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

• Published in: AMB Express Vol. 1; no. 1; p. 41
• Main Authors: 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
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 18-11-2011; BioMed Central Ltd; Springer
• Subjects: Biomedical and Life Sciences; Biotechnology; Life Sciences; Microbial Genetics and Genomics; Microbiology; Original; aquaculture; 16S rRNA; pyrosequencing; carp; biodiversity; intestinal tract
• ISSN: 2191-0855; 2191-0855
• DOI: 10.1186/2191-0855-1-41

The microbes in the gastrointestinal (GI) tract are of high importance for the health of the host. In this study, Roche 454 pyrosequencing was applied to a pooled set of different 16S rRNA gene amplicons obtained from GI content of common carp (
Cyprinus carpio
) to make an inventory of the diversity of the microbiota in the GI tract. Compared to other studies, our culture-independent investigation reveals an impressive diversity of the microbial flora of the carp GI tract. The major group of obtained sequences belonged to the phylum
Fusobacteria
.
Bacteroidetes
,
Planctomycetes
and
Gammaproteobacteria
were other well represented groups of micro-organisms.
Verrucomicrobiae
,
Clostridia
and
Bacilli
(the latter two belonging to the phylum
Firmicutes
) had fewer representatives among the analyzed sequences. Many of these bacteria might be of high physiological relevance for carp as these groups have been implicated in vitamin production, nitrogen cycling and (cellulose) fermentation.