Search results for "metagenomic"
showing 10 items of 177 documents
Bacterial Community Structure of an IFAS-MBRs Wastewater Treatment Plant
2017
TIn this work, the bacterial community putatively involved in BNR events of a UCT-MBMBR pilot plant was elucidated by both culture-dependent and metagenomics DNA analyses. The presence of bacterial isolates belonging to Bacillus (in the anoxic compartment) and to Acinetobacter, Stenotrophomonas, Rhodococcus, Escherichia and Aeromonas (in the aerobic compartment) is in agreement with the nitrification/denitrification processes observed in the plant. Moreover, the study of bacterial community structure by NGS revealed a microbial diversity suggesting a biochemical complexity which can be further explored and exploited to improve UCT-MBMBR plant performance.
Microbial Diversity in the Midguts of Field and Lab-Reared Populations of the European Corn Borer Ostrinia nubilalis
2011
Background: Insects are associated with microorganisms that contribute to the digestion and processing of nutrients. The European Corn Borer (ECB) is a moth present world-wide, causing severe economical damage as a pest on corn and other crops. In the present work, we give a detailed view of the complexity of the microorganisms forming the ECB midgut microbiota with the objective of comparing the biodiversity of the midgut-associated microbiota and explore their potential as a source of genes and enzymes with biotechnological applications. Methodological/Principal Findings: A high-throughput sequencing approach has been used to identify bacterial species, genes and metabolic pathways, parti…
Big Data in metagenomics: Apache Spark vs MPI.
2020
The progress of next-generation sequencing has lead to the availability of massive data sets used by a wide range of applications in biology and medicine. This has sparked significant interest in using modern Big Data technologies to process this large amount of information in distributed memory clusters of commodity hardware. Several approaches based on solutions such as Apache Hadoop or Apache Spark, have been proposed. These solutions allow developers to focus on the problem while the need to deal with low level details, such as data distribution schemes or communication patterns among processing nodes, can be ignored. However, performance and scalability are also of high importance when…
Novel virocell metabolic potential revealed in agricultural soils by virus-enriched soil metagenome analysis
2021
International audience; Viruses are now recognized as important players in microbial dynamics and biogeochemical cycles in the oceans. Yet, compared with aquatic ecosystems, virus discovery in terrestrial ecosystems has been challenging partly due to the inherent complexity of soils. To expand our understanding of soil viruses and their putative contributions to soil microbial processes, we analysed metagenomes of community-level virus-enriched suspensions by tangential flow filtration obtained from two French agricultural soils. We found viral sequences representing a total of 239 viral operational taxonomic units that corresponded to 29.5% of the mapping reads in the metagenomic datasets.…
LSC Abstract – Functional metagenomics of respiratoy microbiome in exacerbated COPD
2015
Background: The course of COPD is frequently aggravated by exacerbations. New molecular techniques have suggested that many bacterial groups, not only the common COPD pathogens, could trigger the exacerbations. Objective: to analyze the microbial community and the gene content of samples obtained during stability and exacerbation of COPD patients. Method: 16S rRNA was pyrosequenced to obtain the taxonomic information. The metabolic information was obtained with the Metagenomics RAST server (MG-RAST) with KEGG database. Results: 8 severe COPD patients were included. At genus level, 68 different OTUs were found. No significant differences in the relative abundance of any of the detected gener…
CRiSPy-CUDA: Computing Species Richness in 16S rRNA Pyrosequencing Datasets with CUDA
2011
Pyrosequencing technologies are frequently used for sequencing the 16S rRNA marker gene for metagenomic studies of microbial communities. Computing a pairwise genetic distance matrix from the produced reads is an important but highly time consuming task. In this paper, we present a parallelized tool (called CRiSPy) for scalable pairwise genetic distance matrix computation and clustering that is based on the processing pipeline of the popular ESPRIT software package. To achieve high computational efficiency, we have designed massively parallel CUDA algorithms for pairwise k-mer distance and pairwise genetic distance computation. We have also implemented a memory-efficient sparse matrix clust…
Insights into the annotated genome sequence of Methanoculleus bourgensis MS2(T), related to dominant methanogens in biogas-producing plants
2014
The final step of the biogas production process, the methanogenesis, is frequently dominated by members of the genus Methanoculleus. In particular, the species Methanoculleus bourgensis was identified to play a role in different biogas reactor systems. The genome of the type strain M. bourgensis MS2(T), originally isolated from a sewage sludge digestor, was completely sequenced to analyze putative adaptive genome features conferring competitiveness within biogas reactor environments to the strain. Sequencing and assembly of the M. bourgensis MS2(T) genome yielded a chromosome with a size of 2,789,773 bp. Comparative analysis of M. bourgensis MS2(T) and Methanoculleus marisnigri JR1 revealed…
PVAmpliconFinder: a workflow for the identification of human papillomaviruses from high-throughput amplicon sequencing
2019
Abstract Background The detection of known human papillomaviruses (PVs) from targeted wet-lab approaches has traditionally used PCR-based methods coupled with Sanger sequencing. With the introduction of next-generation sequencing (NGS), these approaches can be revisited to integrate the sequencing power of NGS. Although computational tools have been developed for metagenomic approaches to search for known or novel viruses in NGS data, no appropriate tool is available for the classification and identification of novel viral sequences from data produced by amplicon-based methods. Results We have developed PVAmpliconFinder, a data analysis workflow designed to rapidly identify and classify kno…
Study of the Viral and Microbial Communities Associated With Crohn's Disease: A Metagenomic Approach
2013
OBJECTIVES: This study aimed to analyze and compare the diversity and structure of the viral and microbial communities in fecal samples from a control group of healthy volunteers and from patients affected by Crohn's disease (CD). METHODS: Healthy adult controls (n=8) and patients affected by ileocolic CD (n=11) were examined for the viral and microbial communities in their feces and, in one additional case, in the intestinal tissue. Using two different approaches, we compared the viral and microbial communities in several ways: by group (patients vs. controls), entity (viruses vs. bacteria), read assembly (unassembled vs. assembled reads), and methodology (our approach vs. an existing pipe…
Metagenomic dynamics in Olea europaea after root damage and Verticillium dahliae infection
2019
AbstractThe olive tree is of particular economic interest in the Mediterranean basin. Researchers have conducted several studies on one of the most devastating disorders affecting this tree, the Verticillium wilt of olive, which causes significant economic damage in numerous areas of this crop. We have analyzed the temporal metagenomic samples of a transcriptomic study in Olea europaea roots and leaves after root-damage and after a root Verticillium dahliae infection (Jimenez-Ruiz et al. 2017). Our results indicate that this infection, although led by Verticillium, is driven not by a single species but by a polymicrobial community, including their natural endophytes, which acts as a consort…