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Best practices for analysing microbiomes
- Source :
- Nature Reviews Microbiology. 16:410-422
- Publication Year :
- 2018
- Publisher :
- Springer Science and Business Media LLC, 2018.
-
Abstract
- Complex microbial communities shape the dynamics of various environments, ranging from the mammalian gastrointestinal tract to the soil. Advances in DNA sequencing technologies and data analysis have provided drastic improvements in microbiome analyses, for example, in taxonomic resolution, false discovery rate control and other properties, over earlier methods. In this Review, we discuss the best practices for performing a microbiome study, including experimental design, choice of molecular analysis technology, methods for data analysis and the integration of multiple omics data sets. We focus on recent findings that suggest that operational taxonomic unit-based analyses should be replaced with new methods that are based on exact sequence variants, methods for integrating metagenomic and metabolomic data, and issues surrounding compositional data analysis, where advances have been particularly rapid. We note that although some of these approaches are new, it is important to keep sight of the classic issues that arise during experimental design and relate to research reproducibility. We describe how keeping these issues in mind allows researchers to obtain more insight from their microbiome data sets.
- Subjects :
- 0301 basic medicine
False discovery rate
Bacteria
General Immunology and Microbiology
Rare biosphere
Microbiota
Systems biology
Best practice
030106 microbiology
Reproducibility of Results
Biology
Microbiology
Data science
Molecular analysis
03 medical and health sciences
030104 developmental biology
Infectious Diseases
Metagenomics
Environmental Microbiology
Animals
Humans
Taxonomic resolution
Microbiome
Subjects
Details
- ISSN :
- 17401534 and 17401526
- Volume :
- 16
- Database :
- OpenAIRE
- Journal :
- Nature Reviews Microbiology
- Accession number :
- edsair.doi.dedup.....17bf59482e204e44611c179c8a94faad