Integration of Microbial Ecology and Statistics: a Test To Compare Gene Libraries

By Patrick D. Schloss, Bret Larget, Jo Handelsman. Applied and Environmental Microbiology, 2004

363 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/45ef9a96a32858d8be653b26c134a557e3d2c2e2

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Ecology

In Molecular Biology

Citations in the corpus

Total and active microbial communities and phoD as affected by phosphate depletion and pH in soil (2016, methodology): “OTU matrices were then normalized to the smallest library size using the normalized.shared command as implemented in MOTHUR to allow comparison between plots (Supplementary Table S4).”
Symbiotic gut microbes modulate human metabolic phenotypes (2008, result): “-LIBSHUFF analysis (16) also showed that each individual appears to have a unique gut microbial community even within this one family (details in SI Text: Results) in agreement with previous reports about the individuality of human gut microbiota.”
One hundred new species of lichenized fungi : a signature of undiscovered global diversity (2011, background): “…400,000 plants, 100,000 fungi (including 17,500 lichens), 1.5 million animals, 200,000 protists, and 10,000 bacteria (Prance et al. 2000, Govaerts 2001, Pitman & Jørgensen 2002, Scotland & Wortley 2003, Schloss et al. 2004, Williamson & Day 2007, Feuerer & Hawksworth 2007, Kirk et al. 2008).”
UniFrac – An online tool for comparing microbial community diversity in a phylogenetic context (2006, background): “This could occur if one environment contains only sequences that also appear in the other (analogous to what can be detected using Lib-Shuff [13,30]), or if the sequences in one environment are more tightly clustered or are on longer branches.”
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].”
Bacterial diversity of terra preta and pristine forest soil from the Western Amazon (2007, methodology): “Calculation of Shannon index values using DOTUR yielded significantly different (P40:05) values for terra preta and forest soil (5.2 and 4.37, respectively).”
Remarkably diverse and contrasting archaeal communities in a large arctic river and the coastal Arctic Ocean (2006, neutral): “Mackenzie River sites: R1 and R2; Beaufort Shelf sites: Z2 (inshore) and 65 (offshore) 60° W 30° W 0° 50° N 50° N 150° W 180° W 70° NCanada Russia Alaska Greenland Beaufort Sea Aquat Microb Ecol 44: 115–126, 2006 (http://www.plantpath.wisc.edu/fac/joh/S-libshuff.html) (Schloss et al. 2004).”
Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples (2009, background): “DOTUR [9], Libshuff [10], # -libshuff [11], SONs [12], MEGAN [13], UniFrac [14], and TreeClimber [15] all focus on different aspects of such an analysis.”
Towards the definition of a core of microorganisms involved in anaerobic digestion of sludge (2009, methodology): “The seven digesters were compared bilaterally with R -Libshuff (Schloss et al., 2004) using the distance matrix calculated by DNAdist as input.”
Diversity of rock varnish bacterial communities from Black Canyon, New Mexico (2010, methodology): “The similarity between each clone library was calculated using S‐Libshuff (http:// www.plantpath.wisc.edu/joh/s‐libshuff.html [Schloss et al., 2004; Singleton et al., 2001]) and SONS [Schloss and Handelsman, 2006].”
Introducing SONS, a Tool for Operational Taxonomic Unit-Based Comparisons of Microbial Community Memberships and Structures (2006, methodology): “In contrast to the (cid:10) -LIBSHUFF analyses, the SONS-based analyses suggested that when comparing OTU 0.03 memberships and structures, the ob/ (cid:1) and ob/ob groups were more similar to each other than they were to the (cid:1) / (cid:1) group.”
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities (2009, methodology): “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.”
High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease (2011, methodology): “To test this we first performed whole community comparisons using ∫-LIBSHUFF [38], unweighted and weighted UniFrac [39] and the parsimony P-test [40] which all test whether or not two communities are significantly different overall without indicating which phylotypes cause the significance.”