Best practices for analysing microbiomes

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.

Emerging Role of the Gut Microbiome in Nonalcoholic Fatty Liver Disease: From Composition to Function

“…Advances in profiling and analytic techniques are transforming microbiome research and have been recently reviewed elsewhere 5, 6 , so we will limit our discussion to an overview of methods that have been utilized in human studies in NAFLD. (Figure 1) To date, the majority of studies have utilized culture-independent, biomarker-based profiling techniques.…”

“…5, 6 These approaches include next generation sequencing approaches to determine the functional genes encoded (metagenomics) or expressed (metatranscriptomics) by a microbial community, and mass spectrometry platforms to identify proteins (metaproteomics) and bioactive small molecules (metabolomics) collectively produced by a microbial community. 1 …”

Experimental old nest material predicts hoopoe Upupa epops eggshell and uropygial gland microbiota

“…1.9.1 (Caporaso et al 2010) and following recommendations on genomic data processing (Navas-Molina et al 2013, Dumbrell et al 2017, Knight et al 2018. nlm.nih.gov/bioproject/559797>).…”

“…Moreover, although reference-based methods are subject to more errors when assigning taxonomies to OTUs than de-novo approaches (Westcott and Schloss 2015), recent clustering methods improve the accuracy of OTU assignations and preserve estimated diversity also for reference based approaches, and several of them are implemented in QIIME (Kopylova et al 2016). Such tools are being improved continuously and the best available approaches change from year to year (Callahan et al 2017, Knight et al 2018, being difficult to work updated. Such tools are being improved continuously and the best available approaches change from year to year (Callahan et al 2017, Knight et al 2018, being difficult to work updated.…”

An overview of microbiome based strategies on anti‐obesity

“…The microbiome data of a fecal sample comes from a mixture of mucosal and luminal contents from different gut regions. To investigate the microbiota composition on mucosal surface or perform a prospective study may help further elucidate the roles of host genetics in colonization, diversity and stability of microbiomes in gut . Whether host genetics will affect the effectiveness of probiotics supplement, microbiota‐replacement, and FMT should be carefully considered and studied.…”