Quantitative and Qualitative β Diversity Measures Lead to Different Insights into Factors That Structure Microbial Communities

By Catherine A. Lozupone, Micah Hamady, Scott T. Kelley, Rob Knight. Applied and Environmental Microbiology, 2007

2,384 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/9e9c7eea95d9d2cd61c2f6559009175549cf46f0

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Citations in the corpus

Microbiota regulate intestinal absorption and metabolism of fatty acids in the zebrafish (2012, methodology): “UniFrac principal coordinates analysis (PCoA) plots derived from both unweighted (an evaluation of community composition) and weighted (an evaluation of community structure) algorithms (Lozupone et al., 2007) provided several insights.”
Bacterial Communities in Women with Bacterial Vaginosis: High Resolution Phylogenetic Analyses Reveal Relationships of Microbiota to Clinical Criteria (2012, methodology): “As described in [35], the KR metric in this context is a generalization of weighted UniFrac [36], allowing assignments to internal edges of the tree and for mass to be split according to probabilistic assignment.”
Normalization and microbial differential abundance strategies depend upon data characteristics (2017, methodology): “Also, the negative values pose a problem to the branch length of UniFrac [57, 58].”
Deciphering microbial interactions and detecting keystone species with co-occurrence networks (2014, background): “Association metrics are used to compare the similarity of microbial communities in a variety of applications and it is known that metrics differ in their performance in detecting different patterns (Lozupone et al., 2007).”
UniFrac: an effective distance metric for microbial community comparison (2011, methodology): “We have also used sequence jackknifing to visualize the effects of sample depth and evenness on PCoA results (Ley et al., 2008, Lozupone et al., 2007).”
Forensic identification using skin bacterial communities (2010, methodology): “Plots were generated using the pairwise unweighted (A) and weighted (B) UniFrac distances (22, 23), respectively.”
Phylogenetic and functional alpha and beta diversity in temperate and tropical tree communities (2012, methodology): “This approach was refined using phylogenetic trees by microbial ecologists that 143 have necessarily been at the leading edge of phylogenetically-based analyses of 144 communities (Martin 2002; Lozupone and Knight 2005; Lozupone et al. 2007).”
Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible (2013, neutral): “The Weighted UniFrac distance [49].”
High-level classification of the Fungi and a tool for evolutionary ecological analyses (2018, methodology): “For each sample, we calculated the phylogenetic diversity (total branch length for all OTUs per sample) and uniqueness (unique branch length for each sample) metrics (cf. Lozupone et al. 2007) as well as the nearest taxon index (NTI) and net relatedness index (NRI).”