title: Estimating beta diversity for under-sampled communities using the variably weighted Odum dissimilarity index and OTUshuff.
abstract: BACKGROUND
  In profiling the composition and structure of complex microbial communities via high throughput amplicon sequencing, a very low proportion of community members are typically sampled. As a result of this incomplete sampling, estimates of dissimilarity between communities are often inflated, an issue we term pseudo β-diversity.
  
  
  RESULTS
  We present a set of tools to identify and correct for the presence of pseudo β-diversity in contrasts between microbial communities. The variably weighted Odum dissimilarity (DwOdum) allows for down-weighting the influence of either abundant or rare taxa in calculating a measure of similarity between two communities. We show that down-weighting the influence of rare taxa can be used to minimize pseudo β-diversity arising from incomplete sampling. Down-weighting the influence of abundant taxa can increase the sensitivity of hypothesis testing. OTUshuff is an associated test for identifying the presence of pseudo β-diversity in pairwise community contrasts.
  
  
  METHODS
  A Perl script for calculating the DwOdum score from a taxon abundance table and performing pairwise contrasts with OTUshuff can be obtained at http://www.ars.usda.gov/services/software/software.htm?modecode=30-12-10-00.
  
  
  BACKGROUND
  daniel.manter@ars.usda.gov
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: USDA-ARS, Soil-Plant-Nutrient Research, Fort Collins, CO 80526, USA and.
authors.forename: Daniel K
authors.initials: DK
authors.lastname: Manter
authors.affiliation: USDA-ARS, National Laboratory for Agriculture and the Environment, Ames, IA 50011 USA.
authors.forename: Matthew G
authors.initials: MG
authors.lastname: Bakker
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000235:genetics*; D044822:Biodiversity; D003198:Computer Simulation; D004269:DNA, Bacterial / Q000235:genetics; D006801:Humans; D056186:Metagenomics; D008962:Models, Theoretical; D016133:Polymerase Chain Reaction; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D015983:Selection Bias; D012988:Soil Microbiology
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S