Structure, function and diversity of the healthy human microbiome. | Sharpton Lab
Adolescent, Adult, Bacteria, Biodiversity, Ecosystem, Female, Health, Humans, Male, Metabolic Networks and Pathways, Metagenome ...http://sharptonlab.cgrb.oregonstate.edu/?q=node/35
A framework for human microbiome research. | Sharpton Lab
Adolescent, Adult, Bacteria, Female, Humans, Male, Metagenome, Metagenomics, Reference Standards, RNA, Ribosomal, 16S, ...http://sharptonlab.cgrb.oregonstate.edu/?q=node/36
Metagenome sequence of Elaphomyces granulatus from sporocarp tissue reveals Ascomycota ectomycorrhizal fingerprints of genome...
Metagenome sequence of Elaphomyces granulatus from sporocarp tissue reveals Ascomycota ectomycorrhizal fingerprints of genome ... Metagenome sequence of Elaphomyces granulatus from sporocarp tissue reveals Ascomycota ectomycorrhizal fingerprints of genome ...http://sharptonlab.cgrb.oregonstate.edu/?q=node/24
Interrelationship between gut microbiota composition an | Open-i
Metagenome/drug effects/physiology. *Mice. *Mice, Inbred C57BL. *Molecular Weight. *Prevotella/physiology ...https://openi.nlm.nih.gov/detailedresult.php?img=PMC3111466_pone.0020944.g006&req=4
RAPD Primer Design from Metagenomes 1.0 - RAPD Primer Design from Metagenomes (RPD-M) scans metagenome sequences identifying...
RAPD Primer Design from Metagenomes RPDM scans metagenome sequences identifying and determining relative frequency of candidate ... RAPD Primer Design from Metagenomes (RPD-M) scans metagenome sequences identifying and determining relative frequency of ...http://www.filetransit.com/view.php?id=215312
SciCafe: Mapping the Urban Microbiome, Genome, Metagenome
... by AMNH on 03/04/2015 11:15 am. ...https://www.amnh.org/explore/news-blogs/podcasts/scicafe-mapping-the-urban-microbiome-genome-metagenome
Los Alamos creates bioinformatics tool for metagenome analysis
Bioinformatics tool for metagenome analysis. Los Alamos creates bioinformatics tool for metagenome analysis. Scientists have ... In a paper this week in the journal Nucleic Acids Research, "Accurate read-based metagenome characterization using a ... metagenome datasets that can be used to re-validate any current or future tools; and 3) addresses the issue of false positives ... and then it classifies the individual metagenome sequences or "reads." They have established a unique method to query these ...http://lanl.gov/discover/news-release-archive/2015/March/03.18-bioinformatics-tool-for%20metagenome-analysis.php
Carnoules arsenic-contaminated mine drainage metagenome, Carnoules bin - Nucleotide - NCBI
Carnoules arsenic-contaminated mine drainage metagenome, Carnoules bin 1, Contig491a, whole genome shotgun sequence. GenBank: ... Carnoules arsenic-contaminated mine drainage metagenome, Carnoules bin 1, Contig... Carnoules arsenic-contaminated mine ... drainage metagenome, Carnoules bin 1, Contig491a, whole genome shotgun sequence. gi,318099972,emb,CABL01000009.1, ...https://www.ncbi.nlm.nih.gov/nuccore/318099972?report=genbank
Fast genome and metagenome distance estimation using MinHash
... 7th February 2015 - BioRxiv. Given a massive collection of ... to reduce large sequences to a representative sketch and rapidly estimate pairwise distances between genomes or metagenomes. ...https://nanoporetech.com/index.php/resource-centre/publications/fast-genome-and-metagenome-distance-estimation-using-minhash
2014) Metagenomes from two microbial consortia associated with Santa Barbara seep oil. Mar Genomics . 10.1016/j.margen.2014.06. ... 2014) Tackling soil diversity with the assembly of large, complex metagenomes. Proc Natl Acad Sci U S A 111(13), 4904-9. ... 2008) The airborne metagenome in an indoor urban environment. PLoS One 3(4), e1862. 10.1371/journal.pone.0001862. More Details ... 2012) IMG/M-HMP: a metagenome comparative analysis system for the Human Microbiome Project. PLoS One 7(7), e40151. 10.1371/ ...https://jgi.doe.gov/our-science/science-programs/metagenomics/metagenome-publications/
Advances in computational analysis of metagenome sequences - Davenport - 2012 - Environmental Microbiology - Wiley Online...
