Quantitative Comparisons of 16S rRNA Gene Sequence Libraries from Environmental Samples

By D. Singleton, M. Furlong, Stephen L. Rathbun, William B. Whitman. Applied and Environmental Microbiology, 2001

664 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/e61dec84d395ebc165e79f7e055f95895fe54032

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Citations in the corpus

Dynamics of organic‐aggregate‐associated bacterial communities and related environmental factors in Lake Taihu, a large eutrophic shallow lake in China (2010, result): “0043 (Singleton et al. 2001).”
Synchrony and seasonality in bacterioplankton communities of two temperate rivers (2005, methodology): “The two clone libraries were compared statistically using the LIBSHUFF computer program (Singleton et al. 2001), which calculates coverage (Good 1953) at various levels of evolutionary distance determined using the Jukes–Cantor model for nucleic acid substitution.”
UniFrac: a New Phylogenetic Method for Comparing Microbial Communities (2005, background): “Techniques with this limitation include the Sørenson and Jaccard indices of group overlap (28), the LibShuff (40; http://www.arches .uga.edu/ (cid:2) whitman/libshuff.html) and (cid”
Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy (2007, methodology): “However, most comparison methods, whether from traditional macroecology, such as Sorensen’s and the Jaccard indices, or designed speciﬁcally for sequence data, such as LIBSHUFF (22), Martin’s P and F tests (19), and UniFrac (17), provide only summary information about the degree of difference betwee”
Hypothesis Testing and Power Calculations for Taxonomic-Based Human Microbiome Data (2012, methodology): “Several methods to analyze metagenomic data have been proposed based on exploratory cluster analysis, bootstrap or resampling methods, and application of univariate and non-parametric statistics to subsets of the data [4–12].”
The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data (2006, methodology): “However, most comparison methods, whether from traditional macroecology, such as Sorensen’s index (9), or designed specifically for sequence library data, such as LIBSHUFF (10) or Martin’s P-test (11), only provide summary information about the degree of difference between communities.”
Composition and temporal variability of picoeukaryote communities at a coastal site of the English Channel from 18S rDNA sequences (2004, methodology): “Restriction patterns were compared by using the software Fragment Analysis (Amersham BioSciences) and clone diversity analyzed by rarefaction curves (Singleton et al. 2001).”
The Distribution of Microbial Taxa in the Subsurface Water of the Kalahari Shield, South Africa (2006, methodology): “Evolutionary relatedness between clone libraries was calculated using LIBSHUFF analyses (Singleton et al. 2001).”
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities (2009, positive): “Because of the development of tools including ARB (13), DOTUR (22), SONS (23), LIBSHUFF (25, 26), UniFrac (11, 12), AMOVA and HOMOVA (15, 21), TreeClimber (24), and rRNA-speciﬁc databases (3, 4, 20), microbial ecology has progressed from being a descriptive to an experimental endeavor.”
Archaeal diversity associated with in situ samplers deployed on hydrothermal vents on the East Pacific Rise (13°N) (2003, methodology): “The different 16S rDNA clonal libraries were compared by determining homologous coverage (C) as in Singleton et al. (2002).”
Novel and Unexpected Prokaryotic Diversity in Water and Sediments of the Alkaline, Hypersaline Lakes of the Wadi An Natrun, Egypt (2007, methodology): “The statistical significance in the compositions of pairs of libraries was calculated using the LIBSHUFF program [42].”
Diversity and Succession of the Intestinal Bacterial Community of the Maturing Broiler Chicken (2003, background): “In order to study the changes of the bacterial community as the birds matured, we compared the libraries at different ages in a pair-wise manner (49).”
Microbial community diversity and heterotrophic production in a coastal Arctic ecosystem: A stamukhi lake and its source waters (2008, methodology): “We did find rare sequences such as Marine Group I.1a sequences present in the lake only, but such rare sequences did not influence the outcome of the LIBSHUFF test.”
Molecular Evidence for a Uniform Microbial Community in Sponges from Different Oceans (2002, neutral): “swinhoei, respectively, were harvested (38).”