New funding!
On September 4, Jianbo received the ERC Starting Grant to lead the NeoGutChip project entitled “A neonatal anaerobic gut-microbiome-on-a-chip to decode bacterial colonization and infant gut T cell maturation”. Over the next five years, the group will develop anaerobic GuMI platforms tailored for infants and use them to study the early bacterial colonization and immune development.
FEMS conference 2025
On July 15-17, Jianbo spoke at FEMS 2025 in the interaction session focusing on Functional Microbiome on Gut-Brain axis, organized by Prof. Stanley Brul. PhD candidate Yangwei presented a poster on the interaction of infant gut microbiota and human milk oligosaccharides.
New member!
On July 1, Dr. Michail Mamantopoulos officially joined the lab as a postdoctoral researcher. His research focuses on probiotics and early life immunity in collaboration wtih SURI Biotech. Welcome Michail!
GuMI lab at MPS World Summit 2025
On June 9-13, MPS World Summit 2025 took place in the Brussels, Belgium. This year, GuMI lab was represented by PhD student Virginia Bruno, who was selected for a 3-minute thesis talk to present her work on how Candida albicans clinical isoaltes affect intestinal epithelial function and pain, and presented her poster. Jianbo presented new development of GuMI model. Our guest PhD student Eloïse Bouges presented her work on modeling irradiation toxicity using tumor organoids during the poster session. MPS World Summit is a go-to place for microphysiological system connecting MPS developers and users from both academic and industry.
New member!
On May 1, Aliki Antoniou officially joined the lab and METAHEALTH consortium as a PhD candidate. Her research focuses on infant gut microbiota and metabolic health. Welcome Aliki!
Virginia and Yangwei presented their work at KNVM
Every spring, Dutch microbiologists meet up together to discuss their research, exchange ideas, and networking at Scientific Spring Meeting KNVM. This year, our group were represented by two presentations. Virgnia Bruno gave a oral presentation in the Session 19 "Host-microbe interactions beyond bacteria". She talked about how to leverage GuMI model to study the impact fungi Candid albicans on colonic epithelium. In the poster session, Yangwei Shan presented his work on the interaction between human milk oligosaccharides and infant gut microbiota using synthetic communities. We are joined by other colleagues in Microbiology Theme at SILS.
BabyPro project is funded!
Glad to share that our project BabyPro is awarded by the Top Sector LSH via the program 'Health~Holland International (HHINT) Kickstarter for public-private partnership'. This project is in collaboration with Prof. Stanley Brul at SILS and Dr. Vanesa Rocha at SURI BioTech in Switzerland. BabyPro aims to identify probiotic bacteria boosting the newborn’s immune development by using ex vivo assays and in vitro GuMI models. More about this project can be found here.
New member!
On February 3, Dr. Inês Parente joined the lab as a postdoc researcher. Her research focuses on host-microbiome-nutrient interactions in the human gut. Welcome Inês!
New paper!
The work on identifying a defined medium for coculture of Candida albicans, Staphylococcus aureus, and human oral epithelial cells is now published online at journal Applied and Environmental Microbiology (29 July 2024). This work is led by PhD candidate Raymond Pasman, in collaboration with senior authors Sebastian Zaat, Stanley Brul, and Bastiaan Krom. In this paper, Raymond thoroughly tested the impact of different media components and culture conditions on the growth and morphology of C. albicans and S. aureus, as well as the toxicity to human oral cells. The optimized medium will allow us to probing the multi-kingdom interactions in a more defined settings. Congratulations!
Read more about the paper
SILS Research Day 2024
On June 26, PhD candidate Yangwei Shan gave a oral presentation at the SILS Research Day 2024. He presented his work on infant gut microbiota and its interaction with human milk oligosaccharides. SILS day is an annual event organized by Swammerdam Institute for Life Sciences PhD-PD council, showcasing the breath and diversity of research in the institute.
Read more about the event and the PhD-PD council.
MasterClass on Intestine and intestinal-microbiome on a chip 2024!
On June 26-28, the MasterClass on Intestine and Intestinal microbiome on a chip was organized in Amsterdam for the second time in a row. This event was co-organized by Dr. Hossein Eslami Amireabadi from Azar Innovations and Dr. Jianbo Zhang, with the help from our group Dr. Marco Lezzerini. We aim to introduce different gut microphysiological systems to the participants by online e-learning, interactive lectures, hands-on lab training, and demos. By the end of the MasterClass, the participants learned the pros and cons of each system and can evaluate which system suits the best for their applications.
Read more about the event
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.
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 at UvA, Bastiaan P. Krom at ACTA, Sebastiaan A.J. Zaat at AUMC, and Jianbo Zhang at UvA). More to come and stay tuned!
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.
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)
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)
