Susannah G Tringe
Affiliation: Lawrence Berkeley National Laboratory
- Differences in sequencing technologies improve the retrieval of anammox bacterial genome from metagenomesFabio Gori
Radboud University Nijmegen, Institute for Computing and Information Science, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
BMC Genomics 14:7. 2013..fulgida). These datasets were obtained using Roche 454 FLX and Sanger sequencing with two different libraries (shotgun and fosmid)...
- Bioprospecting metagenomics of decaying wood: mining for new glycoside hydrolasesLuen Luen Li
Brookhaven National Laboratory, Upton, NY, USA
Biotechnol Biofuels 4:23. 2011..Our goal was to discover and characterize new glycoside hydrolases (GHases) from microbial biomass decay communities, especially those from unknown or never previously cultivated microorganisms...
- A renaissance for the pioneering 16S rRNA geneSusannah G Tringe
DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
Curr Opin Microbiol 11:442-6. 2008..The standard conclusion that microbial ecosystems are remarkably complex and diverse is now being replaced by detailed insights into microbial ecology and evolution based only on this one historically important marker gene...
- High-resolution phylogenetic microbial community profilingEsther Singer
US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
ISME J 10:2020-32. 2016..Thus, PhyloTags provide a reliable adjunct or alternative to cost-effective iTags, enabling more accurate phylogenetic resolution of microbial communities and predictions on their metabolic potential. ..
- Plant compartment and biogeography affect microbiome composition in cultivated and native Agave speciesDevin Coleman-Derr
Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
New Phytol 209:798-811. 2016..Agaves shared core prokaryotic and fungal taxa known to promote plant growth and confer tolerance to abiotic stress, which suggests common principles underpinning Agave-microbe interactions. ..
- Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial communityRobert M Bowers
Microbial Genomics Program Lead, DOE Joint Genome Institute, 2800 Mitchell Dr, Walnut Creek, CA, USA
BMC Genomics 16:856. 2015..Until recently, one of the major bottlenecks of shotgun metagenomics has been the requirement for large initial DNA template quantities during library preparation...
- Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cowsFilipa Godoy-Vitorino
Department of Biology, University of Puerto Rico, Rio Piedras, San Juan, Puerto Rico
ISME J 6:531-41. 2012..Regardless of the independent origin of foregut fermentation in birds and mammals, organ function has led to convergence of the microbial community structure in phylogenetically distant hosts...
- Validation of two ribosomal RNA removal methods for microbial metatranscriptomicsShaomei He
Department of Energy Joint Genome Institute, Walnut Creek, California, USA
Nat Methods 7:807-12. 2010..Illumina sequencing itself also can compromise quantitative data analysis by introducing a G+C bias between runs...
- Metagenomic discovery of biomass-degrading genes and genomes from cow rumenMatthias Hess
Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
Science 331:463-7. 2011..These data sets provide a substantially expanded catalog of genes and genomes participating in the deconstruction of cellulosic biomass...