Advances and Challenges in Metatranscriptomic Analysis

Shakya, Migun; Lo, Chien-Chi; Chain, Patrick Sam Guy

doi:10.3389/fgene.2019.00904

Title: Advances and Challenges in Metatranscriptomic Analysis

Journal Article · 25 September 2019 · Frontiers in Genetics

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

^[1];

^[1]

Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

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.

View Journal Article

Cite

Export

Save

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

OSTI ID:: 1566265

Alternate ID(s):: OSTI ID: 1597345

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

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

Publisher:: FrontiersCopyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 181 works

Citation information provided by
Web of Science

References (154)

Accurate read-based metagenome characterization using a hierarchical suite of unique signatures Freitas, Tracey Allen K.; Li, Po-E; Scholz, Matthew B. Nucleic Acids Research, Vol. 43, Issue 10 https://doi.org/10.1093/nar/gkv180	journal	March 2015
Cloning the Soil Metagenome: a Strategy for Accessing the Genetic and Functional Diversity of Uncultured Microorganisms Rondon, M. R.; August, P. R.; Bettermann, A. D. Applied and Environmental Microbiology, Vol. 66, Issue 6 https://doi.org/10.1128/AEM.66.6.2541-2547.2000	journal	June 2000
Metagenome and Metatranscriptome Analyses Using Protein Family Profiles Zhong, Cuncong; Edlund, Anna; Yang, Youngik PLOS Computational Biology, Vol. 12, Issue 7 https://doi.org/10.1371/journal.pcbi.1004991	journal	July 2016
Enterotypes of the human gut microbiome Arumugam, Manimozhiyan; Raes, Jeroen; Pelletier, Eric Nature, Vol. 473, Issue 7346 https://doi.org/10.1038/nature09944	journal	April 2011
How to normalize metatranscriptomic count data for differential expression analysis Klingenberg, Heiner; Meinicke, Peter PeerJ, Vol. 5 https://doi.org/10.7717/peerj.3859	journal	January 2017
GAGE: generally applicable gene set enrichment for pathway analysis Luo, Weijun; Friedman, Michael S.; Shedden, Kerby BMC Bioinformatics, Vol. 10, Issue 1 https://doi.org/10.1186/1471-2105-10-161	journal	January 2009
MetaTrans: an open-source pipeline for metatranscriptomics Martinez, Xavier; Pozuelo, Marta; Pascal, Victoria Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep26447	journal	May 2016
FMAP: Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies Kim, Jiwoong; Kim, Min Soo; Koh, Andrew Y. BMC Bioinformatics, Vol. 17, Issue 1 https://doi.org/10.1186/s12859-016-1278-0	journal	October 2016
The MG-RAST metagenomics database and portal in 2015 Wilke, Andreas; Bischof, Jared; Gerlach, Wolfgang Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1322	journal	December 2015
Dual Transcriptomic Profiling of Host and Microbiota during Health and Disease in Pediatric Asthma Pérez-Losada, Marcos; Castro-Nallar, Eduardo; Bendall, Matthew L. PLOS ONE, Vol. 10, Issue 6 https://doi.org/10.1371/journal.pone.0131819	journal	June 2015
Dynamics of metatranscription in the inflammatory bowel disease gut microbiome Schirmer, Melanie; Franzosa, Eric A.; Lloyd-Price, Jason Nature Microbiology, Vol. 3, Issue 3 https://doi.org/10.1038/s41564-017-0089-z	journal	January 2018
Metatranscriptome Sequencing Reveals Insights into the Gene Expression and Functional Potential of Rumen Wall Bacteria Mann, Evelyne; Wetzels, Stefanie U.; Wagner, Martin Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.00043	journal	January 2018
Long reads: their purpose and place Pollard, Martin O.; Gurdasani, Deepti; Mentzer, Alexander J. Human Molecular Genetics, Vol. 27, Issue R2 https://doi.org/10.1093/hmg/ddy177	journal	May 2018
Meta-transcriptomics reveals a diverse antibiotic resistance gene pool in avian microbiomes Marcelino, Vanessa R.; Wille, Michelle; Hurt, Aeron C. BMC Biology, Vol. 17, Issue 1 https://doi.org/10.1186/s12915-019-0649-1	journal	April 2019
Species-level functional profiling of metagenomes and metatranscriptomes Franzosa, Eric A.; McIver, Lauren J.; Rahnavard, Gholamali Nature Methods, Vol. 15, Issue 11 https://doi.org/10.1038/s41592-018-0176-y	journal	October 2018
