Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla

By K. Wrighton, Brian C. Thomas, Itai Sharon, Christopher S. Miller, C. Castelle, N. Verberkmoes, M. Wilkins, R. Hettich, M. Lipton, K. Williams and 2 more. Science, 2012

615 citations recorded by the source corpus.

Subfields: Building and Construction, Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/bfe542b0ca0fb63ed26fc9615235308e2b2ad8c6

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Citations in the corpus

Microbial Biodiversity and Bioremediation Assessment Through Omics Approaches (2020, background): “It has been used to new and existing microbial community, analyze new viruses (Yozwiak et al., 2012; Quince et al., 2017; Vermote et al., 2018), uncultured bacteria (Wrighton et al., 2012), unique proteins (Godzik, 2011), and metabolic pathways (Morgan et al., 2012).”
MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm (2014, background): “A number of approaches have been developed to bin assembled sequences from metagenomic data [2,4-9].”
Unusual biology across a group comprising more than 15% of domain Bacteria (2015, methodology): “However, rp16 was also used for phylogenetic analysis because (1) it is encoded in genomes as a syntenic block and is found in only one copy, and thus can be used as a proxy for a particular genotype independent of binning, (2) it encodes ribosomal proteins that provide a robust phylogenetic signal,”
Implications of streamlining theory for microbial ecology (2014, background): “The studies from Wrighton et al. (2012) and Kantor et al. (2013), referred to above, differed markedly from others that reported streamlining, in that they focused on a freshwater aquifer that had been amended with acetate.”
Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life (2017, neutral): “Only metagenomes submitted to the SRA before 31 December 2015 were considered with a predominant focus on environmental and non-human gastrointestinal samples NCBI UBA NCBI UBA Total PD Taxon PD UBA PG NCBI PD UBA PD UBA PG/PD Total Dereplicated Relative Archaea 100.0% 30.7% UAP (all) 1.1% 100.0% Eu”
MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences (2014, background): “Culture-independent whole-genome shotgun (WGS) DNA sequencing has revolutionized the study of the diversity and ecology of microbial communities during the last decade (1,2).”
Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples (2018, background): “Results can also generate clues about the lifestyle of candidate phyla that elude cultivation efforts (Wrighton et al. 2012; Kantor et al. 2013; Brown et al. 2015).”
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes (2015, background): “We compared the quality estimates obtained for the 90 putative population genomes recovered from the acetate-amended aquifer (Wrighton et al. 2012) community using domain-level and lineage-specific marker sets (Supplemental Table S22).”
DRAM for distilling microbial metabolism to automate the curation of microbiome function (2020, background): “Reciprocal best hits (RBHs) are defined by searches where the database sequence that is the top hit from a forward search of the input gene has a bit score >60 (by default) and is the top hit from the reverse search of the database hit against the all genes from the input FASTA file with a bit score”
Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system (2016, methodology): “We used genome-resolved metagenomics to study sediment and groundwater-associated bacteria and archaea from a shallow sediment-hosted perennially suboxic/anoxic aquifer adjacent to the Colorado River, near Riﬂe, CO, USA 7,13,14,16,17,21,22 .”