Advances and Challenges in Metatranscriptomic Analysis

Shakya, Migun; Lo, Chien-Chi; Chain, Patrick S. G.

doi:10.3389/fgene.2019.00904

Title: Advances and Challenges in Metatranscriptomic Analysis

Journal Article · Wed Sep 25 00:00:00 EDT 2019 · Frontiers in Genetics

DOI:https://doi.org/10.3389/fgene.2019.00904· OSTI ID:1566265

Shakya, Migun; Lo, Chien-Chi; Chain, Patrick S. G.

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.

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Research Organization:: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)

Sponsoring Organization:: USDOE National Nuclear Security Administration (NNSA); Defense Threat Reduction Agency (DTRA); USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: KP1601010, 4000150817; 89233218CNA000001; CB10152; R-00480-16-0; CB10623; LANLF59T; LANLF59C; KP1601010; 4000150817-877

OSTI ID:: 1566265

Alternate ID(s):: OSTI ID: 1597345

Report Number(s):: LA-UR-19-24619; 904

Journal Information:: Frontiers in Genetics, Journal Name: Frontiers in Genetics Vol. 10; ISSN 1664-8021

Publisher:: FrontiersCopyright Statement

Country of Publication:: Switzerland

Language:: English

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Cited by: 172 works

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