TABLE 1.

The merits and limitations of common animal models (mice, rats, and zebrafish) in gut microbiome research

Animal model	Advantages	Limitations	Ref.
Mice and rats	1.Similarity with human Genetic conservation (~80%–90%) Similarity in microbial structure (dominated by Firmicutes and Bacteroidetes) Stable gut microenvironment High similarity in tissue and organ structure, cellular function, and metabolic features 2.Experimental operation Collect feces in a noninvasive, sustaining, and easy way for metagenome sequencing Mature techniques for constructing various disease models	1.Shortcomings Long reproductive cycle, small litter size per fetus, long lifespan Low throughput for toxicity testing Cage effects on individual gut microbial structure 2.Experimental techniques Sterile model preparation is inefficient, small scale, high expense, and maintenance cost Manipulation of gut microbial composition by oral gavage	14, 15, 16, 17
Zebrafish	1.Similarity with human/mammals Genetic conservation (~70%) Similarity in the development and physiology function of the digestive system The mode of behavior, internal secretion, and molecular changes are usually similar to clinical data 2.Intrinsic superiorities High fecundity, rapid development, short lifespan, strong genetic and development coherence, high degree of biological replication Transparency in early development, available for intravital imaging in vivo Lack of functional adaptive immune system in early development, capable of studying the innate immune system in the absence of adaptive immunity system High‐throughput model for pharmacological and toxicological evaluation 3.Experimental techniques Powerful manipulatable genetic systems and large availability of genetically modified models, including knock‐out/in, GFP or mCherry fluorescent proteins, casper and crystal mutants Diversity of automated and species‐specific behavioral assays for gut‐microbiome‐brain axis assessment Acquirement and quality control of sterile embryos are easy, practical, and economical Manipulation of gut microbial composition by immersion	1.Shortcomings Difference in microbial structure (dominated by Proteobacteria [76%–82%]) 2.Experimental techniques Difficulty to obtain a series of organ samples in individual operations for its small size Difficulty in modeling of GF adult zebrafish Interference in metagenome sequencing from the mixture of nucleic acid substances from other sources	5, 7, 9, 11, 18, 19, 20, 21