Designs and methodologies to recreate in vitro human gut microbiota models

Biagini, Francesco; Daddi, Costanza; Calvigioni, Marco; Maria, Carmelo De; Zhang, Yu Shrike; Ghelardi, Emilia; Vozzi, Giovanni

doi:10.1007/s42242-022-00210-6

Cited by 17 publications

(5 citation statements)

References 183 publications

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“…This observation aligns with a prior study that reported low variability among 3D organoids derived from multiple human donors (Mohammadi et al, 2021). A possible explanation for the similarity observed between donors is that RepliGut® Planar does not contain an intestinal microbiome or immune cells, both of which are significant variables among humans that can influence clinical outcomes (Parlesak, 2004;Trujillo-de Santiago et al, 2018;Khan et al, 2019;Biagini et al, 2023). Developing strategies to model host-microbe interactions in RepliGut® Planar is a promising next step to enhance the clinical relevance and translatability of this platform.…”

Section: Discussionsupporting

confidence: 86%

Characterization and optimization of variability in a human colonic epithelium culture model

2024

ALTEX

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Animal models have historically been poor preclinical predictors of gastrointestinal (GI) directed therapeutic efficacy and drug-induced GI toxicity. Human stem and primary cell-derived culture systems are a major focus of efforts to create biologically relevant models that enhance preclinical predictive value of intestinal efficacy and toxicity. The inherent variability in stem-cell-based cultures makes development of useful models a challenge; the stochastic nature of stem-cell differentiation interferes with the ability to build and validate reproducible assays that query drug responses and pharmacokinetics. In this study, we aimed to characterize and reduce sources of variability in a complex stem cellderived intestinal epithelium model, termed RepliGut® Planar, across cells from multiple human donors, cell lots, and passage numbers. Assessment criteria included barrier formation and integrity, gene expression, and cytokine responses. Gene expression and culture metric analyses revealed that controlling cell passage number reduces variability and maximizes physiological relevance of the model. In a case study where passage number was optimized, distinct cytokine responses were observed among four human donors, indicating that biological variability can be detected in cell cultures originating from diverse human sources. These findings highlight key considerations for designing assays that can be applied to additional primary-cell derived systems, as well as establish utility of the RepliGut® Planar platform for robust development of human-predictive drug-response assays. Plain language summaryAnimal models are frequently used as tools for studying gastrointestinal (GI) disease, but they poorly replicate the complexities of the human gut limiting the clinical translation of new therapeutics in development. Human stem cell derived models can better recapitulate human GI physiology, but the inherent dynamic nature of stem cells introduces variability in culture performance. We identified sources of variability in the primary stem-cell derived RepliGut® Planar model to develop robust and reliable assays that can improve preclinical therapeutic development for GI disease. Analysis of barrier formation, gene expression, and cytokine responses demonstrated that controlling cell passage number reduces variability and maximizes physiological relevance of the model. These findings highlight key assay design considerations that can be applied to additional primary-cell derived systems. Availability of reliable and physiologically relevant cell-based models can reduce animal testing, improve research accuracy, and make new treatments more relevant and effective for patients.

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Section: Discussionsupporting

confidence: 86%

Characterization and optimization of variability in a human colonic epithelium culture model

2024

ALTEX

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“…Among the known disadvantages of short-term and non-dynamic experiments are the limited nutrient availability and accumulation of metabolic waste products [ 3 , 5 ]. We limited this study to 48 h due to our previous experiences that showed us that 24 h was sufficient to reach a relative stabilization of the microbial communities present in the batch systems and that not many differences are commonly observed when compared to 48 h and 72 h in terms of metabolic production and microbial content [ 22 ].…”

Section: Discussionmentioning

confidence: 99%

“…Batch culture or static colonic fermentation models are popular screening experiments conducted in individual bioreactors where the test substance is maintained in contact with microbial communities and basal media. These assays are generally performed for short durations, ranging from 24 to 48 h, with a maximum of 72 h. Several parameters can be controlled, including pH, temperature, and the maintenance of an anaerobic atmosphere [ 2 , 3 ].…”

Section: Introductionmentioning

confidence: 99%

M-Batches to Simulate Luminal and Mucosal Human Gut Microbial Ecosystems: A Case Study of the Effects of Coffee and Green Tea

Goya-Jorge,

Gonza,

Douny

et al. 2024

Microorganisms

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Gastrointestinal simulations in vitro have only limited approaches to analyze the microbial communities inhabiting the mucosal compartment. Understanding and differentiating gut microbial ecosystems is crucial for a more comprehensive and accurate representation of the gut microbiome and its interactions with the host. Herein is suggested, in a short-term and static set-up (named “M-batches”), the analysis of mucosal and luminal populations of inhabitants of the human colon. After varying several parameters, such as the fermentation volume and the fecal inoculum (single or pool), only minor differences in microbial composition and metabolic production were identified. However, the pool created with feces from five donors and cultivated in a smaller volume (300 mL) seemed to provide a more stable luminal ecosystem. The study of commercially available coffee and green tea in the M-batches suggested some positive effects of these worldwide known beverages, including the increase in butyrate-producing bacteria and lactobacilli populations. We hope that this novel strategy can contribute to future advances in the study of intestinal ecosystems and host-microbe relationships and help elucidate roles of the microbiome in health and disease.

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“…However, there is currently a lack of in vitro studies investigating whether and how salidroside selectively alters bacterial function or competitiveness. In-vitro models of the human gut microbiota, such as Transwell culture models ( Biagini et al, 2023 ), could be an effective approach to delineate the specific mechanisms through which salidroside protects against atherosclerosis by interacting with the gut microbiota and its metabolites.…”

Section: Conclusion and Future Perspectivesmentioning

confidence: 99%

Effects of salidroside on atherosclerosis: potential contribution of gut microbiota

Fei,

Hou,

Jia

2024

Front. Pharmacol.

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Graphical AbstractThis review seeks to offer a comprehensive look at how salidroside impacts gut microbiota and its potential therapeutic role in treating atherosclerosis. (A) Salidroside has been shown to have a positive impact on atherosclerosis by promoting the growth of beneficial bacteria and decreasing the levels of harmful bacteria in the body. (B) Salidroside has been shown to enhance the integrity and function of the intestinal mucosal barrier through its ability to suppress NF-κB and p38 MAPK signaling pathways, modulate the NF-κB/MAPK/JAK-STAT3 signaling pathways and increase the expression of antimicrobial peptides HD-5 and HD-6. (C) Salidroside can reduce TMAO production through reducing the abundance of Firmicutes and Proteobacteria. (D) Salidroside can improve the expression of SCFAs, through increasing the abundance of some special bacteria. (E) Salidroside can reduce LPS-induced inflammation, which is associated with the inhibition of the ROS-mediated PI3K/AKT/mTOR signaling pathway, the downregulation of exosome miR-199a-5p, and the attenuation of the Notch-Hes signaling pathway. (F) Salidroside can inhibit NLRP3-associated gut-coronary axis, including TLR4/MyD88/NF-κB/NLRP3 signaling pathway, AMPK/NF-κB/NLRP3 signaling pathway, and P2X7/NF-κB/NLRP3 signaling pathway.

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Designs and methodologies to recreate in vitro human gut microbiota models

Cited by 17 publications

References 183 publications

Characterization and optimization of variability in a human colonic epithelium culture model

Characterization and optimization of variability in a human colonic epithelium culture model

M-Batches to Simulate Luminal and Mucosal Human Gut Microbial Ecosystems: A Case Study of the Effects of Coffee and Green Tea

Effects of salidroside on atherosclerosis: potential contribution of gut microbiota

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