Meta-analyses of environmental sequence data identify anoxia and salinity as parameters shaping ciliate communities

2012 ◽  
Vol 10 (3) ◽  
pp. 277-288 ◽  
Author(s):  
Dominik Forster ◽  
Anke Behnke ◽  
Thorsten Stoeck
Keyword(s):  
Sequence Data ◽  
Environmental Sequence ◽  
Meta Analyses

scholarly journals Advantages and limits of metagenomic assembly and binning of a giant virus

2020 ◽  
Author(s):  
Frederik Schulz ◽  
Julien Andreani ◽  
Rania Francis ◽  
Jacques Yaacoub Bou Khalil ◽  
Janey Lee ◽  
...  
Keyword(s):  
Size Range ◽  
Sequence Data ◽  
Giant Virus ◽  
Sample Matrix ◽  
Environmental Sequence ◽  
Successful Recovery ◽  
Metagenome Assembly ◽  
Giant Viruses ◽  
Metagenomic Assembly ◽  
Virus Genomes

AbstractGiant viruses have large genomes, often within the size range of cellular organisms. This distinguishes them from most other viruses and demands additional effort for the successful recovery of their genomes from environmental sequence data. Here we tested the performance of genome-resolved metagenomics on a recently isolated giant virus, Fadolivirus, by spiking it into an environmental sample from which two other giant viruses were isolated. At high spike-in levels, metagenome assembly and binning led to the successful genomic recovery of Fadolivirus from the sample. A complementary survey of viral hallmark genes indicated the presence of other giant viruses in the sample matrix, but did not detect the two isolated from this sample. Our results indicate that genome-resolved metagenomics is a valid approach for the recovery of near-complete giant virus genomes given that sufficient clonal particles are present. Our data also underline that a vast majority of giant viruses remain currently undetected, even in an era of terabase-scale metagenomics.

scholarly journals A Need for Improved Cellulase Identification from Metagenomic Sequence Data

2020 ◽  
Vol 87 (1) ◽  
Author(s):  
Rebecca Co ◽  
Laura A. Hug
Keyword(s):  
Sequence Data ◽  
Industrial Applications ◽  
Data Sets ◽  
Metagenomic Sequence ◽  
Environmental Sequence ◽  
Sequencing Technologies ◽  
Current Classification ◽  
Applied Microbiology ◽  
Environmental Surveys ◽  
Metagenomic Sequence Data

ABSTRACT Improved sequencing technologies and the maturation of metagenomic approaches allow the identification of gene variants with potential industrial applications, including cellulases. Cellulase identification from metagenomic environmental surveys is complicated by inconsistent nomenclature and multiple categorization systems. Here, we summarize the current classification and nomenclature systems, with recommendations for improvements to these systems. Addressing the issues described will strengthen the annotation of cellulose-active enzymes from environmental sequence data sets—a rapidly growing resource in environmental and applied microbiology.

scholarly journals Ontology-Enriched Specifications Enabling Findable, Accessible, Interoperable, and Reusable Marine Metagenomic Datasets in Cyberinfrastructure Systems

2021 ◽  
Vol 12 ◽  
Author(s):  
Kai L. Blumberg ◽  
Alise J. Ponsero ◽  
Matthew Bomhoff ◽  
Elisha M. Wood-Charlson ◽  
Edward F. DeLong ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Sequence Data ◽  
Technical Specification ◽  
Global Ocean ◽  
Metagenomic Data ◽  
Use Of Data ◽  
Machine Systems ◽  
Future Direction ◽  
Meta Analyses ◽  
Machine Readable