KEGG: Kyoto Encyclopedia of Genes and Genomes Kanehisa, Minoru; Goto, Susumu Nucleic Acids Research, Vol. 28, Issue 1, p. 27-30 https://doi.org/10.1093/nar/28.1.27	journal	January 2000
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications Yilmaz, Pelin; Kottmann, Renzo; Field, Dawn Nature Biotechnology, Vol. 29, Issue 5 https://doi.org/10.1038/nbt.1823	journal	May 2011
Microbiota and Metatranscriptome Changes Accompanying the Onset of Gingivitis Nowicki, Emily M.; Shroff, Raghav; Singleton, Jacqueline A. mBio, Vol. 9, Issue 2 https://doi.org/10.1128/mBio.00575-18	journal	April 2018
A multi-source domain annotation pipeline for quantitative metagenomic and metatranscriptomic functional profiling Ugarte, Ari; Vicedomini, Riccardo; Bernardes, Juliana Microbiome, Vol. 6, Issue 1 https://doi.org/10.1186/s40168-018-0532-2	journal	August 2018
Dissection of Microbial Community Functions during a Cyanobacterial Bloom in the Baltic Sea via Metatranscriptomics Berg, Carlo; Dupont, Chris L.; Asplund-Samuelsson, Johannes Frontiers in Marine Science, Vol. 5 https://doi.org/10.3389/fmars.2018.00055	journal	February 2018
Combining metagenomics, metatranscriptomics and viromics to explore novel microbial interactions: towards a systems-level understanding of human microbiome Bikel, Shirley; Valdez-Lara, Alejandra; Cornejo-Granados, Fernanda Computational and Structural Biotechnology Journal, Vol. 13 https://doi.org/10.1016/j.csbj.2015.06.001	journal	January 2015
Trees, fungi and bacteria: tripartite metatranscriptomics of a root microbiome responding to soil contamination Gonzalez, E.; Pitre, F. E.; Pagé, A. P. Microbiome, Vol. 6, Issue 1 https://doi.org/10.1186/s40168-018-0432-5	journal	March 2018
Trimmomatic: a flexible trimmer for Illumina sequence data Bolger, Anthony M.; Lohse, Marc; Usadel, Bjoern Bioinformatics, Vol. 30, Issue 15 https://doi.org/10.1093/bioinformatics/btu170	journal	April 2014
A human gut microbial gene catalogue established by metagenomic sequencing Qin, Junjie; Li, Ruiqiang; Raes, Jeroen Nature, Vol. 464, Issue 7285 https://doi.org/10.1038/nature08821	journal	March 2010
IDBA-MT: De Novo Assembler for Metatranscriptomic Data Generated from Next-Generation Sequencing Technology Leung, Henry C. M.; Yiu, Siu-Ming; Parkinson, John Journal of Computational Biology, Vol. 20, Issue 7 https://doi.org/10.1089/cmb.2013.0042	journal	July 2013
MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph Li, Dinghua; Liu, Chi-Man; Luo, Ruibang Bioinformatics, Vol. 31, Issue 10 https://doi.org/10.1093/bioinformatics/btv033	journal	January 2015
Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis Ye, Yuzhen; Tang, Haixu Bioinformatics, Vol. 32, Issue 7 https://doi.org/10.1093/bioinformatics/btv510	journal	August 2015
Microbial community gene expression in ocean surface waters Frias-Lopez, J.; Shi, Y.; Tyson, G. W. Proceedings of the National Academy of Sciences, Vol. 105, Issue 10 https://doi.org/10.1073/pnas.0708897105	journal	March 2008
Centrifuge: rapid and sensitive classification of metagenomic sequences Kim, Daehwan; Song, Li; Breitwieser, Florian P. Genome Research, Vol. 26, Issue 12 https://doi.org/10.1101/gr.210641.116	journal	October 2016
A Parsimony Approach to Biological Pathway Reconstruction/Inference for Genomes and Metagenomes Ye, Yuzhen; Doak, Thomas G. PLoS Computational Biology, Vol. 5, Issue 8 https://doi.org/10.1371/journal.pcbi.1000465	journal	August 2009
Metagenomic and Metatranscriptomic Analyses of Diverse Watermelon Cultivars Reveal the Role of Fruit Associated Microbiome in Carbohydrate Metabolism and Ripening of Mature Fruits Saminathan, Thangasamy; García, Marleny; Ghimire, Bandana Frontiers in Plant Science, Vol. 9 https://doi.org/10.3389/fpls.2018.00004	journal	January 2018
metaSPAdes: a new versatile metagenomic assembler Nurk, Sergey; Meleshko, Dmitry; Korobeynikov, Anton Genome Research, Vol. 27, Issue 5 https://doi.org/10.1101/gr.213959.116	journal	March 2017
Prodigal: prokaryotic gene recognition and translation initiation site identification Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F. BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-119	journal	March 2010
Enhancing the Resolution of Rumen Microbial Classification from Metatranscriptomic Data Using Kraken and Mothur Neves, Andre L. A.; Li, Fuyong; Ghoshal, Bibaswan Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.02445	journal	December 2017
