Table 3.

Comparisons of different animal models for FMT

	Advantages	Limitations
Gnotobiotic animals GF	Microbial depletion guaranteed (within detection limits) No competition with the commensal microbiota to colonize the gut Best for testing specific mechanisms of interventions on host	No similar condition in humans to which it can be compared Experimental groups to which we can compare recolonized GF animals to: conventional animals, GF animals, or re-colonized animals? Expensive, requires access to specialized equipment and training Altered development (immune system very impacted)
Gnotobiotic animals -Defined microbiota (SPF)	Absence of specific pathogen	Basal composition unknown Competition with commensal microbiota to colonize the gut
Gnotobiotic animals -Defined microbiota (ASF)	Simplified model of a commensal microbiota	Competition with commensal microbiota to colonize the gut Not representative of a real microbiome-host interaction
Antibiotic-treated animals	Born and raised with a conventional microbiota Allow us to study specific life stages	Overgrowth of pathogenic species possible Antibiotic resistance genes Systemic side effects Antibiotic treatment varies across studies
Conventional animals	No abnormal development or side effects of a treatment	Unknown basal composition Native gut microbiota exert different selective pressures on exogenous colonizers
Laxative-depletion	Comparable to what is currently done in human Depletion seems to be effective at certain doses	Side effects of laxative use are not well-known Paucity of studies using this model in pre-clinical settings
Vertical microbiota transmission model	Natural transmission of the gut microbiota No abnormal development or side effects of a treatment	Not enough information on vertically or horizontally transmissible strains
Bedding material/coprophagy	Alters cecal content but also metabolic features and cognition Frequency of coprophagy can be beneficial (not a one-time screenshot of the donor’s microbiota) Easiest and least invasive/stressful model of transferring microbes	Not suitable for human to mice FMT Dose and frequency of transfer is not controlled or guaranteed Could imply single housing of rodents to control for coprophagy Bacterial transmission not targeted and probably restricted to oxygen-friendly microorganism