Abstract
BackgroundGraphene oxide (GO) has been suggested as an efficient assistant additive to eliminate non-specific amplification of the polymerase chain reaction (PCR). Although many studies have focused on exploring its molecular mechanism, the practice of GO on the quantitation of microbial community has not been implemented yet. In this study, GO was added in PCR system to explore the changes on removing typical amplification errors, such as chimera and mismatches on two kinds of mock communities (an evenly mixed and a staggered mock communities) and environmental samples.ResultsHigh-throughput sequencing of bacterial and fungal communities, based on 16S rRNA genes and internal transcribed spacers (ITS) respectively, showed that GO could significantly increase large segmental error (chimeric sequence) in PCR procedure while had no specific effect on point error (mismatched sequence). Besides, GO reduced the α-diversity of community, and changed the composition of fungal community more obviously than bacterial community.ConclusionsOur study provides the first quantitative data on microbial community level to prove the negative effect of GO, and also indicates that there may be a more complex interaction between GO and comprehensive DNA fragments in PCR process.
Highlights
Graphene oxide (GO) has been suggested as an efficient assistant additive to eliminate non-specific amplification of the polymerase chain reaction (PCR)
GO affects amplification errors in mock communities Sequences of mock communities were filtered based on quality score, and retained sequences were firstly used to explore the influence of GO on chimeras and mismatches
Bacterial community generated a larger proportion of chimeric sequences than fungal community in both even and staggered mock communities, and it seemed that chimera proportion increased more significantly in fungi than in bacteria after the addition of GO (Fig. 1)
Summary
Graphene oxide (GO) has been suggested as an efficient assistant additive to eliminate non-specific amplification of the polymerase chain reaction (PCR). Many studies have focused on exploring its molecular mechanism, the practice of GO on the quantitation of microbial community has not been implemented yet. GO was added in PCR system to explore the changes on removing typical amplification errors, such as chimera and mismatches on two kinds of mock communities (an evenly mixed and a staggered mock communities) and environmental samples. The study of environmental microbiome is undergoing a great revolution by the development of next-generation sequencing approaches and the establishment of robust bioinformatic tools [1, 2]. It has been a common consent that PCR has become one of the most ubiquitous and important tools in molecular biology since it was developed in 1985 [4].
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