project, we will characterize the microplastics and study their health impacts in human intestine using GuMI microphysiological system. Congratulations to all partners and look forward to the collaboration!


New preprint! Our research is available on preprint platform Research Square. This new immune-competent GuMI physiomimetic system builds on the original GuMI system to coculture Faecalibacterium prausnitzii A2-165 (now renamed F. duncaniae) with colonic epithelium and defined population of immune cells including dendritic cells, macrophages, and naïve T cells. Using this system, we found that colonic epithelial cells respond to F. prausnitzii differently in the presence and absence of T cells. The results demonstrated that the immune-competent GuMI could be used to understand the interaction between gut microbes and specific type of immune cells in an in vivo-like microenvironment.



FEMS 2023 

Our PhD student Raymond Pasman presented his work at the 10th FEMS Congress of European Microbiologists in Hamburg, Germany from July 9 -13th, 2023. His poster was selected for a flash talk entitled “Candida albicans and Staphylococcus aureus reciprocally promote virulence”. Raymond has done a great job on leading this project and his supervisors (Stanley Brul @UvA, Bastiaan P. Krom @ACTA, Sebastiaan A.J. Zaat @AUMC, and Jianbo Zhang @UvA). More to come and stay tuned! 

Master Class on Intestine and Intestine-microbiome on a chip

On 15th and 16th of June, Jianbo Zhang (UvA) and Hossein Eslami Amirabadi (Azar Innovations) co-hosted a MasterClass on Intestine and Intestine-microbiome-on-a-chip.  The participants were introduced to different physiomimetic systems that mimic gastrointestinal tract. The fun part is the participants were asked to pick an application and design their own fit-for-purpose system. 

Our PhD student Raymond Pasman was selected to give a oral presentation at the Annual Meeting Royal Netherlands Society for Microbiology held on 4th and 5th of April. His PhD thesis focuses on the inter-kingdom interactions between Candida, Staphylococcus, and human immune system. Stay tuned!

2023.03.23 Visiting PhD student Eloïse Bouges received an ENEN2plus mobility grant. Congratulations Eloïse! ENEN2plus is one of the largest and most integrative nuclear Education and Training (E&T) efforts up to date in nuclear E&T, funded by European Union.  This grant will support Eloïse's training in gut organoids and gut microphysiological systems at University of Amsterdam. After that, she will apply these technologies at SCK CEN and test protective agents in alleviating radiotherapy-associated side effects. 

2023.03.17 New paper! Our review paper is published online today in the journal FEMS Microbiology Reviews. PhD student Pim T van Leeuwen is the first author. In this review, we discussed the synthetic microbial communities (SynComs) of the human gut, what strategies are currently used to design, assemble, and test a SynCom, and what challenges we are facing. 

2023.01.16 Eloïse Bouges joined the lab as a visiting PhD student. Eloïse will explore the organoids and tumoroids culture. Welcome!

2022.11.21 Yangwei Shan joined the lab. Welcome Yangwei!

2022.11.17 Jianbo received 2022 Honorable Mentions in The Global 3Rs Awards program.

2022.08.15 Yangwei Shan is awarded a PhD fellowship funded by Guangzhou Elite Program! He will soon join the lab in November. 

2022.07.25 A pilot project is funded in collaboration with Dutch non-profit organization Proefdiervrij. The project will focus on establishing animal-free protocols on culturing human intestinal organoids.

New paper!

Biopreservation is defined as the use of microbes or microbially produced compounds to enhance the safety and shelf-life of food, which includes food fermentation. It is a promising and sustainable solution for alleviating microbial decay of foods and feeds. Food cultures, e.g., starter and adjunct cultures added as bioprotectants, contribute to food biopreservation by forming antimicrobial metabolites. Concurrently, microbial biopreservation can lead to the formation of unwanted compounds. One example of that is acrolein formation by food cultures during glycerol transformation. Jianbo Zhang together with Clarissa Schwab from Aarhus University wrote a review on key challenges for reducing the health risk imposed by microbially derived acrolein, suggesting new strategies to monitor the secondary formation of acrolein, and determine whether the levels of acrolein are high enough to cause any harm. The release of acrolein should be considered for safety assessments to reduce the potential risk. The findings can be found in Food Chemistry Advances. (news credit: A. van de Moosdijk)

Grant application funded!

The project METAHEALTH: Health in a microbial, sociocultural and care context in the first 1000 days of life is funded in the NWO program Research along Routes by Consortia (NWA-ORC). This project is led by Dr. Egija Zaura, professor at the Academic Centre for Dentistry Amsterdam. Our group will focus on investigating the mechanisms underlying the host-microbiome-immune interactions and identify potential interventions that can help strengthen the immune system via the microbiome, to increase oral and gut health. Read more. (news credit: J. Zhang)