Table 2.

Niche and possible function of the bacterial classes present within the 16S rRNA amplicons obtained from the GI tract of common carp.

Class/Subclass	Phylum	Metabolism	Niche and function	Reference
Aeromodales	Proteobacteria	Facultative anaerobes	Well-known pathogen in fish, known member of the endogenous flora of freshwater fish, fermentation of organic compounds, cellulose activity, antibacterial activity	Lee et al. 2009; Huber et al. 2004; Namba et al. 2007; Wu et al. 2010; Jiang et al. 2011; Sugita et al. 1995; Sugita et al. 1997
Bacilli	Firmicutes	Aerobic heterotrophs	Bacilli, especially lactobacilli, are known members of the microbial flora of the fish gut, able to ferment various carbon hydrates, pathogens	Ringo and Gatesoupe 1998
Bacterioidaceae	Bacteriodetes	Obligate anaerobes	Polysaccharide (especially from plants) degradation, known member of the intestinal microbiota of various organisms	Van der Meulen et al. 2006; Flint et al. 2008
Cetobacterium	Fusobacteria	Obligate anaerobes	Known member of the endogenous flora of fish intestines, vitamin B12 production	Sugita et al. 1991; Wu et al. 2010; Tsuchiya et al. 2008
Clostridia	Firmicutes	Obligate anaerobes	Known member of the endogenous flora of intestines of various organisms including fish, polysaccharide degradation, pathogen, antibacterial activity	Flint et al. 2008; Wu et al. 2010; Sugita et al. 1990; Sugita et al. 1997
Enterobacteriales	Proteobacteria	Facultative anaerobes	Sugar fermentation, pathogen, known member of the intestinal microbiota of fish (including carp)	Wu et al. 2010; Sugita et al. 1990
Gemmata	Planctomycetes	Aerobic heterotrophs	Abundant in freshwater ecosystems	Wang et al. 2002
Isosphaera	Planctomycetes	Aerobic hetetotrophs	Common in aquatic environments	Wang et al. 2002
Marinilabiaceae	Bacteriodetes	Facultative anaerobic chemo-organotrophs	Sugar/starch fermentation, members of this family can decompose plant polymers and some have low cellulose activity	Denger et al. 2002; Detkova et al. 2009
Pirellula	Planctomycetes	Aerobic heterotrophs	Carbohydrate fermentation, present in aquatic environments, present in guts of some animals and associated to sponges	Fuerst et al. 1997; Pimental-Elardo 2003
Planctomyces	Planctomycetes	Aerobic heterotrophs, anaerobic chemoautotrophs	Known member of the intestinal microbiota of various organisms including fish	Ley et al. 2008; Rawls et al. 2006
Porphyromonadaceae	Bacteriodetes	Obligate anaerobes	Pathogen, major members of the human gut microbiota, present in fish intestines, glucose fermentation	Mulder et al. 2009; Wu et al. 2010; Li et al. 2009
Schlesneria	Planctomycetes	Facultative aerobic chemo-organotrophs	Present in wetlands, degradation of biopolymers	Kulichevskaya et al. 2007
Sphingobacteria	Bacteriodetes	Obligate anaerobes	Endosymbiont in insects, plant polysaccharide degradation	Zhou et al. 2009
Verrucomicrobiae	Verrucomicrobia	Aerobes, facultative anaerobes	Fermentation, known members of the fish microbiota	Schlesner et al. 2006; Rawls et al. 2006
Vibrio	Proteobacteria	Facultative anaerobes	Fermentation, pathogen, obligate endosymbionts, known to be present in fish intestines	Wu et al. 2010; Thompson et al. 2004
Zavarzinella	Planctomycetes	Aerobic heterotrophs	Acidic wetlands, newly identified genus related to Gemmata	Kulichevskaya et al. 2009