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*  Microbiology Society Journals | Lactobacillus micheneri sp. nov., Lactobacillus timberlakei sp. nov. and Lactobacillus quenuiae...
19. Coil D, Jospin G, Darling AE. A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data. ... Microbial species delineation using whole genome sequences. Nucleic Acids Res 2015;43:6761-6771 [CrossRef][PubMed]. [Google ... 21. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the ... 7. Anderson KE, Sheehan TH, Mott BM, Maes P, Snyder L et al. Microbial ecology of the hive and pollination landscape: bacterial ...
  http://ijs.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.002758
*  Microbiology Society Journals | Campylobacter hepaticus sp. nov., isolated from chickens with spotty liver disease
Coil D., Jospin G., Darling A. E..( 2015;). A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq ... The GenBank/EMBL/DDBJ/PIR accession number for the whole genome shotgun project for Campylobacter hepaticus sp. nov. NCTC 13823 ... DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. . Int J Syst Evol Microbiol57:81--91 ...
  http://ijs.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.001383
*  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/
*  The advantages of SMRT sequencing | Genome Biology | Full Text
... detection and high accuracy make SMRT a useful technology and an ideal approach to the complete sequencing of small genomes. ... Koren et al. [6] showed that most microbial genomes could be assembled into a single contig per chromosome with this approach; ... The resultant assembled (epi)genomes would be inherently more valuable: the usefulness of a closed genome with associated ... finished microbial genome assemblies from long-read SMRT sequencing data.Nat Methods 2013, 10:563-569.View ArticlePubMedGoogle ...
  https://genomebiology.biomedcentral.com/articles/10.1186/gb-2013-14-6-405
*  Publications
Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes." ... "Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea ( ... "Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. ... "Community-wide analysis of microbial genome sequence signatures." Genome Biol, 10(8), R85. ...
  http://www.mbl.edu/jbpc/publicationsparentpage/
*  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
*  Metagenomic discovery of biomass-degrading genes and genomes from cow rumen
We also assembled 15 uncultured microbial genomes, which were validated by complementary methods including single-cell genome ... The microbial pan-genome.. Medini D, Donati C, Tettelin H, Masignani V, Rappuoli R., Curr. Opin. Genet. Dev. 15(6), 2005 PMID: ... Assembling the marine metagenome, one cell at a time.. Woyke T, Xie G, Copeland A, Gonzalez JM, Han C, Kiss H, Saw JH, Senin P ... Partial genome assembly for a candidate division OP11 single cell from an anoxic spring (Zodletone Spring, Oklahoma).. Youssef ...
  https://pub.uni-bielefeld.de/publication/1991643
*  Distilled single-cell genome sequencing and de novo assembly for sparse microbial communities. - PubMed - NCBI
Here, we present a novel divide and conquer method to sequence and de novo assemble all distinct genomes present in a microbial ... Distilled single-cell genome sequencing and de novo assembly for sparse microbial communities.. Taghavi Z1, Movahedi NS, ... Identification of every single genome present in a microbial sample is an important and challenging task with crucial ... Distilled single-cell genome sequencing and de novo assembly for sparse microbial communities ...
  https://www.ncbi.nlm.nih.gov/pubmed/23918251
*  Smallest life forms have smallest working CRISPR system | Research UC Berkeley
... of microbial genomes and metagenomes assembled over the past 15 years by colleagues at the Department of Energy's Joint Genome ... The Integrated Microbial Genomes & Microbiomes (IMG/M) system is the world's largest collection of microbial genes, currently ... The smallest known CRISPR gene-editing system was found in a database of all microbial genomes sequenced from soil at a toxic ... though other variants were discovered in microbial genomes sequenced from other environments. ...
  https://vcresearch.berkeley.edu/news/smallest-life-forms-have-smallest-working-crispr-system
*  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
*  Frontiers | CowPI: A Rumen Microbiome Focussed Version of the PICRUSt Functional Inference Software | Microbiology
Census and Hungate 1000 have resulted in a wide sampling of 16S rDNA profiles and over 500 fully sequenced microbial genomes ... Census and Hungate 1000 have resulted in a wide sampling of 16S rDNA profiles and over 500 fully sequenced microbial genomes ... The rumen microbiome is an example of a community traditionally underrepresented in genome and sequence databases, but recent ... but its accuracy relies on the availability of completely sequenced genomes of representative organisms from the community ...
  https://www.frontiersin.org/articles/10.3389/fmicb.2018.01095/full
*  The signaling helix: a common functional theme in diverse signaling proteins | Biology Direct | Full Text
The logo was generated using the WebLogo program [50]. All completely sequenced and assembled microbial genomes that were ... A complete list of these genomes and the predicted proteomes in fasta format can be downloaded from the NCBI Genomes division ... Methe B, Fraser CM: Roll with the flow: microbial masters of redox chemistry. Trends Microbiol 2004,12(10):439-441. 10.1016/j. ... Crooks GE, Hon G, Chandonia JM, Brenner SE: WebLogo: a sequence logo generator. Genome Res 2004,14(6):1188-1190. 10.1101/gr. ...
  https://0-biologydirect-biomedcentral-com.brum.beds.ac.uk/articles/10.1186/1745-6150-1-25
*  The Smallpox Destruction Debate: Could a Grand Bargain Settle the Issue? | Arms Control Association
... to produce long fragments of synthetic DNA in the laboratory and assemble them into genes and even entire microbial genomes ( ... In January 2008, the J. Craig Venter Institute announced the synthesis of a stripped-down bacterial genome made up of 582,970 ... Daniel G. Gibson et al., "Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome," Science, ... strictly forbid the chemical synthesis of full-length smallpox virus genomes or their assembly from smaller DNA fragments, (b) ...
  https://www.armscontrol.org/act/2009_03/tucker
*  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
*  Generation of Multimillion-Sequence 16S rRNA Gene Libraries from Complex Microbial Communities by Assembling Paired-End...
GAIIx genome analyzer, Hiseq 2000 platform, and MiSeq genome analyzer) to assemble ∼200-base hypervariable region 3 (V3) ... Generation of Multimillion-Sequence 16S rRNA Gene Libraries from Complex Microbial Communities by Assembling Paired-End ... Generation of Multimillion-Sequence 16S rRNA Gene Libraries from Complex Microbial Communities by Assembling Paired-End ... Generation of Multimillion-Sequence 16S rRNA Gene Libraries from Complex Microbial Communities by Assembling Paired-End ...
  https://aem.asm.org/content/77/11/3846
*  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/
*  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
*  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
*  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/