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"study-abstract": "In this study we compared methods for quantifying taxonomic composition of microbial communities. The compared methods included metagenomics, 16S rRNA amplicon sequencing and metaproteomics. This ENA study contains the metagenomic and the 16S rRNA amplicon data. The metaproteomic data is available from ProteomeXchange via the PRIDE repository(PXD006118). For the comparison of the methods we analyzed three types of mock communities with all three methods. The communities contain between 28 to 32 species and strains of bacteria, archaea, eukaryotes and bacteriophage. For each community type 4 biological replicate communities were generated. All four replicates were analyzed by 16S rRNA sequencing. Three replicates of each community type were analyzed with metagenomics. The \"C\" type communities have same cell/phage particle number for all community members (C1 to C4). The \"P\" type communities have the same protein content for all community members (P1 to P4). The \"U\" (uneven) type communities cover a large range of protein amounts and cell numbers (U1 to U4). The 16S rRNA libraries were sequenced twice in independent runs. The prefixes \"rep1_\" and \"rep2_\" indicate the two individual runs. The 16S rRNA read files without prefix are rep1 and rep2 merged.",
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"study-abstract": "The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB6941. This project includes samples from the following biomes: root:Engineered:Modeled:Simulated communities (microbial mixture).",
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"study-abstract": "In this study we used an in vitro assembled microbiota sample to evaluate the efficiency and biases of purification methods used to purify virus-like particles from gut content for metagenome sequencing. The artificial microbiome sample contained six bacteriophages (P22, phiVPE25, phi6, T3, T7 and M13)two bacterial strains (gr+: Listeria monocytogenes EGD-e and gr-: Bacteroides thetaiotaomicron VPI5482), which were mixed into feces from germ-free mice. Three purification methods were tested: (1) Filtration + DNase (FD), (2) DTT treatment + filtration + DNase (DTT), (3) filtration + DNase + CsCl density gradient (CsCl). Additionally, metagenomes of the complete microbiome sample were sequenced (MG). Each treatment was done in duplicate.",
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"study-abstract": "The goal of this work is to develop and test synthetic 16S rRNA gene spike-in standards for use in high-throughput 16S rRNA gene amplicon sequencing experiments. The newly developed spike-in standards were tested using mock community mixtures and environmental microbiome samples.",
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"study-abstract": "Study the bacterial community structure and discuss the environmental relatedness. Collected from seawater and sediment from the ECS.",
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"study-abstract": "Sequencing a mock community consisting of T. roseus DSM 18391, C. akajimensis DSM 45221, P. stutzeri DSM 4166, P. inhibens DSM17395, and G. obscurus DSM 43160 for a comparative analysis of multiple displacement amplification performed in standard bulk reactions or in emulsions. Samples also include unamplified controls and no template negative controls.",
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"secondary-accession": "SRP050185",
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"study-abstract": "The goals of this project are to quantify and characterize bias in 16S rRNA Studies due to a particular choice of DNA extraction, PCR amplification, and sequencing and taxonomic classification protocols. Labs will make choices in protocol based on the environment of interest, but bias will always remain. This experiment is designed to quantify the differences between actual and observed community compositions when equal numbers of 1) cells, 2) DNA, and 3) PCR product are blended. By comparing the results of the experiments, one can quantify the contribution to bias of each step. Also, one can build models to predict true community composition based on the observed community composition.",
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"secondary-accession": "SRP016523",
"centre-name": "Oak Ridge National Lab",
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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": "Profiling differences in microbiome composition regarding a healthy or a disease phenotype is central in microbiome research. It typically involves the sequencing, the data processing, the statistical analysis and the graphical representation of the detected signatures. This process is currently addressed through several separated applications that requires expertise for installation, data pre-processing and in some case, programming skills. We present SHAMAN, which is an interactive web application that facilitates the use of a workflow for OTU calculation, the robust statistical modelling proposed by the DESeq2 package and provides more than ten interactive visualisations. It also implements new normalization methods which account for the sparsity of metagenomic data. %which is relevant for the DESeq2 approach.SHAMAN is primary designed for biologist with no experience in metagenomics, but can also meet the needs of specialist who can easily access to the configuration of processed tools and packages. It is freely accessible at http://shaman.pasteur.fr/, but also work as a standalone application with docker (aghozlane/shaman) or in R with packrat. The source code is written in R and is available at https://github.com/aghozlane/shaman. Using a mock community sequencing and a published 16S metagenomic dataset, we show here that SHAMAN allows to perform a complete meta-taxonomic analysis.",
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"study-abstract": "To study which genes are specifically induced during the different growth phases in toluene, which could indicate the changes in BTEX metabolism as well as the biological processes affected during the different growth phases, a controlled RNA-seq transcriptome analysis was carried out. Gene expression levels were analyzed from cultures upon inoculation (T0), after 4(T4) and 24(T24) hours after inoculation in minimal medium with toluene.",
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"study-abstract": "Entomopathogenic nematodes from the genus Steinernema are used in biological control of insect pests. The free form of the nematode (infective juvenile) is in closed symbiotic association with the intestinal bacteria Xenorhabdus (Enterobacteriaceae). In the well-studied Steinernema carpocapsae - Xenorhabdus nematophila couple, it was largely shown that the bacterial symbiont played an important role in the death of the insect and in the elimination of the microbial competitors inside the insect cadaver. However, in addition to symbiotic bacteria, other cultivable bacteria have been regularly isolated from infective juveniles nematodes.In this study,we used both culture-dependent and multigenic metabarcoding methods to obtain a comprehensive survey of S. carpocapsae bacterial microbiota. We used two markers, the V3-V4 region of the 16S rRNA gene and a region of the rpoB gene, for which a database was built. We identified a core-microbiota of about 10 OTUs that were present in more than 70% of the samples. Representative bacterial strains of the core-microbiota were tested for their insecticidal performances and their ability to produce antimicrobial molecules.",
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"secondary-accession": "ERP106234",
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"study-abstract": "All of the raw sequence data for the mock communities that have been sequenced by the Langille Lab.",
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"secondary-accession": "ERP022334",
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"study-abstract": "As part of ELIXIR project, six different semi-synthetic marine metagenomes were created to analyse and evaluate the available metagenomic tools/pipelines.",
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"last-update": "2017-04-06T15:08:48",
"secondary-accession": "ERP022257",
"centre-name": "RADBOUD UNIVERSITY NIJMEGEN",
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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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