*  Microbial Influences in Cardio-Metabolic Diseases | The New York Academy of Sciences
... including 360 fully assembled microbial genomes comprised of 7 million microbial genes, as well as 325 serum metabolites, and ... Microbial Influences in Cardio-Metabolic Diseases. Academy eBriefings. 2016. Available at: www.nyas.org/Metabolic2016-eB ... In mice, there were significant microbial differences in subjects fed cooked or raw sweet potato diets, likely due to the ... On November 3, the Microbiome Science Discussion Group at the New York Academy of Sciences presented Microbial Influences in ...
  https://www.nyas.org/ebriefings/microbial-influences-in-cardio-metabolic-diseases/
*  Whole-genome assembly of Akkermansia muciniphila sequenced directly from human stool | Biology Direct | Full Text
We obtained draft genome of the Akkermansia muciniphila strain Urmite with only 56 gaps. The absence of particular metabolic ... We used a mapping method consisting of aligning metagenomic sequencing reads against the reference genome of the Akkermansia ... This work highlights the potential of metagenomics to facilitate the assembly of genomes directly from human stool. This ... Here, we propose an original approach of genome sequencing for Akkermansia muciniphila directly from the stool sample collected ...
  https://0-biologydirect-biomedcentral-com.brum.beds.ac.uk/articles/10.1186/s13062-015-0041-1
*  Frontiers | Novel, Deep-Branching Heterotrophic Bacterial Populations Recovered from Thermal Spring Metagenomes | Microbiology
... and harbor deeply-branching lineages that provide insight regarding the nature of early microbial life. We characterized ... and harbor deeply-branching lineages that provide insight regarding the nature of early microbial life. We characterized ... Metagenomes were assembled using the Celera assembler; automated tools in the Integrated Microbial Genomes server (IMG; ... coupled with genome coverage's of ~2-3.5x and robustness of Sanger sequencing methodologies indicate that these genomes were ...
  https://www.frontiersin.org/articles/10.3389/fmicb.2016.00304/full
*  Metagenome Publications
... that automatically groups large genomic fragments assembled from metagenome sequences to reconstruct single microbial genomes. ... 2013) Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. J Comput Biol 20(10), 714-37. 10.1089/cmb ... 2015) The integrated microbial genome resource of analysis. Methods Mol Biol 1231, 289-95. 10.1007/978-1-4939-1720-4_18. More ... 2015) Ten Years of Maintaining and Expanding a Microbial Genome and Metagenome Analysis System. Trends Microbiol 23(11), 730-41 ...
  https://jgi.doe.gov/our-science/science-programs/metagenomics/metagenome-publications/
*  Inference of Microbial Recombination Rates from Metagenomic Data
Projects that sample environments dominated by only a few microbial "species" are able to assemble near-complete genomes [13],[ ... Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature. 2004;428:37-43. [ ... Inference of a genome-wide, fine-scale recombination map requires both extensive genome-wide sampling of the genetic diversity ... Despite our motivation from microbial populations, our method itself makes no assumptions inherent to microbial populations. ...
  http://pubmedcentralcanada.ca/pmcc/articles/PMC2745702/?lang=en-ca
*  Future challenges to microbial food safety.
... in molecular techniques make it possible to rapidly assemble information on the genome of various isolates of microbial species ... as well as to models that predict microbial behavior. In addition, the increasing complexity of the global food systems ...
  https://dspace.library.uu.nl/handle/1874/191401
*  Frontiers | Single gene-based distinction of individual microbial genomes from a mixed population of microbial cells |...
Furthermore, the detection of low copy targets such as genes present in single copies in the microbial genomes, has remained ... of MC1061 genomes can be differentiated using this method. Using a spiked sediment microbial sample, we demonstrate that the ... of MC1061 genomes can be differentiated using this method. Using a spiked sediment microbial sample, we demonstrate that the ... of a single copy of a tetracycline resistance gene per genome, we demonstrate that XL1 genomes present at 0.1% ...
  https://www.frontiersin.org/articles/10.3389/fmicb.2015.00195/full
*  Viral dark matter and virus-host interactions resolved from publicly available microbial genomes | eLife
VirSorter revealed 12,498 viral genome sequences that expand the map of the global virosphere and whose analyses improve ... genome fragments assembled outside of the host chromosome (i.e., no microbial gene was detected on the contig, Figure 3A, ... all microbial genomes, (ii) only genomes from a different species than the actual host (i.e., the genome in which the viral ... all microbial genomes, (ii) excluding specifically all genomes from the host species, and (iii) excluding all genomes from the ...
  https://elifesciences.org/articles/08490
*  Frontiers | The Microbial Community of a Passive Biochemical Reactor Treating Arsenic, Zinc, and Sulfate-Rich Seepage |...