Davenport, C. F. and Tümmler, B. (2013), Advances in computational analysis of metagenome sequences. Environmental Microbiology ...http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2012.02843.x/references?globalMessage=0
Argonne Technology Aids Largest Metagenome Study to Date | Argonne National Laboratory
National Laboratory recently completed a study that compared more than 14 million microbial sequences from 90 metagenomes ... Using this database, the researchers then isolated matches between the metagenomes and the sequences in SEED. Up until the ... a high-throughput pipeline designed specifically for metagenome sequencing by researchers at Argonne. In order to make sense of ... Eventually the researchers found that more than 1 million sequences from the microbial metagenomes, and over 500,000 from the ...http://www.mcs.anl.gov/articles/argonne-technology-aids-largest-metagenome-study-date
Frontiers | Glucose-tolerant β-glucosidase retrieved from a Kusaya gravy metagenome | Microbiology
The metagenome was purified, fragmented by partial digestion with Sau3AI, and ligated into a p18GFP vector at the BamHI site, ... Glucose-tolerant β-glucosidase retrieved from a Kusaya gravy metagenome. Taku Uchiyama1, Katusro Yaoi1 and Kentaro Miyazaki1,2* ... Citation: Uchiyama T, Yaoi K and Miyazaki K (2015) Glucose-tolerant β-glucosidase retrieved from a Kusaya gravy metagenome. ... Uchiyama, T., and Watanabe, K. (2008). Substrate-induced gene expression (SIGEX) screening of metagenome libraries. Nat. Protoc ...https://www.frontiersin.org/articles/10.3389/fmicb.2015.00548/full
Denoising PCR-amplified metagenome data | BMC Bioinformatics | Full Text
DADA infers both the sample genotypes and error parameters that produced a metagenome data set. We demonstrate performance on ... For non-test metagenome data that is more diverse and less oversampled, we have seen evidence that using much larger values of ... There are two broad approaches to high-throughput sequencing of metagenomes: in amplicon sequencing (also called gene-centric ... Early studies using this approach on high-throughput metagenome data sets reported large numbers of low-abundance, previously ...https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-13-283
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NutNet soil metagenomes. Terrestrial ecosystems worldwide are receiving elevated inputs of nitrogen and recent studies suggest ... DAS Tool for Genome Reconstruction from Metagenomes. Through the JGI's Emerging Technologies Opportunity Program (ETOP), ... allowing them to reconstruct more near-complete genomes from soil metagenomes compared to other methods. The work was published ... effort will allow researchers to examine how experimental additions of nitrogen to grassland ecosystems affect soil metagenomes ...https://jgi.doe.gov/nutnet-soil-metagenomes/
Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes. - PubMed - NCBI
The Shotgun Metagenome Annotation Pipeline (ShotMAP) is an end-to-end metagenome annotation and analysis workflow. It takes as ... We identify best practices in metagenome annotation and use them to guide the development of the Shotgun Metagenome Annotation ... Optimal bit-score thresholds error for metagenomes in (C). (E) Relative abundance error for simulated metagenomes of varying ... Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes.. Nayfach S1, Bradley PH1, Wyman SK1, ...https://www.ncbi.nlm.nih.gov/pubmed/26565399?dopt=Abstract
Phylogenetic Diversity and Metabolic Potential Revealed in a Glacier Ice Metagenome
... in the glacial ice metagenome is higher than that of metagenomes with different temperature settings such as the metagenomes ... in the glacial metagenome was in the range of the values determined for the other metagenomes (lake in Antarctica, 1.53%; farm ... The fraction of genes in the category methane metabolism was higher in the glacial metagenome (0.63%) than in the metagenomes ... Phylogenetic Diversity and Metabolic Potential Revealed in a Glacier Ice Metagenome. † Carola Simon,1 Arnim Wiezer,2 Axel W. ...http://pubmedcentralcanada.ca/pmcc/articles/PMC2786415/
The Tree of Life: Open Metagenomics Highlight - Metagenome Annotation using massively parallel undergrads.
In it Pascal Hingamp et al discuss an Open Source, Open Science system for metagenome annotation (see PLoS Biology - Metagenome ... They do this as part of a course on metagenome annotation. And the software for running this is all Open Source and available. ...https://phylogenomics.blogspot.com/2008/11/open-metagenomics-highlight-metagenome.html
MetaSAMS--a novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome...
