The Gut Microbiota of Marine Fish

Abstract

The body of work relating to the gut microbiota of fish is dwarfed by that on humans and mammals. However, it is a field that has had historical interest and has grown significantly along with the expansion of the aquaculture industry and developments in microbiome research. Research is now moving quickly in this field. Much recent focus has been on nutritional manipulation and modification of the gut microbiota to meet the needs of fish farming, while trying to maintain host health and welfare. However, the diversity amongst fish means that baseline data from wild fish and a clear understanding of the role that specific gut microbiota play is still lacking. We review here the factors shaping marine fish gut microbiota and highlight gaps in the research.

Switching on the light: using metagenomic shotgun sequencing to characterize the intestinal microbiome of Atlantic cod

“…Several T6SSs are involved in antibacterial processes, including in the human gut (Russell et al ., ). This suggests that P. iliopiscarium and P. kishitanii may provide antagonistic activity toward bacterial pathogens in the Atlantic cod gut, as has previously been observed for several members of the Photobacterium genus (MacDonald et al ., ; Caipang et al ., ; Ray et al ., ; Egerton et al ., ). Le Doujet et al ., also observed a high relative abundance of genes involved in chitin and N‐acetylglucosamine utilization, indicating that the Photobacterium species may aid in the breakdown of the exoskeleton of crustacean prey, of which chitin is the major component.…”

“…Further, histamine biosynthesis by P. kishitanii associated with marine fish has been observed in several studies (Bjornsdottir-Butler et al, 2016;Machado and Gram, 2017), suggesting that this bacterium may be involved in immune responses in the Atlantic cod gut. Members of the Photobacterium genus have also been shown to aid in the digestive process of Dover sole (Solea solea), i.e., by degrading chitin (MacDonald et al, 1986), while others show antagonistic activity towards common bacterial pathogens in Atlantic cod (MacDonald et al, 1986;Caipang et al, 2010;Ray et al, 2012;Egerton et al, 2018). Such roles in protective immunity or digestion suggest an evolutionary benefit of host selection for the colonization by Photobacterium.…”

“…16S rRNA amplicon sequencing (Star et al, 2013;Ye et al, 2014;Llewellyn et al, 2016;Riiser et al, 2018) or dependence on bacterial cultivation (Kim et al, 2007;Martin-Antonio et al, 2007;Valdenegro-Vega et al, 2013). Therefore, there remains a lack of detailed, baseline compositional data comparing healthy wild fish from the same species that live in different habitats with a variety of environmental conditions (Uchii et al, 2006;Egerton et al, 2018).…”

Diet and diet‐associated bacteria shape early microbiome development in Yellowtail Kingfish (Seriola lalandi)

“…In recent years, there has been an increased awareness of the importance of the host microbiome for digestion, immune function and development of animals, including fish (Bates et al, 2006;Fraune and Bosch, 2010;Stephens et al, 2016;Egerton et al, 2018;Wang et al, 2018). It has been shown that early bacterial colonization of the fish gastrointestinal (GI) tract is caused by the uptake of waterborne (Han et al, 2010) and/or feed-associated bacteria (Hansen and Olafsen, 1999).…”

Using fish models to investigate the links between microbiome and social behaviour: The next step for translational microbiome research?

“…Most were purely descriptive or assessed the effects of diet (e.g., food substitution or supplements with prebiotics or probiotics) or host factors (ontogenetic, genetic or species‐specific) on gut microbiota. Since 2014, the number of fish microbiome studies has more than doubled (see for example Tarnecki, Burgos, Ray, & Arias, , for a review on fish gut microbiome studies) and now the dominant phyla in fish microbiomes are well established, belonging to Proteobacteria, Bacteroidetes, Actinobacteria, Firmicutes and Fusobacterium (e.g., Egerton, Culloty, Whooley, Stanton, & Ross, ; Wang, Ran, Ringø, & Zhou, ). While the focus of these new studies continues to be merely descriptive (e.g., Rosado, Pérez‐Losada, Severino, Cable, & Xavier, ) or rather addressing the effects of diet supplements on gut microbiota (e.g., Ray et al., ; Wang et al., ), more effort has been placed in finding which ecological factors are determinants of microbiome composition.…”