Full-length transcriptome assembly from RNA-Seq data without a reference genome Grabherr, Manfred G.; Haas, Brian J.; Yassour, Moran Nature Biotechnology, Vol. 29, Issue 7 https://doi.org/10.1038/nbt.1883	journal	May 2011
IDBA-tran: a more robust de novo de Bruijn graph assembler for transcriptomes with uneven expression levels Peng, Yu; Leung, Henry C. M.; Yiu, Siu-Ming Bioinformatics, Vol. 29, Issue 13 https://doi.org/10.1093/bioinformatics/btt219	journal	June 2013
Analysis of environmental transcriptomes by DNA microarrays Parro, Víctor; Moreno-Paz, Mercedes; González-Toril, Elena Environmental Microbiology, Vol. 9, Issue 2 https://doi.org/10.1111/j.1462-2920.2006.01162.x	journal	February 2007
Fast and sensitive protein alignment using DIAMOND Buchfink, Benjamin; Xie, Chao; Huson, Daniel H. Nature Methods, Vol. 12, Issue 1 https://doi.org/10.1038/nmeth.3176	journal	November 2014
Fast and sensitive taxonomic classification for metagenomics with Kaiju Menzel, Peter; Ng, Kim Lee; Krogh, Anders Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms11257	journal	April 2016
Kraken: ultrafast metagenomic sequence classification using exact alignments Wood, Derrick E.; Salzberg, Steven L. Genome Biology, Vol. 15, Issue 3 https://doi.org/10.1186/gb-2014-15-3-r46	journal	January 2014
Comparative Metatranscriptomics of Wheat Rhizosphere Microbiomes in Disease Suppressive and Non-suppressive Soils for Rhizoctonia solani AG8 Hayden, Helen L.; Savin, Keith W.; Wadeson, Jenny Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.00859	journal	May 2018
Comparative metagenomic and metatranscriptomic analyses reveal the breed effect on the rumen microbiome and its associations with feed efficiency in beef cattle Li, Fuyong; Hitch, Thomas C. A.; Chen, Yanhong Microbiome, Vol. 7, Issue 1 https://doi.org/10.1186/s40168-019-0618-5	journal	January 2019
De novo assembly and analysis of RNA-seq data Robertson, Gordon; Schein, Jacqueline; Chiu, Readman Nature Methods, Vol. 7, Issue 11 https://doi.org/10.1038/nmeth.1517	journal	October 2010
Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform Li, Po-E; Lo, Chien-Chi; Anderson, Joseph J. Nucleic Acids Research, Vol. 45, Issue 1 https://doi.org/10.1093/nar/gkw1027	journal	November 2016
Analysis of Microbial Gene Transcripts in Environmental Samples Poretsky, R. S.; Bano, N.; Buchan, A. Applied and Environmental Microbiology, Vol. 71, Issue 7 https://doi.org/10.1128/AEM.71.7.4121-4126.2005	journal	July 2005
Strand-specific community RNA-seq reveals prevalent and dynamic antisense transcription in human gut microbiota Bao, Guanhui; Wang, Mingjie; Doak, Thomas G. Frontiers in Microbiology, Vol. 6 https://doi.org/10.3389/fmicb.2015.00896	journal	September 2015
Virus-host relationships of marine single-celled eukaryotes resolved from metatranscriptomics Moniruzzaman, Mohammad; Wurch, Louie L.; Alexander, Harriet Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/ncomms16054	journal	June 2017
Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels Schulz, Marcel H.; Zerbino, Daniel R.; Vingron, Martin Bioinformatics, Vol. 28, Issue 8 https://doi.org/10.1093/bioinformatics/bts094	journal	February 2012
Moleculo Long-Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil Metagenomes White, Richard Allen; Bottos, Eric M.; Roy Chowdhury, Taniya mSystems, Vol. 1, Issue 3 https://doi.org/10.1128/mSystems.00045-16	journal	June 2016
SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads Xie, Y.; Wu, G.; Tang, J. Bioinformatics, Vol. 30, Issue 12 https://doi.org/10.1093/bioinformatics/btu077	journal	February 2014
Metatranscriptomics and Amplicon Sequencing Reveal Mutualisms in Seagrass Microbiomes Crump, Byron C.; Wojahn, John M.; Tomas, Fiona Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.00388	journal	March 2018
BinPacker: Packing-Based De Novo Transcriptome Assembly from RNA-seq Data Liu, Juntao; Li, Guojun; Chang, Zheng PLOS Computational Biology, Vol. 12, Issue 2 https://doi.org/10.1371/journal.pcbi.1004772	journal	February 2016
IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth Peng, Y.; Leung, H. C. M.; Yiu, S. M. Bioinformatics, Vol. 28, Issue 11 https://doi.org/10.1093/bioinformatics/bts174	journal	April 2012
