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Mascarenhas R, Ruziska FM, Moreira EF, Campos AB, Loiola M, Reis K, Trindade-Silva AE, Barbosa FAS, Salles L, Menezes R, Veiga R, Coutinho FH, Dutilh BE, Guimarães PR, Assis APA, Ara A, Miranda JGV, Andrade RFS, Vilela B, Meirelles PM. Integrating Computational Methods to Investigate the Macroecology of Microbiomes. Front Genet 2020; 10:1344. [PMID: 32010196 PMCID: PMC6979972 DOI: 10.3389/fgene.2019.01344] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 12/09/2019] [Indexed: 12/15/2022] Open
Abstract
Studies in microbiology have long been mostly restricted to small spatial scales. However, recent technological advances, such as new sequencing methodologies, have ushered an era of large-scale sequencing of environmental DNA data from multiple biomes worldwide. These global datasets can now be used to explore long standing questions of microbial ecology. New methodological approaches and concepts are being developed to study such large-scale patterns in microbial communities, resulting in new perspectives that represent a significant advances for both microbiology and macroecology. Here, we identify and review important conceptual, computational, and methodological challenges and opportunities in microbial macroecology. Specifically, we discuss the challenges of handling and analyzing large amounts of microbiome data to understand taxa distribution and co-occurrence patterns. We also discuss approaches for modeling microbial communities based on environmental data, including information on biological interactions to make full use of available Big Data. Finally, we summarize the methods presented in a general approach aimed to aid microbiologists in addressing fundamental questions in microbial macroecology, including classical propositions (such as “everything is everywhere, but the environment selects”) as well as applied ecological problems, such as those posed by human induced global environmental changes.
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Affiliation(s)
| | - Flávia M Ruziska
- Institute of Biology, Federal University of Bahia, Salvador, Brazil
| | | | - Amanda B Campos
- Institute of Biology, Federal University of Bahia, Salvador, Brazil
| | - Miguel Loiola
- Institute of Biology, Federal University of Bahia, Salvador, Brazil
| | - Kaike Reis
- Chemical Engineering Department, Polytechnic School of Federal University of Bahia, Salvador, Brazil
| | - Amaro E Trindade-Silva
- Institute of Biology, Federal University of Bahia, Salvador, Brazil.,Department of Ecology, Biosciences Institute, University of Sao Paulo, Sao Paulo, Brazil
| | | | - Lucas Salles
- Institute of Geology, Federal University of Bahia, Salvador, Brazil
| | - Rafael Menezes
- Department of Ecology, Biosciences Institute, University of Sao Paulo, Sao Paulo, Brazil.,Institute of Physics, Federal University of Bahia, Salvador, Brazil
| | - Rafael Veiga
- Center of Data and Knowledge Integration for Health (CIDACS), Instituto Gonçalo Muniz, Fundação Oswaldo Cruz, Brazil
| | - Felipe H Coutinho
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández de Elche, San Juan de Alicante, Spain
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands.,Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Paulo R Guimarães
- Department of Ecology, Biosciences Institute, University of Sao Paulo, Butantã, Brazil
| | - Ana Paula A Assis
- Department of Ecology, Biosciences Institute, University of Sao Paulo, Butantã, Brazil
| | - Anderson Ara
- Institute of Mathematics, Federal University of Bahia, Salvador, Brazil
| | - José G V Miranda
- Institute of Physics, Federal University of Bahia, Salvador, Brazil
| | - Roberto F S Andrade
- Institute of Physics, Federal University of Bahia, Salvador, Brazil.,Center of Data and Knowledge Integration for Health (CIDACS), Instituto Gonçalo Muniz, Fundação Oswaldo Cruz, Brazil
| | - Bruno Vilela
- Institute of Biology, Federal University of Bahia, Salvador, Brazil
| | - Pedro Milet Meirelles
- Institute of Biology, Federal University of Bahia, Salvador, Brazil.,Department of Ecology, Biosciences Institute, University of Sao Paulo, Sao Paulo, Brazil
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