Table 1.

Advantages and disadvantages of in vitro and ex vivo models of inflammatory bowel disease.

Sr. no.	Models/systems	Advantages	Disadvantages
1.	Caco-2 cell line	Features identical to small bowel enterocytes (presence of brush-border microvilli) [16]. Produces specific digestive enzymes (e.g., peptidase and lactase) [16]. Ability to produce various cytokines [18–20]. Absorption-related studies are easy to perform [21–24].	Presence of other cells other than enterocytes in the epithelium [12]. Mucus and unstirred water are unable to be considered [12]. Various non-cellular factors hinder the study [12].
2.	HT29 cell line	Cytokine release pattern similar to Caco-2 cells [34]. Higher mucin production [35]. Cell differentiation pattern similar to Caco-2 cells [33]. Produces typical digestive enzymes (e.g., peptidase and lactase) [33].	A longer time of differentiation [33]. High consumption of glucose [36]. Undifferentiated cells even when high glucose concentration is provided [36].
3.	Organoids	Imitate physiology of intestinal cells [62, 63]. Co-culturing of gut organoids with non-epithelial cells is also possible. [62, 63] Imitate gut microbial ecology [64–66]. Investigation of innate immune systems possible [67]. Patient-derived organoids can be used [68–70].	Lacks specific cells/tissues [49]. Unable to recreate the complex environment of an organism [60]. Uncommon cell types (e.g., tuft cells) are difficult to cultivate [49]. Unable to replicate mucosal barrier [49].
4.	Caco-2/HT29-MTX co-culture	Excellent for research involving microbial adhesion, colonic permeability, etc. [81]. Able to generate mucus membranes [82]. Stability and reproducibility similar to monocultures [82]. Increased mucin production [82].	Unable to generate some transporters [82]. Perfect ratio between Caco-2 and HT29 cells required for a homogenous mucin layer [82]. Cell viability is challenging [82].
5.	T84 cell lines	Development into crypt-like cells [92].	Similar to Caco-2 and HT29 cells [92].
6.	Intestinal-immunological cultures	Appropriate for use of studying immune-related mechanisms.	Variations between immune cells and intestinal cells.
7.	Ussing chamber	Presence of two compartments [147]. Presence of electrodes to measure transport of ion [147]. Used to study intestinal permeability [149]. Used to study host-microbiome interactions [151]. Use of both animal and human tissue possible [149]. Physiology of receptors can easily be studied [157–160].	Cell viability up to 5 h only [92]. Since viability of cell is less, long-term studies not possible [92]. Poor throughput [92]. Complex handling [92].
8.	Everted gut sac	Intestinal tissue is intact [92]. Mucus layer is present [92]. Presence of large surface area [92].	Not much relevant to human as it is ideal for rat tissue. System sensitivity depends on a number of factors. Tissue viability is 2 h only [164].
9.	Microfluidic gut-on-chip	Location-based organ-on-chip can be developed [174–177]. Co-culturing of cells and macrophages possible [177]. Pluripotent stem cells can also be used [180].	Complex system [92]. PDMS used can itself adsorb compounds, hindering the research [185, 186]. High labor intensive [92].