Microbiota-dependent influence of prebiotics on the resilience of infant gut microbiota to amoxicillin/clavulanate perturbation in an in vitro colon model

Development of an infant colon simulating in vitro model, I-TIM-2, to study the effects of modulation strategies on the infant gut microbiome composition and function

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.

Modulation of human gut microbiota by linear and branched fructooligosaccharides in an in vitro colon model (TIM-2)

AIMS

This study aimed to compare the effects of linear and branched fructooligosaccharides (FOS) extracted from chicory and grass (Lolium perenne), respectively on human microbiota composition, diversity, and metabolism.

METHODS AND RESULTS

To test the effects of linear and branched FOS on human microbiota we used the artificial in vitro human colon model (TIM-2). Microbiota composition and diversity were assessed by V3-V4 16S rRNA metagenomic sequencing, followed by differential taxa abundance and alpha/beta diversity analyses. SCFA/BCFA production was evaluated by gas chromatography-mass spectrometry. As a result, branched FOS had the most beneficial effects on microbial diversity and metabolite production. Also, branched FOS significantly increased the abundance of commensal bacteria associated with maintaining healthy gut functions and controlling inflammation, such as Butyricicoccus, Erysipelotrichaceae, Phascolarctobacterium, and Sutterella. Linear FOS also significantly increased the abundance of some other commensal gut bacteria (Anaerobutyricum, Lachnospiraceae, Faecalibacterium), but there were no differences in diversity metrics compared to the control.

CONCLUSIONS

The study revealed that branched FOS had the most beneficial effects compared to the linear FOS in vitro, concerning microbiota modulation, and metabolite production, making this a good candidate for further studies in food biotechnology.

Gut Microbiome Integration in Drug Discovery and Development of Small Molecules

Human microbiomes, particularly in the gut, could have a major impact on the efficacy and toxicity of drugs. However, gut microbial metabolism is often neglected in the drug discovery and development process. Medicen, a Paris-based human health innovation cluster, has gathered more than 30 international leading experts from pharma, academia, biotech, clinical research organizations, and regulatory science to develop proposals to facilitate the integration of microbiome science into drug discovery and development. Seven subteams were formed to cover the complementary expertise areas of 1) pharma experience and case studies, 2) in silico microbiome-drug interaction, 3) in vitro microbial stability screening, 4) gut fermentation models, 5) animal models, 6) microbiome integration in clinical and regulatory aspects, and 7) microbiome ecosystems and models. Each expert team produced a state-of-the-art report of their respective field highlighting existing microbiome-related tools at every stage of drug discovery and development. The most critical limitations are the growing, but still limited, drug-microbiome interaction data to produce predictive models and the lack of agreed-upon standards despite recent progress. In this paper we will report on and share proposals covering 1) how microbiome tools can support moving a compound from drug discovery to clinical proof-of-concept studies and alert early on potential undesired properties stemming from microbiome-induced drug metabolism and 2) how microbiome data can be generated and integrated in pharmacokinetic models that are predictive of the human situation. Examples of drugs metabolized by the microbiome will be discussed in detail to support recommendations from the working group. SIGNIFICANCE STATEMENT: Gut microbial metabolism is often neglected in the drug discovery and development process despite growing evidence of drugs' efficacy and safety impacted by their interaction with the microbiome. This paper will detail existing microbiome-related tools covering every stage of drug discovery and development, current progress, and limitations, as well as recommendations to integrate them into the drug discovery and development process.

Presence of digestible starch impacts in vitro fermentation of resistant starch

Starch is an important energy source for humans. Starch escaping digestion in the small intestine will transit to the colon to be fermented by gut microbes. Many gut microbes express α-amylases that can degrade soluble starch, but only a few are able to degrade intrinsic resistant starch (RS), which is insoluble and highly resistant to digestion (≥80% RS). We studied the in vitro fermentability of eight retrograded starches (RS-3 preparations) differing in rapidly digestible starch content (≥70%, 35-50%, ≤15%) by a pooled adult faecal inoculum and found that fermentability depends on the digestible starch fraction. Digestible starch was readily fermented yielding acetate and lactate, whereas resistant starch was fermented much slower generating acetate and butyrate. Primarily Bifidobacterium increased in relative abundance upon digestible starch fermentation, whereas resistant starch fermentation also increased relative abundance of Ruminococcus and Lachnospiraceae. The presence of small fractions of total digestible starch (±25%) within RS-3 preparations influenced the fermentation rate and microbiota composition, after which the resistant starch fraction was hardly fermented. By short-chain fatty acid quantification, we observed that six individual faecal inocula obtained from infants and adults were able to ferment digestible starch, whereas only one adult faecal inoculum was fermenting intrinsic RS-3. This suggests that, in contrast to digestible starch, intrinsic RS-3 is only fermentable when specific microbes are present. Our data illustrates that awareness is required for the presence of digestible starch during in vitro fermentation of resistant starch, since such digestible fraction might influence and overrule the evalution of the prebiotic potential of resistant starches.

Galactooligosaccharide Mediates NF-κB Pathway to Improve Intestinal Barrier Function and Intestinal Microbiota

The use of antibiotics to treat diarrhea and other diseases early in life can lead to intestinal disorders in infants, which can cause a range of immune-related diseases. Intestinal microbiota diversity is closely related to dietary intake, with many oligosaccharides impacting intestinal microorganism structures and communities. Thus, oligosaccharide type and quantity are important for intestinal microbiota construction. Galactooligosaccharides (GOS) are functional oligosaccharides that can be supplemented with infant formula. Currently, information on GOS and its impact on intestinal microbiota diversity and disorders is lacking. Similarly, GOS is rarely reported within the context of intestinal barrier function. In this study, 16S rRNA sequencing, gas chromatography, and immunohistochemistry were used to investigate the effects of GOS on the intestinal microbiota and barrier pathways in antibiotic-treated mouse models. The results found that GOS promoted Bifidobacterium and Akkermansia proliferation, increased short-chain fatty acid levels, increased tight junction protein expression (occludin and ZO-1), increased secretory immunoglobulin A (SIgA) and albumin levels, significantly downregulated NF-κB expression, and reduced lipopolysaccharide (LPS), interleukin-IL-1β (IL-1β), and IL-6 levels. Also, a high GOS dose in ampicillin-supplemented animals provided resistance to intestinal damage.