The Gut Microbiota of Fish

The fish microbiome and its interactions with mucosal tissues

“…The bacterial communities in the GI tracts of fish are diverse, comprising 100s-1000s of OTUs, and are present in levels of up to log 11 cells per gram of fecal material (Zhou et al, 2014). Although these communities are complex and are influenced by a number of factors, species from the phyla Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, Fusobacteria, and Tenericutes are commonly reported to be amongst the most dominant members present in the GI tracts of fish species (Nayak 2010;Llewellyn et al, 2014;Romero et al, 2014). There is some information available in regards to the factors that influence these communities, their functionality, and why these communities are of importance to the host.…”

“…A meta-analysis of environmental and ecological factors associated with twenty-five 16S rRNA libraries derived from the GI tracts of freshwater and marine fish species revealed that salinity and trophic level shape the composition of fish gut bacteria (Sullam et al, 2012). An in-depth discussion of these factors is beyond the scope of this chapter, but readers with an interest are referred to the review of Romero et al (2014).…”

“…For example, Cetobacterium somerae is known to produce abundant amounts of vitamin B12 (cobalamin), and this organism is commonly present in the GI tract of a number of fish species (Tsuchiya et al, 2008). Its contribution to the vitamin B12 requirements of the host is inferred not only by the bacterium's high abundance and production of vitamin B12, but also by the fact that various fish species in which the bacterium is present in the GI tract, such as Nile tilapia and common carp Cyprinus carpio, have no dietary vitamin B12 requirement, whereas species in which the bacteria is not commonly present, such as channel catfish Ictalurus punctatus and Japanese eel Anguilla japonica, have a requirement for dietary vitamin B12 (Tsuchiya et al, 2008;NRC, 2011;Romero et al, 2014). Fermentation of dietary fiber by the GI microbiota leads to the production of various short-chain fatty acids (SCFAs); high acetate (along with smaller quantities of propionate and butyrate) levels have been detected in the hindgut sections of herbivorous fish species (Clements and Choat, 1995;Mountfort et al, 2002).…”

“…Typically the yeast identified from the fish GI tract belong to the Ascomycota or Basidiomycota (for reviews see Gatesoupe (2007) and Romero et al (2014)). Metschnikowia zobelii, Candida tropicalis, and Trichosporon cutaneum are reportedly the dominant yeasts in some marine fish species and Debaryomyces hansenii, Candida spp., Saccharomyces cerevisiae, and Leucosporidium spp.…”

The fish egg microbiome : diversity and activity against the oomycete pathogen Saprolegnia

“…Besides the bacterial microbiome, the yeast microbiome of fish gut has attracted wide attention, mainly due to the fact that several yeasts can stimulate the host immune response, growth, development and metabolism of the hosts (Gatesoupe, 2007). The population density of yeast in fish gut ranges from undetectable quantities to 10 7 CFU per gram of gut matter and the two most reported fungal phyla are the Ascomycota and Basidiomycota (Gatesoupe, 2007;Romero et al, 2014b). Concerning filamentous fungi, only little is known: a condition and eating habit (e.g.…”