Table 1.

Comparison of vertebrate and invertebrate models used for microorganism—host, microorganism—microorganism and microorganism—microorganism—host interactions.

	Vertebrates models			Invertebrates models
	Mus musculus	Rattus norvegicus	Danio rerio	Drosophila melanogaster	Galleria mellonella	Caenorhabditis elegans
Full genome sequence available	Yes	Yes	Yes	Yes	Yes	Yes
Resources needed in the laboratory	Very high	Very high	High	Low	Low	Low to high
Ease of implementation	High	High	Low	Low	Low	Low
Mutants available in public bank	Yes	No	Yes	Yes	No	Yes
RNAi bank available	No	No	No	Yes	No	Yes
Major intestinal taxa	Firmicutes, Bacteroidetes, Actinobacteria	Firmicutes, Bacteroidetes, Proteobacteria	Proteobacteria, Fusobacteria	Lactobacillus, Acetobacter	No microbiota in laboraroty condition	No microbiota in laboratory condition
Survival at 37°C (human body temperature)	Yes	Yes	No	No	Yes	No
Immunity	Innate and adaptative	Innate and adaptative	Innate and adaptative	Innate	Innate	Innate
Axenic animals	Yes but technically demanding and very expensive	Yes but technically demanding and very expensive	Yes but limited in time	Yes	Yes	Yes
Compatibility with human origin microorganisms	Variable	Variable	Yes but limited to aerobic taxa	Yes but limited to aerobic taxa	Yes but limited to aerobic taxa	Yes
Screening platform	No	No	Yes	Yes	Yes	Yes
Usable for high-throughput studies	No	No	Yes	Variable	Yes	Yes
Microscopic observation on live whole animal	No	No	Yes	No	No	Yes
Ethical issues	Yes	Yes	No	No	No	No
Other limitations	Impact of skin, fur, digestive tract and behavior on microbial communities	Impact of skin, fur, digestive tract and behavior on microbial communitiesLack of mutants	High variability of the gut microbiota based on experimental and environmental conditions	Low diversity of the gut microbiotaHigh-throughput methods difficult to implementInjecting a pathogen bypasses the early stages of infection	No mutants Low standardization between laboratories	Time consuming without automationImpact of temperature on microbial metabolism

Adapted from Douglas (7) and Nathan (39).