Prokka: rapid prokaryotic genome annotation Seemann, T. Bioinformatics, Vol. 30, Issue 14 https://doi.org/10.1093/bioinformatics/btu153	journal	March 2014
Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere microbiome of plants Turner, Thomas R.; Ramakrishnan, Karunakaran; Walshaw, John The ISME Journal, Vol. 7, Issue 12 https://doi.org/10.1038/ismej.2013.119	journal	July 2013
FragGeneScan: predicting genes in short and error-prone reads Rho, Mina; Tang, Haixu; Ye, Yuzhen Nucleic Acids Research, Vol. 38, Issue 20 https://doi.org/10.1093/nar/gkq747	journal	August 2010
SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data Kopylova, Evguenia; Noé, Laurent; Touzet, Hélène Bioinformatics, Vol. 28, Issue 24 https://doi.org/10.1093/bioinformatics/bts611	journal	October 2012
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data Robinson, M. D.; McCarthy, D. J.; Smyth, G. K. Bioinformatics, Vol. 26, Issue 1 https://doi.org/10.1093/bioinformatics/btp616	journal	November 2009
limma powers differential expression analyses for RNA-sequencing and microarray studies Ritchie, Matthew E.; Phipson, Belinda; Wu, Di Nucleic Acids Research, Vol. 43, Issue 7 https://doi.org/10.1093/nar/gkv007	journal	January 2015
iPath2.0: interactive pathway explorer Yamada, Takuji; Letunic, Ivica; Okuda, Shujiro Nucleic Acids Research, Vol. 39, Issue suppl_2 https://doi.org/10.1093/nar/gkr313	journal	May 2011
UniProt: a worldwide hub of protein knowledge Consortium, The UniProt Nucleic Acids Research https://doi.org/10.1093/nar/gky1049		November 2018
IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses Narayanasamy, Shaman; Jarosz, Yohan; Muller, Emilie E. L. Genome Biology, Vol. 17, Issue 1 https://doi.org/10.1186/s13059-016-1116-8	journal	December 2016
Environmental Genome Shotgun Sequencing of the Sargasso Sea Venter, J. C. Science, Vol. 304, Issue 5667 https://doi.org/10.1126/science.1093857	journal	April 2004
MetaPhlAn2 for enhanced metagenomic taxonomic profiling Truong, Duy Tin; Franzosa, Eric A.; Tickle, Timothy L. Nature Methods, Vol. 12, Issue 10 https://doi.org/10.1038/nmeth.3589	journal	September 2015
Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation O'Leary, Nuala A.; Wright, Mathew W.; Brister, J. Rodney Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1189	journal	November 2015
Metatranscriptomic census of active protists in soils Geisen, Stefan; Tveit, Alexander T.; Clark, Ian M. The ISME Journal, Vol. 9, Issue 10 https://doi.org/10.1038/ismej.2015.30	journal	March 2015
Comparison of assembly algorithms for improving rate of metatranscriptomic functional annotation Celaj, Albi; Markle, Janet; Danska, Jayne Microbiome, Vol. 2, Issue 1 https://doi.org/10.1186/2049-2618-2-39	journal	January 2014
SAMSA2: a standalone metatranscriptome analysis pipeline Westreich, Samuel T.; Treiber, Michelle L.; Mills, David A. BMC Bioinformatics, Vol. 19, Issue 1 https://doi.org/10.1186/s12859-018-2189-z	journal	May 2018
SqueezeMeta, A Highly Portable, Fully Automatic Metagenomic Analysis Pipeline Tamames, Javier; Puente-Sánchez, Fernando Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.03349	journal	January 2019
Relating the metatranscriptome and metagenome of the human gut Franzosa, E. A.; Morgan, X. C.; Segata, N. Proceedings of the National Academy of Sciences, Vol. 111, Issue 22 https://doi.org/10.1073/pnas.1319284111	journal	May 2014
UProC: tools for ultra-fast protein domain classification Meinicke, Peter Bioinformatics, Vol. 31, Issue 9 https://doi.org/10.1093/bioinformatics/btu843	journal	December 2014
Data quality aware analysis of differential expression in RNA-seq with NOISeq R/Bioc package Tarazona, Sonia; Furió-Tarí, Pedro; Turrà, David Nucleic Acids Research https://doi.org/10.1093/nar/gkv711	journal	July 2015
Metatranscriptomics Reveals the Diversity of Genes Expressed by Eukaryotes in Forest Soils Damon, Coralie; Lehembre, Frédéric; Oger-Desfeux, Christine PLoS ONE, Vol. 7, Issue 1 https://doi.org/10.1371/journal.pone.0028967	journal	January 2012
Rapid evaluation and quality control of next generation sequencing data with FaQCs Lo, Chien-Chi; Chain, Patrick S. G. BMC Bioinformatics, Vol. 15, Issue 1 https://doi.org/10.1186/s12859-014-0366-2	journal	November 2014
