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Updated: Jun 11, 2025
An In Vitro Batch-culture Model to Estimate the Effects of Interventional Regimens on Human Fecal Microbiota
Published on: July 31, 2019
Development of an infant colon simulating in vitro model, I-TIM-2, to study the effects of modulation strategies on
Olivia Colberg1,2, Gerben D A Hermes1, Tine Rask Licht2
1Novonesis, Human Health Research, Hørsholm, Denmark.
Insights
We developed a new infant gut model to study microbiome development. Human milk oligosaccharides (HMOs) promote beneficial Bifidobacterium growth, impacting infant gut health and metabolism.
Area of Science:
- Microbiology
- Gastroenterology
- Developmental Biology
Background:
- Infant gut microbiome development is crucial for long-term health.
- Factors like antibiotics, C-section birth, and formula feeding can disrupt this development.
- Ethical constraints limit direct infant studies on microbiome modulation.
Purpose of the Study:
- To develop and validate an infant in vitro colonic model (I-TIM-2) for studying gut microbiome dynamics.
- To investigate the impact of human milk oligosaccharides (HMOs) on the infant gut microbiome and its metabolic output.
Main Methods:
- Utilized a computer-controlled, dynamic colon model (TIM-2) with four compartments.
- Inoculated with fecal samples from healthy, breastfed infants.
- Compared diet-adapted medium with and without physiological concentrations of five HMOs over 96 hours.
- Analyzed bacterial composition via shotgun metagenomics and qPCR, and metabolites (SCFAs, HMOs) using LC-MS.
Main Results:
- The I-TIM-2 model successfully preserved microbial diversity and inoculum-derived species.
- Microbiome composition and short-chain fatty acid (SCFA) concentrations mirrored infant data.
- HMOs significantly modulated the microbiome, increasing Bifidobacterium proportions.
- This modulation led to increased acetic and formic acid production, characteristic of HMO metabolism.
Conclusions:
- The I-TIM-2 model is a valid system for studying infant gut microbiome dynamics and modulations.
- HMOs play a key role in shaping the infant gut microbiome by promoting Bifidobacterium.
- This model can assess strategies for modulating the infant gut microbiome and its host interactions.
Abstract:
The early life stages are critical for the development of the gut microbiome. Variables such as antibiotics exposure, birth-mode via Cesarean section, and formula feeding are associated with disruptions in microbiome development and are related to adverse health effects later in life. Studying the effects of microbiome-modulating strategies in infants is challenged by appropriate ethical constraints. Therefore, we developed I-TIM-2, an infant in vitro colonic model based on the validated, computer-controlled, dynamic model of the colon, TIM-2. The system, consisting of four separate compartments, was inoculated with feces from four healthy, primarily breastfed infants, displaying distinctive microbiome profiles. For each infant's fecal sample, a 96-h experiment was performed, with two compartments receiving an infant diet adapted medium and two compartments additionally receiving five human milk oligosaccharides (HMOs) in physiological concentrations and proportions. Bacterial composition was determined by shotgun metagenomics and qPCR. Concentrations of short-chain fatty acids (SCFAs) and HMOs were determined by LC-MS. Microbial diversity and high amounts of inoculum-derived species were preserved in the model throughout each experiment. Microbiome composition and SCFA concentrations were consistent with published data from infants. HMOs strongly modulated the microbiome composition by stimulating relative proportions of Bifidobacterium. This affected the metabolic output and resulted in an increased production of acetic and formic acid, characteristic of bifidobacterial HMO metabolism. In conclusion, these data demonstrate the development of a valid model to study the dynamics and modulations of the infant gut microbiome and metabolome.IMPORTANCEThe infant gut microbiome is intricately linked to the health of its host. This is partly mediated through the bacterial production of metabolites that interact with the host cells. Human milk shapes the establishment of the infant gut microbiome as it contains human milk sugars that select for primarily bifidobacteria. The establishment can be disrupted by modern interventions such as formula feeding. This can alter the microbiome composition and metabolite production profile, which can affect the host. In this article, we set up an infant in vitro colonic model to study microbiome interactions and functions. In this model, we investigated the effects of human milk sugars and their promotion of bifidobacteria at the expense of other bacteria. The model is an ideal system to assess the effects of various modulating strategies on the infant gut microbiome and its interactions with its host.
