Table 1.

Comparison of in vitro, organoids, organ-on-a-chip, ex vivo and in vivo models.

	Cell type	Advantages	Limitations	Potential Improvements	Ref
In vitro (MTP- and flow-based systems)	Bacteria only	Inexpensive; High-throughput; Real-time visualization; Incorporation of flow conditions; Well defined experimental conditions	Lack of immune response; Use of abiotic surfaces; Lack of 3D structure of native substrates	Use of synthetic media to mimic native chemical environment	[27,52]
Organoid	PSCs and ASCsa	Near-physiological conditions; Specific stem cell propagation; Access to varieties of patient-derived organoids, sufficient tissue mass for analytical approaches	Lack of biomechanical forces and flow conditions; Unable to study interactions between environmental cues	Incorporate microfluidic techniques; establish co-culture systems	[53] [54]
Organ-On-a-Chip	Primary cells or cell lines	Enable cell-cell and cell-environment interactions; Introduce biomechanical forces and fluidic flow that mimic microenvironments in vivo; Real-time monitor and high-resolution imaging; Ability to model ADMET properties	Only partial tissue function is presented; Poly-dimethylsiloxane (PDMS) substrates are not ideal for mimicking extracellular matrices; Limited spaces and tissue mass	Improve fabrication techniques; Use ESCs or iPSCs to serve as cell sources	[55,56]
Ex vivo	Tissue explants	Native physiochemical environment; Relatively cheap and high-throughput; Real time monitoring; Relatively controlled experimental conditions; Less ethical concerns	Limited life span; Lack of immune response; Lack of standardization	Use of synthetic media to mimic native chemical environments; Use of standardized culture system, e.g. BoDrum®	[[57], [58], [59], [60]]
In vivo (Non-mammalian)	Native cell population	High-throughput; Presence of immune system, low cost, easy maintenance, easy genetic manipulation, less ethic constraints	Limited similarities to humans; Llimited lifespan; Difference in body temperature	Focus on elucidating conserved and universal immune mechanisms	[61,62]
In vivo (Mammalian)	Native cell population	Presence of host immune systems; Native physicochemical environment	Ethical and animal welfare constraints; High costs; interspecies differences; Limited experiment duration to mimic chronic infections	Repeated bacteria exposure to mimic chronic conditions	[13,[63], [64], [65]]

^aPSCs = pluripotent stem cells; ASCs = adult stem cells.