Introducing DOTUR, a Computer Program for Defining Operational Taxonomic Units and Estimating Species Richness

By Patrick D. Schloss, Jo Handelsman. Applied and Environmental Microbiology, 2005

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View Paper: https://www.semanticscholar.org/paper/5d964ace9b56e60214b890d8bd27ca4565999e99

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Citations in the corpus

Dirichlet Multinomial Mixtures: Generative Models for Microbial Metagenomics (2012, methodology): “Alternatively, an unsupervised strategy can be used to identify proxies to traditional taxonomic units by clustering sequences, so called Operational Taxonomic Units (OTUs) [6].”
Effect of inulin on the human gut microbiota: stimulation of Bifidobacterium adolescentis and Faecalibacterium prausnitzii (2008, methodology): “A distance matrix was created with Phylip((35)) and operational taxonomic units at 99 % were obtained with Dotur((36)).”
The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data (2006, methodology): “In addition, a pairwise distance matrix suitable for the DOTUR (17) molecular macroecology package as well as many phylogenetic packages such as Weighbor and PHYLIP can be created and downloaded with either uncorrected or Jukes-Cantor-corrected distances.”
Updating the 97% identity threshold for 16S ribosomal RNA OTUs (2017, methodology): “Several OTU quality metrics have been proposed, including richness (e.g., (Sun et al., 2009)), normalized mutual information (Cai and Sun, 2011; Zheng et al., 2012) and Matthews’ Correlation Coefficient (Schloss and Westcott, 2011).”
Microbial activity and soil respiration under nitrogen addition in Alaskan boreal forest (2008, methodology): “We obtained usable DNA sequences from 57 sporocarps, which were assigned to 13 OTUs ( 99% similarity for 18S region) by DOTUR.”
Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences (2014, methodology): “…identification, including algorithms that typically use pairwise alignments to compute a distance matrix before grouping sequences into OTUs (DOTUR (Schloss and Handelsman, 2005), ESPRIT (Sun et al. , 2009), SLP (Huse et al. , 2010), HPC-CLUST (Matias Rodrigues and von Mering, 2014)) as well as…”
Bacterial diversity in cucumber (Cucumis sativus) rhizosphere in response to salinity, soil pH, and boron (2010, methodology): “The computer program DOTUR (Schloss and Handelsman, 2005, 2006) was used to calculate species richness estimates and diversity indices from sequence data.”
A general suite of fungal endophytes dominate the roots of two dominant grasses in a semiarid grassland (2010, methodology): “Comparisons of the taxonomical database based on NCBI blast results and OTUs defined by the program DOTUR indicated that different genera can be distinguished at this level of similarity (93.1% concordance of Sequencher OTUs and DOTUR OTUs).”
Comparison of free-living, suspended particle, and aggregate-associated bacterial and archaeal communities in the Laptev Sea (2009, methodology): “Phylotypes were defined as sequences of ≥ 97% similarity (for SSP and FL bacterial clone libraries) or ≥ 99% similarity when DOTUR did not provide the 97% option (remaining libraries) due to low diversity or low number of sequences.”
Deciphering Diversity Indices for a Better Understanding of Microbial Communities. (2017, background): “In order to compare the bacterial diversity from samples of microorganisms, a variety of bioinformatics tools have been developed [13-15].”
Land-use history has a stronger impact on soil microbial community composition than aboveground vegetation and soil properties (2011, methodology): “Shannon diversity index (H), Chao1 estimate, and reciprocal of Simpson’s index (1/D) were calculated based on the number of operational taxonomic units (OTUs) at an evolutionary distance (D) of 0.03 using the average neighbor algorithm in DOTUR (Schloss and Handelsman, 2005).”
Salmonella enterica Serovar Typhimurium Exploits Inflammation to Compete with the Intestinal Microbiota (2007, methodology): “To obtain more detailed taxonomic information the sequences were divided into phylotypes by generating distance matrices in ARB (with Olsen correction), which were then entered into the DOTUR program [58] set to the furthest neighbour and 99% similarity settings.”