Abstract
Metagenomics and other meta-omics approaches (including metatranscriptomics) provide insights into the composition and function of microbial communities living in different environments or animal hosts. Metatranscriptomics research provides an unprecedented opportunity to examine gene regulation for many microbial species simultaneously, and more importantly, for the majority that are unculturable microbial species, in their natural environments (or hosts). Current analyses of metatranscriptomic datasets focus on the detection of gene expression levels and the study of the relationship between changes of gene expression and changes of environment. As a demonstration of utilizing metatranscriptomics beyond these common analyses, we developed a computational and statistical procedure to analyze the antisense transcripts in strand-specific metatranscriptomic datasets. Antisense RNAs encoded on the DNA strand opposite a gene’s CDS have the potential to form extensive base-pairing interactions with the corresponding sense RNA, and can have important regulatory functions. Most studies of antisense RNAs in bacteria are rather recent, are mostly based on transcriptome analysis, and have been applied mainly to single bacterial species. Application of our approaches to human gut-associated metatranscriptomic datasets allowed us to survey antisense transcription for a large number of bacterial species associated with human beings. The ratio of protein coding genes with antisense transcription ranges from 0 to 35.8% (median = 10.0%) among 47 species. Our results show that antisense transcription is dynamic, varying between human individuals. Functional enrichment analysis revealed a preference of certain gene functions for antisense transcription, and transposase genes are among the most prominent ones (but we also observed antisense transcription in bacterial house-keeping genes).
Highlights
Advances in sequencing technology have catalyzed the development of metagenomics, which has revolutionized many fields in the study of microbial organisms
They showed that measurements of microbial species, gene, and gene transcript composition within self-collected samples were consistent across sampling methods (Franzosa et al, 2014)
For each sample handling method, we computed a profile of antisense transcription, in which a number represents the ratio of genes with antisense transcription in one species in one human individual
Summary
Advances in sequencing technology have catalyzed the development of metagenomics, which has revolutionized many fields in the study of microbial organisms. Metagenomics has been applied to study microbial communities sampled from various environments and animal hosts (including humans). The research emphasis has shifted toward elucidating the functionality and regulatory mechanisms of the microbial communities using other meta-omics approaches, including metatranscriptomics and metaproteomics. Metatranscriptomics research is creating an unprecedented opportunity to gain knowledge about gene regulation for many microbial species simultaneously, and more importantly, for the vast majority of uncultured microbial species in their natural environments (or hosts). In addition to elucidating functional characteristics of microbial communities, metatranscriptomic data provides information vital for accurate annotations of genes and their regulation in their community—complementary to metagenomic sequencing. Metatranscriptomic data indicate which of the genes encoded in a metagenome are transcribed, and which metabolic pathways are active (and the level of their activities), on the basis of their transcripts within a microbial community under various environmental conditions
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