Analysis of the scallop microbiota by means of 16S rRNA gene pyrosequencing
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1
Universidad de Santiago de Compostela, Spain
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2
Centro Superior de Investigación de la Salud Pública (CSISP-FISABIO, Departamento de Genómica y Salud,, Spain
Bivalve molluscs, due to its filter-feeding mechanism, have an abundant associated bacterial microbiota composed of a large number of species of different genera. The knowledge about the composition of the microbiota associated with bivalve molluscs is based, mostly, on techniques of cultivation of microorganisms, but also on DGGE methods. However, it is estimated that less than 1% of the bacteria are culturable with current methods, which lead to an underestimation of the microbial diversity. On the other hand, DGGE methodology has a limited resolution due to the low number of DNA fragments obtained as representative of a microbial community. The introduction of new molecular approaches allowed the improvement of the knowledge about bacterial communities present in a sample [1]. In recent years, new molecular techniques known as Next Generation Sequencing (NGS) have been developed, based on high- throughput sequencing [2]. In this study, we present the analysis of the microbiota associated to reared scallop gonads before and after spawning by pyrosequencing of the 16S rRNA gene. After the DNA extraction of the samples, amplification was performed using a set of degenerate primers with low stringency conditions. Pyrosequencing of samples was carried out using the sequencer 454 GLX Titanium Plus (Roche). The data obtained was further subjected to bioinformatics analysis using Galaxy and UCHIME program and the Ribosomal Database Project. Rarefaction curves were obtained, the composition of the bacterial community was analysed after the taxonomic assignment, and the total composition of the bacterial communities of the samples were compared using the principal coordinates analysis (PCoA) by FastUnifrac tool [3].
Pyrosequencing of the samples resulted in a total of 18520 sequences (3000 per sample, approximately) with an average length of 325 bp (base pairs). The taxonomic assignment of sequences allowed the identification to the genus level, being observed a large bacterial diversity with over 110 genera. The most prevalent genera in the samples were Hydrotalea, Acinetobacter, Delftia, Sediminibacter and Pseudomonas, among others. Differences in the microbial communities were observed among the samples, and the PCoA analysis allowed their separation by means on their gender and if they proceed from sampling before or after the spawning. Nevertheless, the rarefaction curves obtained for each sample failed to reach a saturation phase, indicating that more sequencing effort would be necessary.
References
[1] L.D. Alcaraz, P. Belda-Ferra, R. Cabrera-Rubio, H. Romero, A. Simón-Soro, M. Pignatelli and A. Mira. Clinical Microbiology and Infection, 18 (2012) 54-57.
[2] M. Carda-Dieguez, A. Mira and B. Fouz. Doi:10.1111/1574-6941.12236.
[3] M. Hamady, C. Lozupone and R. Knight. ISME J, 4 (2010) 17-27.
Keywords:
Bacterial communities,
NGS,
reared scallop.,
pyrosequencing,
16S rRNA gene
Conference:
IMMR | International Meeting on Marine Research 2014, Peniche, Portugal, 10 Jul - 11 Jul, 2014.
Presentation Type:
Poster Presentation
Topic:
AQUACULTURE
Citation:
Lasa
A,
Mira
A,
Camelo-Castillo
A,
Belda-Ferre
P and
Romalde
JL
(2014). Analysis of the scallop microbiota by means of 16S rRNA gene pyrosequencing.
Front. Mar. Sci.
Conference Abstract:
IMMR | International Meeting on Marine Research 2014.
doi: 10.3389/conf.fmars.2014.02.00112
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Received:
09 May 2014;
Published Online:
18 Jul 2014.
*
Correspondence:
Prof. Jesus L Romalde, Universidad de Santiago de Compostela, Santiago de Compostela, Spain, jesus.romalde@usc.es