Table 2.

Animal models for microbiota research (images from Creative Commons).

Animal Model	Main Characteristics of the Model	Aspect of the Microbiota to Study	Methodology Employed	Reference
(A) Hydra (Hydra spp.)	Tube-like body (similar to the human gut) Shares ancestral genes with humans Established protocols for generating germ-free or gnotobiotic animals	Microbe–microbe relationships (including virome) and the impact on the host	In vivo system	[45]
(B) Honeybee (Apis mellifera)	Lower complexity of bacterial diversity All members of the honeybee microbiota can be cultured Established protocols for generating microbiota-free bees and recolonizing bees	Function of bacteria in bee gut species	In vivo system for strain interactions 16s rRNA sequencing	[46]
(C) Zebrafish (Danio rerio)	High reproduction rate Environment can be thoroughly sampled Can be raised with the same diet their entire lives	Changes in microbial communities under a constant diet and trough different stages of age Effects of dietary fat on microbiota composition	16s rRNA sequencing	[20]
(D) Mice (Mus musculus)	Germ-free mice Small size, large litters, and rapid generation time Techniques for maintaining a sterile environment in GF or gnotobiotic animals are critical	Host–microbe interactions Role of microbiota in homeostasis, health, and diseases Role of the interaction between diet and microbiota and the mechanisms of obesity Effect and mechanisms of inoculation with known microbes	16s rRNA sequencing Metabolomics, identification, and quantitation of metabolites	[47]
(E) Rat (Rattus novergicus)	Similar phyla in the gut compared to humans Good models for specific pathogen-free (SPF) experiments	Effect of certain probiotics and prebiotics on the microbiota Effect of diet on the microbiota Role of the microbiota in diseases like obesity	Amplification of bacterial 16S rRNA Microbial metabolites through gas chromatography fitted with a quadrupole mass spectrometry unit	[30]
(F) Pig (Sus scrofa)	Similarities to humans in gastrointestinal tract functions, anatomical structure, metabolism, nutritional requirements, and bacterial phyla (Bacteroidetes and Firmicutes) As an obesity model, pigs are prone to sedentary behavior and fatten, similar to humans Distribution of fat and adipocyte size are similar in both species	In obesity models, the microbiota interactions can be assessed under more controlled conditions in pigs than in human subjects	qPCR available for amplification and quantification of target bacterial group and total bacteria Analysis of microbial metabolites such as ammonia and short chain fatty acids (SCFAs) using gas chromatography	[48]