Organic matter degradation is one driver for shifting the microbial community composition and therefore possibly the ... Organic matter degradation is one driver for shifting the microbial community composition and therefore possibly the ... of a field-based biochemical reactor that had been removing zinc and arsenic for over six years revealed that the microbial ... of a field-based biochemical reactor that had been removing zinc and arsenic for over six years revealed that the microbial ...
  https://www.frontiersin.org/articles/10.3389/fbioe.2015.00027/full
*  ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads
Our test cases consist of five finished and homozygous microbial genomes. Importantly, finished genome sequences represent an ... The five genomes were assembled on a 16-processor Dell server having 128 GB of memory. Some of the code is parallelized. The ... ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads. Iain MacCallum,1 Dariusz ... Using 36 base (fragment) and 26 base (jumping) reads from five microbial genomes of varied GC composition and sizes up to 40 Mb ...
  http://pubmedcentralcanada.ca/pmcc/articles/PMC2784318/?lang=en-ca
*  Social evolution of microbial heavy metal bioremediation | AXA Research Fund
... we have assembled a highly interdisciplinary team specializing in high throughput genome sequencing, microbial experimental ... Moreover, the study will be the first application of the rapidly expanding field of microbial social evolution to a real ... Maximising microbial siderophore production will therefore greatly increase the success of phytoremediation.. Unfortunately, ... Heavy metals are more readily taken up by plants when bound to microbial siderophores, and siderophore production in ...
  https://www.axa-research.org/en/projects/angus-buckling
*  Developing an Ice Plant Gene Atlas - DOE Joint Genome Institute
... that automatically groups large genomic fragments assembled from metagenome sequences to reconstruct single microbial genomes. ... From Genome to Watershed Scales. Microbial Functions at Soil-Aquatic Interfaces. DNA Methylation Role in Basal Fungi. Fungal ... Since I am just learning about the bioinformatics involved in assembling a genome, it's great that they have those online tools ... Better Microbial Genome Binning with MetaBAT. An automated tool called MetaBAT ...
  https://jgi.doe.gov/developing-ice-plant-gene-atlas/
*  Identification and characterization of the polyketide synthase involved in ochratoxin A biosynthesis in Aspergillus carbonarius...
... that automatically groups large genomic fragments assembled from metagenome sequences to reconstruct single microbial genomes. ... Since I am just learning about the bioinformatics involved in assembling a genome, it's great that they have those online tools ... Better Microbial Genome Binning with MetaBAT. An automated tool called MetaBAT ... Scaling Microbial Genomics Discoveries for Ecosystem Modeling. In showing how microbial metabolism is regulated by coupled ...
  https://jgi.doe.gov/publication/identification-and-characterization-of-the-polyketide-synthase-involved-in-ochratoxin-a-biosynthesis-in-aspergillus-carbonarius/
*  Finding A New Major Gene Expression Regulator in Fungi - DOE Joint Genome Institute
... that automatically groups large genomic fragments assembled from metagenome sequences to reconstruct single microbial genomes. ... Since I am just learning about the bioinformatics involved in assembling a genome, it's great that they have those online tools ... Better Microbial Genome Binning with MetaBAT. An automated tool called MetaBAT ... Many of the fungal genomes used in the study were sequenced as part of the DOE JGI's 1000 Fungal Genomes initiative aimed at ...
  https://jgi.doe.gov/finding-major-gene-expression-regulator-fungi/
*  Bay Area Plant Microbe Interaction Symposium II
... that automatically groups large genomic fragments assembled from metagenome sequences to reconstruct single microbial genomes. ... Microbial Genome Reannotation Workshop. *Application of High Performance Computing to the DOE Joint Genomic Institute's Data ... Since I am just learning about the bioinformatics involved in assembling a genome, it's great that they have those online tools ... Better Microbial Genome Binning with MetaBAT. An automated tool called MetaBAT ...
  https://jgi.doe.gov/past-events/bay-area-plant-microbe-interaction-symposium-ii/
*  DOE Joint Genome Institute: A DOE Office of Science User Facility of Lawrence Berkeley National Laboratory
... that automatically groups large genomic fragments assembled from metagenome sequences to reconstruct single microbial genomes. ... Since I am just learning about the bioinformatics involved in assembling a genome, it's great that they have those online tools ... Better Microbial Genome Binning with MetaBAT. An automated tool called MetaBAT ... Scaling Microbial Genomics Discoveries for Ecosystem Modeling. In showing how microbial metabolism is regulated by coupled ...
  https://jgi.doe.gov/
*  The Genomes of the Fungal Plant Pathogens Cladosporium fulvum and Dothistroma septosporum Reveal Adaptation to Different Hosts...
