Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences

By Pablo Yarza, Pelin Yilmaz, Elmar Pruesse, Frank Oliver Glöckner, Wolfgang Ludwig, K. Schleifer, William B. Whitman, J. Euzéby, R. Amann, Ramon Rosselló-Mora. Nature Reviews Microbiology, 2014

2,284 citations recorded by the source corpus.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/c953f7abdd5bee276ccddd6c9b8d3ea97ae51904

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Citations in the corpus

Endophytic bacteria in Miscanthus seed: implications for germination, vertical inheritance of endophytes, plant evolution and breeding (2017, background): “Near-complete 16S rDNA sequences enable accurate taxonomic identification to species level (Yarza et al., 2014) and minimize the risk of chimeric sequences being generated.”
MiDAS: the field guide to the microbes of activated sludge (2015, methodology): “(14) for monophyletic groups in the ARB base tree.”
Phylogeny and taxonomy of Synechococcus-like cyanobacteria (2020, background): “According to Yarza et al. (2014), the threshold sequence identity for recognition is ≤98.7%, indicating that more than one species could be described even they are morphologically cryptic.”
The gut microbiota and inflammatory bowel disease (2014, background): “…time period in order to capture differences in disease activity and other heterogenous features of IBD, 2) patients with new onset IBD to gain more knowledge on the influence of IBD management such as different drug use and surgery, 3) birth cohorts such as Lifelines NEXT 80 to capture microbial…”
RESCRIPt: Reproducible sequence taxonomy reference database management (2020, methodology): “SILVA, GTDB, and NCBI data were all found to contain unusually long and short 16S rRNA gene sequences (using the RESCRIPt action evaluate-seqs), thus Archaea sequences < 900 nt [50] and Bacteria< 1200 nt [25], as performed for the SILVA releases (e.”
Benchmarking Metagenomics Tools for Taxonomic Classification. (2019, methodology): “The most widely used single marker gene for bacterial metagenomics is the highly conserved 16S rRNA sequence (Edgar, 2018; Yarza et al., 2014), though other markers are needed to identify viruses, fungi and other microbes that do not have the 16S marker gene.”
Uncultivated microbes in need of their own taxonomy (2017, background): “Few ecologists might be aware that SAR11 refers to a large monophyletic group of a depth similar to a phylum, whereas the Roseobacter clade encompasses a single family (Yarza et al., 2014).”
The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics (2015, background): “Timeline showing advances in microbial communities studies from Leeuwenhoek to NGS (Ottman et al., 2012; Yarza et al., 2014). restriction-fragment length polymorphism (T-RFLP).”