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

van Kessel, Maartje AHJ; Dutilh, Bas E; Neveling, Kornelia; Kwint, Michael P; Veltman, Joris A; Flik, Gert; Jetten, Mike SM; Klaren, Peter HM; Op den Camp, Huub JM

doi:10.1186/2191-0855-1-41

AMB Express

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

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