Pairwise and incremental multi-stage alignment of metagenomes: A new proposal [PDF]
, 2017 Traditional comparisons between metagenomes are often performed using reference databases as intermediary templates from which to obtain distance metrics.
Pérez-Wohlfeil, Esteban +2 more
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Needle in a Whey-Stack: PhRACS as a Discovery Tool for Unknown Phage-Host Combinations
mBio, 2022 The field of metagenomics has rapidly expanded to become the go-to method for complex microbial community analyses. However, there is currently no straightforward route from metagenomics to traditional culture-based methods of strain isolation ...
Eoghan Casey +17 more
doaj +1 more source
Differential Functional Constraints Cause Strain-Level Endemism in Polynucleobacter Populations. [PDF]
, 2016 The adaptation of bacterial lineages to local environmental conditions creates the potential for broader genotypic diversity within a species, which can enable a species to dominate across ecological gradients because of niche flexibility.
Geeta Rijal +8 more
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Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software [PDF]
Nature Methods, 2017 ISSN:1548 ...
David Koslicki +75 more
openaire +10 more sources
Dissecting the role of the human microbiome in COVID-19 via metagenome-assembled genomes
Nature Communications, 2022 Here, using whole-metagenome shotgun sequencing data from patients with COVID-19 and controls, the authors reconstruct 11,584 microbial metagenome-assembled genomes (MAGs) including 5,403 non-redundant MAGs, revealing microbiota and metabolic pathways ...
Shanlin Ke, Scott T. Weiss, Yang-Yu Liu
doaj +1 more source
Identification of Carbohydrate Metabolism Genes in the Metagenome of a Marine Biofilm Community Shown to Be Dominated by Gammaproteobacteria and Bacteroidetes [PDF]
, 2010 Polysaccharides are an important source of organic carbon in the marine environment and degradation of the insoluble and globally abundant cellulose is a major component of the marine carbon cycle.
Connolly, John +7 more
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Metagenome-assembled genome sequences of three uncultured planktomarina sp. strains from the Northeast Atlantic Ocean [PDF]
, 2020 We report three metagenome-assembled genomes (MAGs) of Planktomarina strains from coastal seawater (Portugal) to help illuminate the functions of understudied Rhodobacteraceae bacteria in marine environments.
Borges, Nuno +6 more
core +1 more source
From metagenomics to the metagenome: Conceptual change and the rhetoric of translational genomic research [PDF]
, 2009 As the international genomic research community moves from the tool-making efforts of the Human Genome Project into biomedical applications of those tools, new metaphors are being suggested as useful to understanding how our genes work – and for ...
Huss, John Edward, Juengst, Eric Thomas
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Carbon assimilation strategies in ultrabasic groundwater: clues from the integrated study of a serpentinization-influenced aquifer [PDF]
, 2020 © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Seyler, L. M., Brazelton, W. J., McLean, C., Putman, L. I., Hyer, A., Kubo, M. D.
Brazelton, William J. +8 more
core +2 more sources
Methodology and ontology in microbiome research [PDF]
, 2014 Research on the human microbiome has gen- erated a staggering amount of sequence data, revealing variation in microbial diversity at the community, species (or phylotype), and genomic levels. In order to make this complexity more manageable and easier to
Huss, John
core +1 more source