Abstract
Sequencing-based analyses of microbiomes have traditionally focused on addressing the question of community membership and profiling taxonomic abundance through amplicon sequencing of 16 rRNA genes. More recently, shotgun metagenomics, which involves the random sequencing of all genomic content of a microbiome, has dominated this arena due to advancements in sequencing technology throughput and capability to profile genes as well as microbiome membership. While these methods have revealed a great number of insights into a wide variety of microbiomes, both of these approaches only describe the presence of organisms or genes, and not whether they are active members of the microbiome. To obtain deeper insights into how a microbial community responds over time to their changing environmental conditions, microbiome scientists are beginning to employ large-scale metatranscriptomics approaches. Here, we present a comprehensive review on computational metatranscriptomics approaches to study microbial community transcriptomes. We review the major advancements in this burgeoning field, compare strengths and weaknesses to other microbiome analysis methods, list available tools and workflows, and describe use cases and limitations of this method. We envision that this field will continue to grow exponentially, as will the scope of projects (e.g. longitudinal studies of community transcriptional responses to perturbations over time) and the resulting data. This review will provide a list of options for computational analysis of these data and will highlight areas in need of development.
Highlights
The past few decades have seen significant advancements in sequencing technologies that have transformed how we conduct biological experiments, when it comes to the study of complex microbiomes
We review the major advancements in this burgeoning field, compare strengths and weaknesses to other microbiome analysis methods, list available tools and workflows, and describe use cases and limitations of this method
Most of the high throughput sequencing has focused on DNA sequencing of entire communities using either targeted approaches like PCR-amplicon sequencing of 16S ribosomal RNA (rRNA) genes or shotgun sequencing of all available DNA from the sample
Summary
The past few decades have seen significant advancements in sequencing technologies that have transformed how we conduct biological experiments, when it comes to the study of complex microbiomes. Metatranscriptomics is not always able to capture the entire metatranscriptome due in part to the complexity (high diversity and relative ratios of members) of some microbial communities, the large dynamic range of transcript expression, the short half-life of RNA, and a number of technology-specific limitations.
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