Differences in sequencing technologies improve the retrieval of anammox bacterial genome from metagenomes

BMC Genomics

Research Article

Sacha AFT van Hijum¹  Susannah G Tringe²  Huub JM Op den Camp³  Mike SM Jetten⁴  Gianluigi Folino⁵  Fabio Gori⁶  Elena Marchiori⁶ 

[1] Center for Molecular and Biomolecular Informatics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands;DOE Joint Genome Institute, 94598, Walnut Creek, CA, USA;Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands;Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands;Department Biotechnology, Delft University of Technology, 2628 BC, Delft, The Netherlands;ICAR-CNR, Rende, Italy;Radboud University Nijmegen, Institute for Computing and Information Science, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands;

关键词: Sequencing Technology;    Population Distribution;    Anammox Bacterium;    Mapping Threshold;    Coverage Depth;   

DOI  :  10.1186/1471-2164-14-7

 received in 2012-03-19, accepted in 2012-12-13,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundSequencing technologies have different biases, in single-genome sequencing and metagenomic sequencing; these can significantly affect ORFs recovery and the population distribution of a metagenome. In this paper we investigate how well different technologies represent information related to a considered organism of interest in a metagenome, and whether it is beneficial to combine information obtained using different technologies. We analyze comparatively three metagenomic datasets acquired from a sample containing the anammox bacterium Candidatus ’Brocadia fulgida’ (B. fulgida). These datasets were obtained using Roche 454 FLX and Sanger sequencing with two different libraries (shotgun and fosmid).ResultsIn each dataset, the abundance of the reads annotated to B. fulgida was much lower than the abundance expected from available cell count information. This was due to the overrepresentation of GC-richer organisms, as shown by GC-content distribution of the reads. Nevertheless, by considering the union of B. fulgida reads over the three datasets, the number of B. fulgida ORFs recovered for at least 80% of their length was twice the amount recovered by the best technology. Indeed, while taxonomic distributions of reads in the three datasets were similar, the respective sets of B. fulgida ORFs recovered for a large part of their length were highly different, and depth of coverage patterns of 454 and Sanger were dissimilar.ConclusionsPrecautions should be sought in order to prevent the overrepresentation of GC-rich microbes in the datasets. This overrepresentation and the consistency of the taxonomic distributions of reads obtained with different sequencing technologies suggests that, in general, abundance biases might be mainly due to other steps of the sequencing protocols. Results show that biases against organisms of interest could be compensated combining different sequencing technologies, due to the differences of their genome-level sequencing biases even if the species was present in not very different abundances in the metagenomes.

【 授权许可】

CC BY   
© Gori et al.; licensee BioMed Central Ltd. 2013