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"study-abstract": "Best practices for making shotgun metagenome sequence libraries from ultra-low biomass specimens have yet to be fully resolved. In this study, we address the utility of spiking in carrier genomic DNA into library preparation protocols to get to minimum input requirements recommended by protocols. Mock microbial genomic DNA (an established mixture of DNA from 8 different bacterial species and 2 fungal species) was mixed together with carrier DNA (lambda DNA) at different ratios and at different input levels starting at 50 pg and decreasing below 1 pg. This study was performed as part of the NASA Planetary Protection Analysis Working Group.",
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"study-abstract": "Next generation sequencing has dramatically changed the landscape of microbial ecology, large scale and in depth diversity studies being now widely accessible. Determining the accuracy of taxonomic and quantitative inferences and comparing results obtained with different approaches are complicated by incongruence of experimental and computational data types and by lack of knowledge of the true ecological diversity. Here we used highly diverse bacterial and archaeal synthetic communities assembled from pure genomic DNAs to compare inferences from metagenomic and SSU rRNA amplicon sequencing. Both Illumina and 454 metagenomic data outperformed amplicon sequencing in quantifying the community diversity but the outcome was dependent on analysis parameters and platform. New approaches in processing and classifying amplicons can reconstruct the taxonomic composition of the community, but all tested primers lead to significant taxon-specific biases. Controlled synthetic communities assembled to broadly mimic the phylogenetic richness in target environments can provide important validation for fine-tuning experimental and computational parameters used to characterize natural communities.",
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"study-abstract": "Bioinformatical research on viruses is still limited because of the low amounts of viral DNA that can be obtained for analysis. To overcome this limitation, DNA is often amplified with multiple displacement amplification (MDA), which causes an unavoidable bias. Here, we describe a DNA-spiking method to avoid the bias that is created when using amplification of DNA before metagenome sequencing. To obtain sufficient DNA for sequencing, a bacterial 16S rRNA gene was amplified and the obtained DNA was spiked to a DNA sample containing DNA from a bacteriophage population before sequencing using Ion Torrent technology. After sequencing, the 16S rRNA gene reads DNA was removed by mapping to the Silva database. The new DNA-spiking method was compared with the MDA technique.The new method provides a simple and inexpensive protocol with very low bias in sequencing of metagenomes for which low amounts of DNA are available.",
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"centre-name": "Virginia Commonwealth University",
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"study-abstract": "This is an artificial metagenome created by pooling various proportions of DNA from four microbe cultures to simulate a simple metagenome for analysis by Oxford nanopore MinION. Single-species cultures of Escherichia coli, Pseudomonas fluorescens, Microcystis aeruginosa, and Synechococcus elongatus were grown to log phase then harvested for DNA extraction. Following mechanical shearing, templates were prepared using either equimolar amounts of each species or combinations of DNAs where one species was rare (0.05%). Libraries were created using his-tag bead purification according to MinION specifications and libraries were sequenced using MinION R7.x flow cells. For validation, a final library was prepared using a mock microbial community with 20 species included in “staggered” proportions (obtained from ATCC, the mixture had 1,000 to 1,000,000 16S rRNA operon copies per organism per μL of material supplied). This latter library, as it was supplied at a low concentration, required pre-amplification with Phi29 prior to library preparation.",
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"secondary-accession": "ERP009740",
"centre-name": "Virginia Commonwealth University",
"public-release-date": null,
"study-abstract": "This is an artificial metagenome created by pooling various proportions of DNA from four microbe cultures to simulate a simple metagenome for analysis by Oxford nanopore MinION. Single-species cultures of Escherichia coli, Paracoccus denitrificans, Microcystis aeruginosa, and Synechococcus elongatus were grown to log phase then harvested for DNA extraction. Following mechanical shearing, templates were prepared using either equimolar amounts of each species or combinations of DNAs where one species was rare (0.05%). Libraries were created using his-tag bead purification according to MinION specifications and libraries were sequenced using MinION R7.x flow cells.",
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"last-update": "2016-01-20T14:12:06",
"secondary-accession": "SRP004311",
"centre-name": "HMP",
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"study-abstract": "The HMP metagenomes mock pilot represents the shotgun sequencing of HMP even and staggered Mock communities, distributed to each of the four HMP sequencing centers. The goal of the pilot was to test the sequencing protocol and to evaluate accuracy and consistency between centers.",
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"study-abstract": "A metagenomic sequencer dataset built from database sequences to compare the accuracy and performance of various metagenomic sequence dataset analysis pipelines",
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