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Table 2 Niche and possible function of the bacterial classes present within the 16S rRNA amplicons obtained from the GI tract of common carp.

From: Pyrosequencing of 16S rRNA gene amplicons to study the microbiota in the gastrointestinal tract of carp (Cyprinus carpio L.)

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