Intestinal microbiota in fishes: what's known and what's not

Abstract

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.

Gut content microbiota of introduced bigheaded carps ( Hypophthalmichthys spp.) inhabiting the largest shallow lake in Central Europe

“…Microorganisms may contribute to fish nutrition either directly as part of the ingested and digested food Matĕna et al, 1995;Kamjunke and Mehner, 2001) or indirectly by colonizing their digestive tracts and participating in digestion processes, influencing absorption and synthesis of important nutrients (Ray et al, 2012;Li et al, 2013;Clements et al, 2014). So far, we have evidence of direct usage of microbes as food only in a limited number of fish species.…”

Divergence across diet, time and populations rules out parallel evolution in the gut microbiomes of Trinidadian guppies

“…A more ancient example of gut microbiota 'resistance' to dietary change includes pandas that show similar gut microbiota compared with their carnivorous relatives in spite of their extensive consumption of foliage (Ley et al, 2008). Their rapid gut processing of large volumes of plant material (Van Soest, 1994), rather than slow digestion and extensive fermentation seen for many mammalian herbivores, may have promoted the retention of their 'ancestral' microbiome instead of shifts to canonical fermenting gut communities (see Clements et al, 2014 for a similar discussion of pertinence to herbivorous fish).…”

Physiology and immunology of mucosal barriers in catfish (Ictalurus spp.)

“…High-throughput sequencing approaches based upon 16s rRNA, have brought about a new appreciation and interest in the diversity and function of the microbiota in different groups of vertebrates. 139 Little is known regarding the microbiome in the catfish model, particularly lacking is a basic characterization of microbial communities and how these communities shift due to changes in health status. Recently however, by utilizing 454 pyrosequencing of 16S rRNA, Larsen et al 141 compared gastrointestinal microbiota across 3 commercially important species of fish (channel catfish; bluegill, Lepomis macrochirus; and largemouth bass, Micropterus salmoides) inhabiting the same lake and consuming natural food items.…”

“…137 Culture-based surveys greatly underestimate the diversity of microbiota, as an estimated <10% of bacteria can be isolated or cultured in laboratory settings. 139,140 The interaction between the assemblages of microbes in fish and host health is a topic that has been out of reach until the advent of recent technological advances such as next generation sequencing, which enable investigators to deeply profile microbial communities in host tissues of interest. High-throughput sequencing approaches based upon 16s rRNA, have brought about a new appreciation and interest in the diversity and function of the microbiota in different groups of vertebrates.…”