... that automatically groups large genomic fragments assembled from metagenome sequences to reconstruct single microbial genomes. ... Since I am just learning about the bioinformatics involved in assembling a genome, it's great that they have those online tools ... The genomes of these fungi have a similar set of genes (70% of gene content in both genomes are homologs), but differ ... Better Microbial Genome Binning with MetaBAT. An automated tool called MetaBAT ...
  https://jgi.doe.gov/publication/the-genomes-of-the-fungal-plant-pathogens-cladosporium-fulvum-and-dothistroma-septosporum-reveal-adaptation-to-different-hosts-and-lifestyles-but-also-signatures-of-common-ancestry/
*  Establishing Standard Definitions for Genome Sequences - DOE Joint Genome Institute
... that automatically groups large genomic fragments assembled from metagenome sequences to reconstruct single microbial genomes. ... Since I am just learning about the bioinformatics involved in assembling a genome, it's great that they have those online tools ... Better Microbial Genome Binning with MetaBAT. An automated tool called MetaBAT ... This is of even greater concern for reference genome sequences, such as those genome projects conducted in support of the U.S. ...
  https://jgi.doe.gov/news_09_10_08/
*  Untangling Whole Genomes Of Individual Species From A Microbial Mix - Redorbit
... while simultaneously assembling their genome sequences," says co-author Maitreya Dunham, a biologist at the University of ... Untangling Whole Genomes Of Individual Species From A Microbial Mix. by editor ... Washington's Department of Genome Sciences.. Microbial communities, whether sampled from the ocean floor or a human mouth, are ... The work is described in an article published May 22 in Early Online form in the journal G3: Genes,Genomes,Genetics, published ...
  http://www.redorbit.com/news/science/1113154606/untangling-whole-genomes-of-individual-species-from-a-microbial-mix/
*  Aerobic proteobacterial methylotrophs in Movile Cave: genomic and metagenomic analyses | Microbiome | Full Text
The assembled draft genome was uploaded to Intergrated Microbial Genome (IMG) (www.img.jgi.doe.gov) for downstream analysis. ... Genome assembly of the isolate LWB was performed as described in [21]. Briefly, the raw sequences were assembled using a range ... LWB and draft genome sequence. Microbial mat with lake water samples collected from Movile Cave were used for isolating MOB in ... LWB from Movile Cave microbial mats and preliminary insights on its metabolic potential from the draft genome sequence. We also ...
  https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-017-0383-2
*  The present and future of de novo whole-genome assembly, Briefings in Bioinformatics | 10.1093/bib/bbw096 | DeepDyve
"The present and future of de novo whole-genome assembly, Briefings in Bioinformatics" on DeepDyve, the largest online rental ... Evaluation and validation of assembling corrected pacbio long reads for microbial genome completion via hybrid approaches. PLoS ... Evaluation and validation of assembling corrected pacbio long reads for microbial genome completion via hybrid approaches. PLoS ... Reducing assembly complexity of microbial genomes with single-molecule sequencing. Genome Biol 2013; 14: R101. Google Scholar ...
  https://www.deepdyve.com/lp/ou_press/the-present-and-future-of-de-novo-whole-genome-assembly-gv0src80eR
*  Untangling whole genomes of individual species from a microbial mix
... while simultaneously assembling their genome sequences," says co-author Maitreya Dunham, a biologist at the University of ... Further reports about: , GSA , Genetics , Genome , Untangling , analyze , genomes , microbes , microbial , sequences , species ... Untangling whole genomes of individual species from a microbial mix. 26.05.2014 ... Washington's Department of Genome Sciences. Microbial communities, whether sampled from the ocean floor or a human mouth, are ...
  http://www.innovations-report.com/html/reports/life-sciences/untangling-whole-genomes-of-individual-species-from-a-microbial-mix.html
*  Researchers sequence and assemble first full genome of a living organism using technology the size
... of smartphone. ... development and using shared computing resources on the Medical Research Council funded Cloud Infrastructure for Microbial ... Researchers sequence and assemble first full genome of a living organism using technology the size of smartphone ... "Long reads are necessary to assemble the most repetitive parts of genomes but we need a lot of reads if we want to sequence ...
  https://www.newswire.ca/news-releases/researchers-sequence-and-assemble-first-full-genome-of-a-living-organism-using-technology-the-size-of-smartphone-517940221.html
*  Frontiers | Metagenomic Analysis Reveals Symbiotic Relationship among Bacteria in Microcystis-Dominated Community | Microbiology
Individual genomes of the colony bacteria were obtained and they provided valuable insights into microbial community structures ... Individual genomes of the colony bacteria were obtained and they provided valuable insights into microbial community structures ... We found that the method was effective in grouping sequences and it did not require reference genome sequence. ... We found that the method was effective in grouping sequences and it did not require reference genome sequence. ...
  https://www.frontiersin.org/articles/10.3389/fmicb.2016.00056/full
*  More than Six Million New Genes, Thousands of New Protein Families, and Incredible Degree of Microbial Diversity Discovered...
... enabled researchers to assemble very large segments of DNA from the abundant but previously hard to analyze genomes of ... One comparative genomic method termed "fragment recruitment," allowed researchers to look at genome structure, microbial ... The availability of the GOS metagenomic data along with other large microbial genome data sets is enabling more research into ... "Given the findings, it's clear that we've only begun to scratch the surface of understanding the microbial world around us." ...
  https://www.jcvi.org/more-six-million-new-genes-thousands-new-protein-families-and-incredible-degree-microbial-diversity