Marine microbial ecology requires the systematic comparison of biogeochemical and sequence data to analyze environmental influences on the distribution and variability of microbial communities. With ever-increasing quantities of metagenomic data, there is a growing need to make datasets Findable, Accessible, Interoperable, and Reusable (FAIR) across diverse ecosystems. FAIR data is essential to developing analytical frameworks that integrate microbiological, genomic, ecological, oceanographic, and computational methods. Although community standards defining the minimal metadata required to accompany sequence data exist, they haven’t been consistently used across projects, precluding interoperability. Moreover, these data are not machine-actionable or discoverable by cyberinfrastructure systems. By making ‘omic and physicochemical datasets FAIR to machine systems, we can enable sequence data discovery and reuse based on machine-readable descriptions of environments or physicochemical gradients. In this work, we developed a novel technical specification for dataset encapsulation for the FAIR reuse of marine metagenomic and physicochemical datasets within cyberinfrastructure systems. This includes using Frictionless Data Packages enriched with terminology from environmental and life-science ontologies to annotate measured variables, their units, and the measurement devices used. This approach was implemented in Planet Microbe, a cyberinfrastructure platform and marine metagenomic web-portal. Here, we discuss the data properties built into the specification to make global ocean datasets FAIR within the Planet Microbe portal. We additionally discuss the selection of, and contributions to marine-science ontologies used within the specification. Finally, we use the system to discover data by which to answer various biological questions about environments, physicochemical gradients, and microbial communities in meta-analyses. This work represents a future direction in marine metagenomic research by proposing a specification for FAIR dataset encapsulation that, if adopted within cyberinfrastructure systems, would automate the discovery, exchange, and re-use of data needed to answer broader reaching questions than originally intended.

scholarly journals Extracting allelic read counts from 250,000 human sequencing runs in Sequence Read Archive

2018 ◽  
Author(s):  
Brian Tsui ◽  
Michelle Dow ◽  
Dylan Skola ◽  
Hannah Carter
Keyword(s):  
Genomic Sequence ◽  
Sequence Data ◽  
Rna Seq ◽  
Dna And Rna ◽  
Human Sequence ◽  
Sequence Read Archive ◽  
Sequencing Library ◽  
Ncbi Dbsnp ◽  
Data Worth ◽  
Meta Analyses

The Sequence Read Archive (SRA) contains over one million publicly available sequencing runs from various studies using a variety of sequencing library strategies. These data inherently contain information about underlying genomic sequence variants which we exploit to extract allelic read counts on an unprecedented scale. We reprocessed over 250,000 human sequencing runs (>1000 TB data worth of raw sequence data) into a single unified dataset of allelic read counts for nearly 300,000 variants of biomedical relevance curated by NCBI dbSNP, where germline variants were detected in a median of 912 sequencing runs, and somatic variants were detected in a median of 4,876 sequencing runs, suggesting that this dataset facilitates identification of sequencing runs that harbor variants of interest. Allelic read counts obtained using a targeted alignment were very similar to read counts obtained from whole genome alignment. Analyzing allelic read count data for matched DNA and RNA samples from tumors, we find that RNA-seq can also recover variants identified by WXS, suggesting that reprocessed allelic read counts can support variant detection across different library strategies in SRA. This study provides a rich database of known human variants across SRA samples that can support future meta-analyses of human sequence variation.

Modeling Taxa-Abundance Distributions in Microbial Communities using Environmental Sequence Data

2006 ◽  
Vol 53 (3) ◽  
pp. 443-455 ◽  
Author(s):  
William T. Sloan ◽  
Stephen Woodcock ◽  
Mary Lunn ◽  
Ian M. Head ◽  
Thomas P. Curtis
Keyword(s):  
Microbial Communities ◽  
Sequence Data ◽  
Environmental Sequence

Associations of coronary and peripheral artery disease with presence, expansion, and rupture of abdominal aortic aneurysm – a grin without a cat!

VASA ◽  
2017 ◽  
Vol 46 (3) ◽  
pp. 151-158 ◽  
Author(s):  
Hisato Takagi ◽  
Takuya Umemoto
Keyword(s):  
Abdominal Aortic Aneurysm ◽  
Aortic Aneurysm ◽  
Peripheral Artery Disease ◽  
Literature Search ◽  
Systematic Literature Search ◽  
Peripheral Artery ◽  
Epidemiological Evidence ◽  
Abdominal Aortic ◽  
Artery Disease ◽  
Meta Analyses

Abstract. Both coronary and peripheral artery disease are representative atherosclerotic diseases, which are also known to be positively associated with presence of abdominal aortic aneurysm. It is still controversial, however, whether coronary and peripheral artery disease are positively associated with expansion and rupture as well as presence of abdominal aortic aneurysm. In the present article, we overviewed epidemiological evidence, i. e. meta-analyses, regarding the associations of coronary and peripheral artery disease with presence, expansion, and rupture of abdominal aortic aneurysm through a systematic literature search. Our exhaustive search identified seven meta-analyses, which suggest that both coronary and peripheral artery disease are positively associated with presence of abdominal aortic aneurysm, may be negatively associated with expansion of abdominal aortic aneurysm, and might be unassociated with rupture of abdominal aortic aneurysm.

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