title: Quantitative Comparison of Abundance Structures of Generalized Communities: From B-Cell Receptor Repertoires to Microbiomes.
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.
authors.affiliation: Bioinformatics and Computational Biophysics, Faculty of Biology, University of Duisburg-Essen, Essen, Germany.
authors.forename: Mohammadkarim
authors.initials: M
authors.lastname: Saeedghalati
authors.affiliation: Bioinformatics and Computational Biophysics, Faculty of Biology, University of Duisburg-Essen, Essen, Germany.
authors.forename: Farnoush
authors.initials: F
authors.lastname: Farahpour
authors.affiliation: Bioinformatics and Computational Biophysics, Faculty of Biology, University of Duisburg-Essen, Essen, Germany.
authors.forename: Bettina
authors.identifier: 0000-0002-9313-8636
authors.initials: B
authors.lastname: Budeus
authors.affiliation: Bioinformatics and Computational Biophysics, Faculty of Biology, University of Duisburg-Essen, Essen, Germany.
authors.forename: Anja
authors.initials: A
authors.lastname: Lange
authors.affiliation: Center for Medical Biotechnology, University of Duisburg-Essen, Essen, Germany.|Institute of Medical Microbiology, Medical Faculty, University of Duisburg-Essen, Essen, Germany.
authors.forename: Astrid M
authors.initials: AM
authors.lastname: Westendorf
authors.affiliation: Institute of Cell Biology (Cancer Research), Medical Faculty, University of Duisburg-Essen, Essen, Germany.
authors.forename: Marc
authors.initials: M
authors.lastname: Seifert
authors.affiliation: Center for Medical Biotechnology, University of Duisburg-Essen, Essen, Germany.|Institute of Cell Biology (Cancer Research), Medical Faculty, University of Duisburg-Essen, Essen, Germany.
authors.forename: Ralf
authors.initials: R
authors.lastname: Küppers
authors.affiliation: Bioinformatics and Computational Biophysics, Faculty of Biology, University of Duisburg-Essen, Essen, Germany.|Center for Medical Biotechnology, University of Duisburg-Essen, Essen, Germany.|Center for Computational Sciences and Simulation, University of Duisburg-Essen, Essen, Germany.|Center for Water and Environmental Research, University of Duisburg-Essen, Essen, Germany.
authors.forename: Daniel
authors.identifier: 0000-0003-2973-7869
authors.initials: D
authors.lastname: Hoffmann
mesh_terms: D000818:Animals; D053265:B-Cell Activation Factor Receptor / Q000235:genetics*; D003198:Computer Simulation; D014644:Genetic Variation / Q000235:genetics*; D005828:Genetics, Population; D006801:Humans; D064307:Microbiota / Q000235:genetics*; D008957:Models, Genetic; D015233:Models, Statistical
chemical_list: D053265:B-Cell Activation Factor Receptor