Detection of Large Numbers of Novel Sequences in the Metatranscriptomes of Complex Marine Microbial Communities Gilbert, Jack A.; Field, Dawn; Huang, Ying PLoS ONE, Vol. 3, Issue 8 https://doi.org/10.1371/journal.pone.0003042	journal	August 2008
Metatranscriptomics reveals unique microbial small RNAs in the ocean’s water column Shi, Yanmei; Tyson, Gene W.; DeLong, Edward F. Nature, Vol. 459, Issue 7244 https://doi.org/10.1038/nature08055	journal	May 2009
Diet affects arctic ground squirrel gut microbial metatranscriptome independent of community structure: Microbiota of fattening arctic ground squirrels Hatton, Jasmine J.; Stevenson, Timothy J.; Buck, C. Loren Environmental Microbiology, Vol. 19, Issue 4 https://doi.org/10.1111/1462-2920.13712	journal	April 2017
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 Love, Michael I.; Huber, Wolfgang; Anders, Simon Genome Biology, Vol. 15, Issue 12 https://doi.org/10.1186/s13059-014-0550-8	journal	December 2014
fastp: an ultra-fast all-in-one FASTQ preprocessor Chen, Shifu; Zhou, Yanqing; Chen, Yaru Bioinformatics, Vol. 34, Issue 17 https://doi.org/10.1093/bioinformatics/bty560	journal	September 2018
COMAN: a web server for comprehensive metatranscriptomics analysis Ni, Yueqiong; Li, Jun; Panagiotou, Gianni BMC Genomics, Vol. 17, Issue 1 https://doi.org/10.1186/s12864-016-2964-z	journal	August 2016
IDBA-MTP: A Hybrid Metatranscriptomic Assembler Based on Protein Information Leung, Henry C. M.; Yiu, Siu-Ming; Chin, Francis Y. L. Journal of Computational Biology, Vol. 22, Issue 5 https://doi.org/10.1089/cmb.2014.0139	journal	May 2015
Virus-host relationships of marine single-celled eukaryotes resolved from metatranscriptomics Moniruzzaman, Mohammad; Wurch, Louie L.; Alexander, Harriet Columbia University https://doi.org/10.7916/d8zk6tjz	text	January 2017
Viruses infecting a warm water picoeukaryote shed light on spatial co-occurrence dynamics of marine viruses and their hosts Bachy, Charles; Yung, Charmaine C. M.; Needham, David M. The ISME Journal https://doi.org/10.1038/s41396-021-00989-9	journal	May 2021
Draft Genome Sequence of Comamonas aquatilis Strain LK (= CSUR P6418 = CECT 9772), Isolated from the Planarian Schmidtea mediterranea Kangale, Luis Johnson; Levasseur, Anthony; Raoult, Didier Microbiology Resource Announcements, Vol. 10, Issue 5 https://doi.org/10.1128/mra.00297-20	journal	February 2021
Datura genome reveals duplications of psychoactive alkaloid biosynthetic genes and high mutation rate following tissue culture Rajewski, Alex; Carter-House, Derreck; Stajich, Jason BMC Genomics, Vol. 22, Issue 1 https://doi.org/10.1186/s12864-021-07489-2	journal	March 2021
Characterization and functional analysis of phytoene synthase gene family in tobacco Wang, Zhaojun; Zhang, Lin; Dong, Chen BMC Plant Biology, Vol. 21, Issue 1 https://doi.org/10.1186/s12870-020-02816-3	journal	January 2021
Polinton-like viruses are abundant in aquatic ecosystems Bellas, Christopher M.; Sommaruga, Ruben Microbiome, Vol. 9, Issue 1 https://doi.org/10.1186/s40168-020-00956-0	journal	January 2021
Long reads: their purpose and place. Pollard, Martin O.; Gurdasani, Deepti; Mentzer, Alexander J. Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.38576	text	January 2018
limma powers differential expression analyses for RNA-sequencing and microarray studies Ritchie, Matthew E.; Phipson, Belinda; Wu, Di Oxford University Press https://doi.org/10.5167/uzh-155268	text	January 2015
Metatranscriptomic census of active protists in soils Geisen, Stefan DataverseNL https://doi.org/10.34894/xess9x	dataset	January 2016
SOAPdenovo-Trans: De novo transcriptome assembly with short RNA-Seq reads Xie, Yinlong; Wu, Gengxiong; Tang, Jingbo arXiv https://doi.org/10.48550/arxiv.1305.6760	preprint	January 2013
MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph Li, Dinghua; Liu, Chi-Man; Luo, Ruibang arXiv https://doi.org/10.48550/arxiv.1409.7208	preprint	January 2014
Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis Ye, Yuzhen; Tang, Haixu arXiv https://doi.org/10.48550/arxiv.1504.01304	preprint	January 2015
Combining metagenomics, metatranscriptomics and viromics to explore novel microbial interactions: towards a systems-level understanding of human microbiome Bikel, Shirley; Valdez-Lara, Alejandra; Cornejo-Granados, Fernanda Computational and Structural Biotechnology Journal, Vol. 13 https://doi.org/10.1016/j.csbj.2015.06.001	journal	January 2015
Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere microbiome of plants Turner, Thomas R.; Ramakrishnan, Karunakaran; Walshaw, John The ISME Journal, Vol. 7, Issue 12 https://doi.org/10.1038/ismej.2013.119	journal	July 2013
Metatranscriptomic census of active protists in soils Geisen, Stefan; Tveit, Alexander T.; Clark, Ian M. The ISME Journal, Vol. 9, Issue 10 https://doi.org/10.1038/ismej.2015.30	journal	March 2015
Metatranscriptomics reveals unique microbial small RNAs in the ocean’s water column Shi, Yanmei; Tyson, Gene W.; DeLong, Edward F. Nature, Vol. 459, Issue 7244 https://doi.org/10.1038/nature08055	journal	May 2009
A human gut microbial gene catalogue established by metagenomic sequencing Qin, Junjie; Li, Ruiqiang; Raes, Jeroen Nature, Vol. 464, Issue 7285 https://doi.org/10.1038/nature08821	journal	March 2010
Enterotypes of the human gut microbiome Arumugam, Manimozhiyan; Raes, Jeroen; Pelletier, Eric Nature, Vol. 473, Issue 7346 https://doi.org/10.1038/nature09944	journal	April 2011
Full-length transcriptome assembly from RNA-Seq data without a reference genome Grabherr, Manfred G.; Haas, Brian J.; Yassour, Moran Nature Biotechnology, Vol. 29, Issue 7 https://doi.org/10.1038/nbt.1883	journal	May 2011
Fast and sensitive taxonomic classification for metagenomics with Kaiju Menzel, Peter; Ng, Kim Lee; Krogh, Anders Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms11257	journal	April 2016
De novo assembly and analysis of RNA-seq data Robertson, Gordon; Schein, Jacqueline; Chiu, Readman Nature Methods, Vol. 7, Issue 11 https://doi.org/10.1038/nmeth.1517	journal	October 2010
MetaPhlAn2 for enhanced metagenomic taxonomic profiling Truong, Duy Tin; Franzosa, Eric A.; Tickle, Timothy L. Nature Methods, Vol. 12, Issue 10 https://doi.org/10.1038/nmeth.3589	journal	September 2015
Commensal Pseudomonas protect Arabidopsis thaliana from a coexisting pathogen via multiple lineage-dependent mechanisms Shalev, Or; Ashkenazy, Haim; Neumann, Manuela The ISME Journal, Vol. 16, Issue 5 https://doi.org/10.1038/s41396-021-01168-6	journal	December 2021
Evolution of the murine gut resistome following broad-spectrum antibiotic treatment de Nies, Laura; Busi, Susheel Bhanu; Tsenkova, Mina Nature Communications, Vol. 13, Issue 1 https://doi.org/10.1038/s41467-022-29919-9	journal	April 2022
Dynamics of metatranscription in the inflammatory bowel disease gut microbiome Schirmer, Melanie; Franzosa, Eric A.; Lloyd-Price, Jason Nature Microbiology, Vol. 3, Issue 3 https://doi.org/10.1038/s41564-017-0089-z	journal	January 2018
The gut microbiota is associated with immune cell dynamics in humans Schluter, Jonas; Peled, Jonathan U.; Taylor, Bradford P. Nature, Vol. 588, Issue 7837 https://doi.org/10.1038/s41586-020-2971-8	journal	November 2020
CXCR4 signaling directs Igk recombination and the molecular mechanisms of late B lymphopoiesis Mandal, Malay; Okoreeh, Michael K.; Kennedy, Domenick E. Nature Immunology, Vol. 20, Issue 10 https://doi.org/10.1038/s41590-019-0468-0	journal	September 2019
High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing Karst, Søren M.; Ziels, Ryan M.; Kirkegaard, Rasmus H. Nature Methods, Vol. 18, Issue 2 https://doi.org/10.1038/s41592-020-01041-y	journal	January 2021
Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain Raldúa, Demetrio; Casado, Marta; Prats, Eva Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-019-57142-y	journal	January 2020
Red versus green leaves: transcriptomic comparison of foliar senescence between two Prunus cerasifera genotypes Vangelisti, Alberto; Guidi, Lucia; Cavallini, Andrea Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-58878-8	journal	February 2020
MetaTrans: an open-source pipeline for metatranscriptomics Martinez, Xavier; Pozuelo, Marta; Pascal, Victoria Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep26447	journal	May 2016
Microbial community gene expression in ocean surface waters Frias-Lopez, J.; Shi, Y.; Tyson, G. W. Proceedings of the National Academy of Sciences, Vol. 105, Issue 10 https://doi.org/10.1073/pnas.0708897105	journal	March 2008