The capabilities of MetaSAMS are demonstrated for two metagenome datasets obtained from a biogas-producing microbial community ... To address current demands in metagenome data analyses, the novel platform MetaSAMS was developed. MetaSAMS automatically ... MetaSAMS--a novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome ... the first pipeline consists of three different classifiers performing the taxonomic profiling of metagenome sequences and (ii) ...https://www.ncbi.nlm.nih.gov/pubmed/23026555
Frontiers | Novel, Deep-Branching Heterotrophic Bacterial Populations Recovered from Thermal Spring Metagenomes | Microbiology
Recovery of Uncharacterized Bacterial Populations from Hot-Spring Metagenomes. The assembled metagenome sequence from Octopus ... Recovery of Uncharacterized Bacterial Populations from Hot-Spring Metagenomes. Details of site sampling, metagenome sequencing ... A 953 bp 16S rRNA gene present in the Octopus Spring metagenome (but not included in the T3 de novo assembly due to length) was ... Inskeep, W. P., Jay, Z. J., Tringe, S. G., Herrgård, M. J., Rusch, D. B., and YNP Metagenome Project Steering Committee et al ...https://www.frontiersin.org/articles/10.3389/fmicb.2016.00304/full
Big Data, Evolution, and Metagenomes: Predicting Disease from Gut Microbiota Codon Usage Profiles | SpringerLink
Human metagenome Cirrhosis Translational optimization Enrichment analysis Variable selection Random forests This is a preview ... Franzosa EA, Morgan XC, Segata N et al (2014) Relating the metatranscriptome and metagenome of the human gut. Proc Natl Acad ... Karlsson FH, Fåk F, Nookaew I et al (2012) Symptomatic atherosclerosis is associated with an altered gut metagenome. Nat Commun ... Fabijanić M., Vlahoviček K. (2016) Big Data, Evolution, and Metagenomes: Predicting Disease from Gut Microbiota Codon Usage ...https://link.springer.com/protocol/10.1007/978-1-4939-3572-7_26
Selection of Appropriate Metagenome Taxonomic Classifiers for Ancient Microbiome Research | mSystems
Selection of Appropriate Metagenome Taxonomic Classifiers for Ancient Microbiome Research. Irina M. Velsko, Laurent A. F. ... Selection of Appropriate Metagenome Taxonomic Classifiers for Ancient Microbiome Research. Irina M. Velsko, Laurent A. F. ... Selection of Appropriate Metagenome Taxonomic Classifiers for Ancient Microbiome Research. Irina M. Velsko, Laurent A. F. ... Thirty-nine total metagenomes were simulated as follows: 40-genome even distribution of ancient (10) and modern (3), 100-genome ...https://msystems.asm.org/content/3/4/e00080-18
Mash: fast genome and metagenome distance estimation using MinHash | Genome Biology | Full Text
We have found the parameters k = 21 and s = 1000 give accurate estimates in most cases (including metagenomes), so this is set ... Metagenomic clustering of ocean and human metagenomes using Mash. a Comparison of Global Ocean Survey (GOS) clustering using ... Mash enables the comparison and clustering of whole genomes and metagenomes on a massive scale. Potential applications include ... Rasheed Z, Rangwala H. A Map-Reduce Framework for Clustering Metagenomes. In: 2013 IEEE International Symposium on Parallel & ...https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0997-x
Frontiers | Highly Effective Inhibition of Biofilm Formation by the First Metagenome-Derived AI-2 Quenching Enzyme |...
2011b). BpiB05, a novel metagenome-derived hydrolase acting on N-acylhomoserine lactones. J. Biotechnol. 155, 86-94. doi: ... Highly Effective Inhibition of Biofilm Formation by the First Metagenome-Derived AI-2 Quenching Enzyme. Nancy Weiland-Bräuer1, ... Screening of soil metagenomes mainly extended the diversity of AHL-lactonases by identifying the metagenomic enzymes QlcA, ... 2007). Selection and characterization of forest soil metagenome genes encoding lipolytic enzymes. J. Microbiol. Biotechnol. 17 ...https://www.frontiersin.org/articles/10.3389/fmicb.2016.01098/full
The environment shapes microbial enzymes: five cold-active and salt-resistant carboxylesterases from marine metagenomes |...
Marine metagenome Metagenomic library Esterase Cold adaptation Salt resistance Polyester hydrolysis Electronic supplementary ... Kourist R, Hari Krishna S, Patel JS, Bartnek F, Hitchman TS, Weiner DP, Bornscheuer UT (2007) Identification of a metagenome- ... Steele HL, Jaeger KE, Daniel R, Streit WR (2009) Advances in recovery of novel biocatalysts from metagenomes. J Mol Microbiol ... The environment shapes microbial enzymes: five cold-active and salt-resistant carboxylesterases from marine metagenomes. ...https://link.springer.com/article/10.1007%2Fs00253-014-6038-3