|
2D cell culture models
|
Ease of useLow costRelatively rapid assessmentScalableModerate/high throughputGood reproducibility |
Limited time in cultureLack of 3D architecture – does not mimic in vivo host–microbiome interactions |
Inflammatory cytokine productionCell viability |
| Primary human cells |
May retain behaviour of human cells in tissues |
Multiple donors needed to reflect inter-person variability |
|
| Cell lines |
Engineered to enable continuous passageProvide consistency across studiesEasier to source |
Does not necessarily retain the behaviours of human cells in tissues |
|
|
3D models
|
3D architectureMore tissue level functionMore representative of microbe-surface interaction (skin) |
Higher costOften require specialized expertise and equipment |
ViabilityCytokine productionGene expressionStructural changes (fluorescence microscopy, electron microscopy, imaging)Can study microbial communities (viability, growth, metabolites, toxins, compositional changes of mixed populations) |
| 3D skin equivalents |
ReproducibilityCommercially available |
Barrier properties do not resemble that of human skin |
|
|
Ex vivo human skin maintained in organ culture |
Gold standardCloser resemblance to barrier properties of real skin maintained (better mimicking of host–microbiome interaction) |
Availability |
|
| Organoids |
Preserving organ, disease and patient-specific characteristics and enabling repeated experiments |
Luminal side of cells oriented towards the centre – obstacle to study host microbiome interactionNot possible to directly co-culture with strictly anaerobic bacteria because it is an aerobic model |
Single or multiple omics readout across many different samples |
| Linearized organoids |
Apical (luminal) side accessibleCan be co-cultured with bacteria and microbial derived metabolites introduced into the culture media |
Not possible to directly co-culture with strictly anaerobic bacteria because it is an aerobic modelMore expensive than normal 3D organoids |
Single or multiple omics readout across samples; TEER (transepithelial electrical resistance) for barrier integrity and imaging |
| Microfluidic devices |
Incorporate organoid cells with other cell types (immune cells and fibroblasts)Can replicate anaerobic conditions (gut) |
Infrastructure and cost needsStandardisation is challenging |
Multiple omics readouts from the same sample under select conditions |
| Organ-on-a chip |
Reproducible and controllable environment for both host and microbial cellsPrecise manipulation of microscale fluids, mimicking the physiological environment of the human organs |
Different platforms have different attributesOften difficult to choose the most adequate one |
Imaging, multi-omics and cytokine measurements |