Relating the metatranscriptome and metagenome of the human gut Franzosa, E. A.; Morgan, X. C.; Segata, N. Proceedings of the National Academy of Sciences, Vol. 111, Issue 22 https://doi.org/10.1073/pnas.1319284111	journal	May 2014
IDBA-MT: De Novo Assembler for Metatranscriptomic Data Generated from Next-Generation Sequencing Technology Leung, Henry C. M.; Yiu, Siu-Ming; Parkinson, John Journal of Computational Biology, Vol. 20, Issue 7 https://doi.org/10.1089/cmb.2013.0042	journal	July 2013
IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth Peng, Y.; Leung, H. C. M.; Yiu, S. M. Bioinformatics, Vol. 28, Issue 11 https://doi.org/10.1093/bioinformatics/bts174	journal	April 2012
SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data Kopylova, Evguenia; Noé, Laurent; Touzet, Hélène Bioinformatics, Vol. 28, Issue 24 https://doi.org/10.1093/bioinformatics/bts611	journal	October 2012
IDBA-tran: a more robust de novo de Bruijn graph assembler for transcriptomes with uneven expression levels Peng, Yu; Leung, Henry C. M.; Yiu, Siu-Ming Bioinformatics, Vol. 29, Issue 13 https://doi.org/10.1093/bioinformatics/btt219	journal	June 2013
UProC: tools for ultra-fast protein domain classification Meinicke, Peter Bioinformatics, Vol. 31, Issue 9 https://doi.org/10.1093/bioinformatics/btu843	journal	December 2014
MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph Li, Dinghua; Liu, Chi-Man; Luo, Ruibang Bioinformatics, Vol. 31, Issue 10 https://doi.org/10.1093/bioinformatics/btv033	journal	January 2015
Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis Ye, Yuzhen; Tang, Haixu Bioinformatics, Vol. 32, Issue 7 https://doi.org/10.1093/bioinformatics/btv510	journal	August 2015
rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data Bushmanova, Elena; Antipov, Dmitry; Lapidus, Alla GigaScience, Vol. 8, Issue 9 https://doi.org/10.1093/gigascience/giz100	journal	September 2019
FragGeneScan: predicting genes in short and error-prone reads Rho, Mina; Tang, Haixu; Ye, Yuzhen Nucleic Acids Research, Vol. 38, Issue 20 https://doi.org/10.1093/nar/gkq747	journal	August 2010
iPath2.0: interactive pathway explorer Yamada, Takuji; Letunic, Ivica; Okuda, Shujiro Nucleic Acids Research, Vol. 39, Issue suppl_2 https://doi.org/10.1093/nar/gkr313	journal	May 2011
The MG-RAST metagenomics database and portal in 2015 Wilke, Andreas; Bischof, Jared; Gerlach, Wolfgang Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1322	journal	December 2015
Accurate read-based metagenome characterization using a hierarchical suite of unique signatures Freitas, Tracey Allen K.; Li, Po-E; Scholz, Matthew B. Nucleic Acids Research, Vol. 43, Issue 10 https://doi.org/10.1093/nar/gkv180	journal	March 2015
Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform Li, Po-E; Lo, Chien-Chi; Anderson, Joseph J. Nucleic Acids Research, Vol. 45, Issue 1 https://doi.org/10.1093/nar/gkw1027	journal	November 2016
Centrifuge: rapid and sensitive classification of metagenomic sequences Kim, Daehwan; Song, Li; Breitwieser, Florian P. Genome Research, Vol. 26, Issue 12 https://doi.org/10.1101/gr.210641.116	journal	October 2016
Analysis of environmental transcriptomes by DNA microarrays Parro, Víctor; Moreno-Paz, Mercedes; González-Toril, Elena Environmental Microbiology, Vol. 9, Issue 2 https://doi.org/10.1111/j.1462-2920.2006.01162.x	journal	February 2007
Environmental Genome Shotgun Sequencing of the Sargasso Sea Venter, J. C. Science, Vol. 304, Issue 5667 https://doi.org/10.1126/science.1093857	journal	April 2004
GAGE: generally applicable gene set enrichment for pathway analysis Luo, Weijun; Friedman, Michael S.; Shedden, Kerby BMC Bioinformatics, Vol. 10, Issue 1 https://doi.org/10.1186/1471-2105-10-161	journal	January 2009
Comparison of assembly algorithms for improving rate of metatranscriptomic functional annotation Celaj, Albi; Markle, Janet; Danska, Jayne Microbiome, Vol. 2, Issue 1 https://doi.org/10.1186/2049-2618-2-39	journal	January 2014
Kraken: ultrafast metagenomic sequence classification using exact alignments Wood, Derrick E.; Salzberg, Steven L. Genome Biology, Vol. 15, Issue 3 https://doi.org/10.1186/gb-2014-15-3-r46	journal	January 2014
