Sequence composition diversity in Alaskan glacier and other metagenomes
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Abstract
Metagenomics by next generation sequencing has become an important tool for interrogating complex microbial communities. In this study we analyzed several pairs of metagenomic samples obtained by different methods and observed biases, resulting in different nucleotide composition of the sequenced reads. The pairwise sample comparison was based on the principal component analysis of dinucleotide word frequencies in sequences obtained from different platforms. We found bias in the sequences obtained from the different platforms for the amplified hypervariable regions in 16S rRNA but not in shotgun metagenome reads aligned to such hypervariable regions. The differences and consistency of the distributions of the nucleotides suggest that the biases are likely due to a combination of biases introduced by PCR and different sequencing protocols, and they are related to the GC content of the reads produced. For this reason, caution should be exercised when interpreting the results of comparative metagenomics studies, as they may vary depending on the sequencing technology.
Cite this as
2014. Sequence composition diversity in Alaskan glacier and other metagenomes. PeerJ PrePrints 2:e734v1 https://doi.org/10.7287/peerj.preprints.734v1Author comment
This is version 1 of a submission to PeerJ for review.
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Competing Interests
The authors declare they have no competing interests.
Author Contributions
Sulbha Choudhari performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables.
Roman J Dial conceived and designed the experiments, contributed reagents/materials/analysis tools.
Dibyendu Kumar contributed reagents/materials/analysis tools, reviewed drafts of the paper.
Daniel H Shain conceived and designed the experiments, reviewed drafts of the paper.
Andrey Grigoriev conceived and designed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.
Funding
This work was supported by funds from the Rutgers University and in part by the NSF grant DBI-1126052 to A.G. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
