Shotgun metagenomics, from sampling to analysis
Diverse microbial communities of bacteria, archaea, viruses and single-celled eukaryotes
have crucial roles in the environment and in human health. However, microbes are …
have crucial roles in the environment and in human health. However, microbes are …
Toward accurate and quantitative comparative metagenomics
S Nayfach, KS Pollard - Cell, 2016 - cell.com
Shotgun metagenomics and computational analysis are used to compare the taxonomic and
functional profiles of microbial communities. Leveraging this approach to understand roles of …
functional profiles of microbial communities. Leveraging this approach to understand roles of …
Genomic features of bacterial adaptation to plants
A Levy, I Salas Gonzalez, M Mittelviefhaus… - Nature …, 2018 - nature.com
Plants intimately associate with diverse bacteria. Plant-associated bacteria have ostensibly
evolved genes that enable them to adapt to plant environments. However, the identities of …
evolved genes that enable them to adapt to plant environments. However, the identities of …
The structure and diversity of human, animal and environmental resistomes
Abstract Background Antibiotic resistance genes (ARGs) are widespread but cause
problems only when present in pathogens. Environments where selection and transmission …
problems only when present in pathogens. Environments where selection and transmission …
Plant microbiomes harbor potential to promote nutrient turnover in impoverished substrates of a Brazilian biodiversity hotspot
The substrates of the Brazilian campos rupestre s, a grassland ecosystem, have extremely
low concentrations of phosphorus and nitrogen, imposing restrictions to plant growth …
low concentrations of phosphorus and nitrogen, imposing restrictions to plant growth …
Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome
S Nayfach, KS Pollard - Genome biology, 2015 - Springer
Average genome size is an important, yet often overlooked, property of microbial
communities. We developed MicrobeCensus to rapidly and accurately estimate average …
communities. We developed MicrobeCensus to rapidly and accurately estimate average …
Impact of long-term N, P, K, and NPK fertilization on the composition and potential functions of the bacterial community in grassland soil
Y Pan, N Cassman, M de Hollander… - FEMS microbiology …, 2014 - academic.oup.com
Soil abiotic and biotic interactions govern important ecosystem processes. However, the
mechanisms behind these interactions are complex, and the links between specific …
mechanisms behind these interactions are complex, and the links between specific …
Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification
KA Ziesemer, AE Mann, K Sankaranarayanan… - Scientific reports, 2015 - nature.com
To date, characterization of ancient oral (dental calculus) and gut (coprolite) microbiota has
been primarily accomplished through a metataxonomic approach involving targeted …
been primarily accomplished through a metataxonomic approach involving targeted …
Accurate read-based metagenome characterization using a hierarchical suite of unique signatures
A major challenge in the field of shotgun metagenomics is the accurate identification of
organisms present within a microbial community, based on classification of short sequence …
organisms present within a microbial community, based on classification of short sequence …
Grinder: a versatile amplicon and shotgun sequence simulator
Abstract We introduce Grinder (http://sourceforge. net/projects/biogrinder/), an open-source
bioinformatic tool to simulate amplicon and shotgun (genomic, metagenomic, transcriptomic …
bioinformatic tool to simulate amplicon and shotgun (genomic, metagenomic, transcriptomic …