High-throughput sequencing approaches have enabled characterizations of the community composition of numerous gut microbial communities, which in turn has enhanced interest in their diversity and functional relationships in different groups of vertebrates. Although fishes represent the greatest taxonomic and ecological diversity of vertebrates, our understanding of their gut microbiota and its functional significance has lagged well behind that of terrestrial vertebrates. In order to highlight emerging issues, we provide an overview of research on fish gut microbiotas and the biology of their hosts. We conclude that microbial community composition must be viewed within an informed context of host ecology and physiology, and that this is of particular importance with respect to research planning and sampling design.

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Epulopiscium fishelsoni n. g., n. sp., is described from the gut of Acanthurus nigrofuscus, an herbivorous surgeonfish (Acanthuridae: Teleostei) from the Red Sea, Israel. The symbiont is placed in the kingdom Protoctista (or Protista) but more specific taxonomic assignment is impossible at this time. The organism is of an elongate oval shape, round in cross‐section, and highly mobile, with the ability to reverse direction rapidly. It lacks a mouth or other external structures, with the exception of fine surface filaments of an undetermined nature. Internally, there is a complex of folded membranes or tubules and a nucleus. No other organelles are evident. Reproduction is characterized by doubling of nuclei within the parental cell and emergence of daughter cells from a perforation in the parental cortex. Symbionts appear to exhibit circadian cycles of growth, reproductive activity, and movement within the gut. Although the organism greatly reduces local gut pH when present in large numbers, we know nothing of interactions between host and symbiont.

Prior studies have described a morphologically diverse group of intestinal microorganisms associated with surgeonfish. Despite their diversity of form, 16S rRNA gene surveys and fluorescent in situ hybridizations indicate that these bacteria are low-G؉C gram-positive bacteria related to Epulopiscium spp. Many of these bacteria exhibit an unusual mode of reproduction, developing multiple offspring intracellularly. Previous reports have suggested that some Epulopiscium-like symbionts produce dormant or phase-bright intracellular offspring. Close relatives of Epulopiscium, such as Metabacterium polyspora and Clostridium lentocellum, are endospore-forming bacteria, which raises the possibility that the phase-bright offspring are endospores. Structural evidence and the presence of dipicolinic acid demonstrate that phase-bright offspring of Epulopiscium-like bacteria are true endospores. In addition, endospores are formed as part of the normal daily life cycle of these bacteria. In the populations studied, mature endospores were seen only at night and the majority of cells in a given population produced one or two endospores per mother cell. Phylogenetic analyses confirmed the close relationship between the endospore-forming surgeonfish symbionts characterized here and previously described Epulopiscium spp. The broad distribution of endospore formation among the Epulopiscium phylogenetic group raises the possibility that sporulation is a characteristic of the group. We speculate that spore formation in Epulopiscium-like symbionts may be important for dispersal and may also enhance survival in the changing conditions of the fish intestinal tract.

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