Advances and Challenges in Metatranscriptomic Analysis
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)more »
- Authors:
- Publication Date:
- Research Org.:
- Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
- Sponsoring Org.:
- USDOE National Nuclear Security Administration (NNSA); Defense Threat Reduction Agency (DTRA); USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1566265
- Alternate Identifier(s):
- OSTI ID: 1597345
- Report Number(s):
- LA-UR-19-24619
Journal ID: ISSN 1664-8021; 904
- Grant/Contract Number:
- KP1601010, 4000150817; 89233218CNA000001; CB10152; R-00480-16-0; CB10623; LANLF59T; LANLF59C; KP1601010; 4000150817-877
- Resource Type:
- Published Article
- Journal Name:
- Frontiers in Genetics
- Additional Journal Information:
- Journal Name: Frontiers in Genetics Journal Volume: 10; Journal ID: ISSN 1664-8021
- Publisher:
- Frontiers
- Country of Publication:
- Switzerland
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; RNASeq; microbiome; workflows; gene expression; omics
Citation Formats
Shakya, Migun, Lo, Chien-Chi, and Chain, Patrick S. G. Advances and Challenges in Metatranscriptomic Analysis. Switzerland: N. p., 2019.
Web. doi:10.3389/fgene.2019.00904.
Shakya, Migun, Lo, Chien-Chi, & Chain, Patrick S. G. Advances and Challenges in Metatranscriptomic Analysis. Switzerland. https://doi.org/10.3389/fgene.2019.00904
Shakya, Migun, Lo, Chien-Chi, and Chain, Patrick S. G. Wed .
"Advances and Challenges in Metatranscriptomic Analysis". Switzerland. https://doi.org/10.3389/fgene.2019.00904.
@article{osti_1566265,
title = {Advances and Challenges in Metatranscriptomic Analysis},
author = {Shakya, Migun and Lo, Chien-Chi and Chain, Patrick S. G.},
abstractNote = {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.},
doi = {10.3389/fgene.2019.00904},
journal = {Frontiers in Genetics},
number = ,
volume = 10,
place = {Switzerland},
year = {Wed Sep 25 00:00:00 EDT 2019},
month = {Wed Sep 25 00:00:00 EDT 2019}
}
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https://doi.org/10.3389/fgene.2019.00904
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