Quantitative Comparison of Abundance Structures of Generalized Communities: From B-Cell Receptor Repertoires to Microbiomes

PLoS Comput Biol. 2017 Jan 23;13(1):e1005362. doi: 10.1371/journal.pcbi.1005362. eCollection 2017 Jan.

Abstract

The community, the assemblage of organisms co-existing in a given space and time, has the potential to become one of the unifying concepts of biology, especially with the advent of high-throughput sequencing experiments that reveal genetic diversity exhaustively. In this spirit we show that a tool from community ecology, the Rank Abundance Distribution (RAD), can be turned by the new MaxRank normalization method into a generic, expressive descriptor for quantitative comparison of communities in many areas of biology. To illustrate the versatility of the method, we analyze RADs from various generalized communities, i.e. assemblages of genetically diverse cells or organisms, including human B cells, gut microbiomes under antibiotic treatment and of different ages and countries of origin, and other human and environmental microbial communities. We show that normalized RADs enable novel quantitative approaches that help to understand structures and dynamics of complex generalized communities.

Publication types

  • Comparative Study
  • Evaluation Study

MeSH terms

  • Animals
  • B-Cell Activation Factor Receptor / genetics*
  • Computer Simulation
  • Genetic Variation / genetics*
  • Genetics, Population*
  • Humans
  • Microbiota / genetics*
  • Models, Genetic*
  • Models, Statistical*

Substances

  • B-Cell Activation Factor Receptor

Grants and funding

This work was supported by grant numbers TRR60/A2, TRR60/B1, KU1315/8-1 from Deutsche Forschungsgemeinschaft, http://www.dfg.de. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.