Comparative Metagenomics of Microbial Communities

By Susannah Tringe, C. von Mering, A. Kobayashi, A. Salamov, Kevin Y. Chen, H. Chang, M. Podar, J. Short, E. Mathur, J. Detter and 3 more. Science, 2004

1,618 citations recorded by the source corpus.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/89d7d2dde80331d35b51fd829348796d4a7d561e

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Citations in the corpus

Towards next‐generation biodiversity assessment using DNA metabarcoding (2012, background): “Such experiments would be similar to the current metagenomic approach (e.g. Riesenfeld et al. 2004; Tringe et al. 2005), except that the goal would not be to assemble whole microorganism genomes or to find the most common functional genes, but to use repetitive DNA to identify the different species.”
Defining the Human Microbiome (2012, background): “Understanding whether this principle holds true for other body sites will be fascinating; cross-biome metagenomic comparisons have been exceedingly rare to date[46, 47].”
Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities (2006, background): “Moreover, shotgun sequencing gives a metagenomic context for dominant organisms by providing low-level genomic coverage of many other community members suitable for a gene-centric analysis that could highlight habitat-specific metabolic trait”
Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation (2007, background): “The amount and diversity of species with at least partial sequence information is rapidly increasing (Cole, et al., 2005; Tringe, et al., 2005) and the tree of life based on completely sequenced genomes is being constantly redrawn (e.g. (Ciccarelli, et al., 2006)).”
The role of organisms in hyporheic processes: gaps in current knowledge, needs for future research and applications (2012, background): “Addressing this gap is one of the most important challenges of modern ecology (e.g. Tringe et al., 2005) and new environmental genomics approaches Diversity What is the real degree of microbial diversity in the hyporheic zone and what is the impact of this diversity on major ecological processes?”
Toward a Census of Bacteria in Soil (2006, methodology): “Comparison of Alaskan and Minnesotan Soils Microbial Communities Recently, the microbial community of a Minnesota farm soil was characterized by metagenomic (direct cloning and analysis of DNA from a soil sample) and 16S rRNA gene sequencing analyses [23].”
Environmental DNA (2012, background): “The ambiguity arose from a seminal paper with ‘metagenomics’ in the title (Tringe et al. 2005) that combined shotgun sequencing with 16S identification.”
Toward an ecological classification of soil bacteria. (2007, neutral): “Key words: Acidobacteria; copiotroph; K-selection; microbial diversity; oligotroph; Proteobacteria; quantitative PCR; real-time PCR; r-selection; soil carbon.”
Bacterial Extracellular Enzymatic Activity in Globally Changing Aquatic Ecosystems (2010, background): “The identities of the particular members of mixed assemblages capable of producing different extracellular enzymes in natural environments is still largely unknown, since most molecular analyses of community composition focus on rRNA sequences that provide little information on the degradative capab”
The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. (2013, background): “…built from 16S rRNA gene sequencing data obtained in a soil metagenome study failed to reach saturation and revealed that, of 150 000 sequencing reads obtained for a soil clone library, 1% exhibited overlap with the sequencing reads of other independent soil clone libraries (Tringe et al., 2005).”