Zebrafish as a vertebrate model have contributed to elucidating the functions of important factors involved in development, metabolism, and various diseases that are shared among human and animals. Zebrafish have also attracted attention as a gut microbiota model and have been studied for host-microbe interaction using diverse approaches, which involve host immune, metabolic, and behavioral responses to specific microbes. Using zebrafish as disease models for diabetes and pathogen infection models has been especially valuable for the elucidation of important factors as candidate targets for pharmaceutical development. Zebrafish offer unique advantages over mammalian models as a gut microbiota model because their transparency enables live imaging of individual microbes and immune cells within the host. Rearing zebrafish and setting up experiments for microbiome research entail consideration of aquatic-specific factors that may significantly impact the microbiota. Although fish are not considered as experimental animals in Japan, the handling of fish with ethical consideration is required, due to the international trend toward the awareness of animal welfare including fish. In this review, we provide an overview of zebrafish as an experimental animal model and summarize recent important studies using zebrafish as a host of microbes. We then discuss perspectives on zebrafish research as an alternative animal model and international ethical differences in handling fish, and review the applicability and prospect of fish models for microbiome research.

Drosophila melanogaster serves as an invaluable model for exploring the symbiotic relationship between hosts and microorganisms. This review summarizes recent findings on the maintenance mechanisms, physiological roles, and dysbiosis of the Drosophila gut microbiota. The gut microbiota of Drosophila is maintained by a balance between continuous intake of microbes from diet and their colonization and proliferation in the gut. Distinct pathways of reactive oxygen species (ROS) production and antimicrobial peptides (AMPs) of Drosophila play crucial roles in recognizing pathogenic and commensal microorganisms. The gut microbiota has a significant impact on the physiological functions of Drosophila. Growth-promoting effects have been reported in the larval stage, and the gut microbiota also exhibits diverse functions in adult flies. Abnormalities in the gut microbiota caused by aging or disease lead to intestinal inflammation and decreased intestinal barrier function, resulting in shortened lifespan. Furthermore, dysbiosis has been suggested to influence the pathology of neurodegenerative disease models. Future advancements in gut microbiota research using Drosophila are expected to elucidate the fundamental mechanisms of host-microbe interactions.

Intestinal epithelial cells face an aerobic environment on their basal side, while their apical side is exposed to an anaerobic environment, where a diverse range of obligate anaerobic microbes dwell and establish a symbiotic relationship with the host. To reconstruct the complex intestinal ecosystem and understand the molecular basis underlying the crosstalk between gut microbes and the host, it is necessary to develop a device that can reproduce these two different oxygen concentration environments experienced by intestinal epithelial cells. I have collaborated with two companies to jointly develop such a device. In this review article, I briefly introduce the development process of this apical anaerobic cultivation device, and highlight some of the results obtained using the prototype and manufactured devices to discuss their effectiveness as research tools.