Rapid evaluation and quality control of next generation sequencing data with FaQCs Lo, Chien-Chi; Chain, Patrick S. G. BMC Bioinformatics, Vol. 15, Issue 1 https://doi.org/10.1186/s12859-014-0366-2	journal	November 2014
FMAP: Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies Kim, Jiwoong; Kim, Min Soo; Koh, Andrew Y. BMC Bioinformatics, Vol. 17, Issue 1 https://doi.org/10.1186/s12859-016-1278-0	journal	October 2016
SAMSA2: a standalone metatranscriptome analysis pipeline Westreich, Samuel T.; Treiber, Michelle L.; Mills, David A. BMC Bioinformatics, Vol. 19, Issue 1 https://doi.org/10.1186/s12859-018-2189-z	journal	May 2018
COMAN: a web server for comprehensive metatranscriptomics analysis Ni, Yueqiong; Li, Jun; Panagiotou, Gianni BMC Genomics, Vol. 17, Issue 1 https://doi.org/10.1186/s12864-016-2964-z	journal	August 2016
Meta-transcriptomics reveals a diverse antibiotic resistance gene pool in avian microbiomes Marcelino, Vanessa R.; Wille, Michelle; Hurt, Aeron C. BMC Biology, Vol. 17, Issue 1 https://doi.org/10.1186/s12915-019-0649-1	journal	April 2019
IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses Narayanasamy, Shaman; Jarosz, Yohan; Muller, Emilie E. L. Genome Biology, Vol. 17, Issue 1 https://doi.org/10.1186/s13059-016-1116-8	journal	December 2016
Trees, fungi and bacteria: tripartite metatranscriptomics of a root microbiome responding to soil contamination Gonzalez, E.; Pitre, F. E.; Pagé, A. P. Microbiome, Vol. 6, Issue 1 https://doi.org/10.1186/s40168-018-0432-5	journal	March 2018
Comparative metagenomic and metatranscriptomic analyses reveal the breed effect on the rumen microbiome and its associations with feed efficiency in beef cattle Li, Fuyong; Hitch, Thomas C. A.; Chen, Yanhong Microbiome, Vol. 7, Issue 1 https://doi.org/10.1186/s40168-019-0618-5	journal	January 2019
A Parsimony Approach to Biological Pathway Reconstruction/Inference for Genomes and Metagenomes Ye, Yuzhen; Doak, Thomas G. PLoS Computational Biology, Vol. 5, Issue 8 https://doi.org/10.1371/journal.pcbi.1000465	journal	August 2009
BinPacker: Packing-Based De Novo Transcriptome Assembly from RNA-seq Data Liu, Juntao; Li, Guojun; Chang, Zheng PLOS Computational Biology, Vol. 12, Issue 2 https://doi.org/10.1371/journal.pcbi.1004772	journal	February 2016
Metagenome and Metatranscriptome Analyses Using Protein Family Profiles Zhong, Cuncong; Edlund, Anna; Yang, Youngik PLOS Computational Biology, Vol. 12, Issue 7 https://doi.org/10.1371/journal.pcbi.1004991	journal	July 2016
Detection of Large Numbers of Novel Sequences in the Metatranscriptomes of Complex Marine Microbial Communities Gilbert, Jack A.; Field, Dawn; Huang, Ying PLoS ONE, Vol. 3, Issue 8 https://doi.org/10.1371/journal.pone.0003042	journal	August 2008
Dual Transcriptomic Profiling of Host and Microbiota during Health and Disease in Pediatric Asthma Pérez-Losada, Marcos; Castro-Nallar, Eduardo; Bendall, Matthew L. PLOS ONE, Vol. 10, Issue 6 https://doi.org/10.1371/journal.pone.0131819	journal	June 2015
Long reads: their purpose and place. Pollard, Martin O.; Gurdasani, Deepti; Mentzer, Alexander J. Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.38576	text	January 2018
Strand-specific community RNA-seq reveals prevalent and dynamic antisense transcription in human gut microbiota Bao, Guanhui; Wang, Mingjie; Doak, Thomas G. Frontiers in Microbiology, Vol. 6 https://doi.org/10.3389/fmicb.2015.00896	journal	September 2015
Enhancing the Resolution of Rumen Microbial Classification from Metatranscriptomic Data Using Kraken and Mothur Neves, Andre L. A.; Li, Fuyong; Ghoshal, Bibaswan Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.02445	journal	December 2017
Metatranscriptomics and Amplicon Sequencing Reveal Mutualisms in Seagrass Microbiomes Crump, Byron C.; Wojahn, John M.; Tomas, Fiona Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.00388	journal	March 2018
Comparative Metatranscriptomics of Wheat Rhizosphere Microbiomes in Disease Suppressive and Non-suppressive Soils for Rhizoctonia solani AG8 Hayden, Helen L.; Savin, Keith W.; Wadeson, Jenny Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.00859	journal	May 2018
Metagenomic and Metatranscriptomic Analyses of Diverse Watermelon Cultivars Reveal the Role of Fruit Associated Microbiome in Carbohydrate Metabolism and Ripening of Mature Fruits Saminathan, Thangasamy; García, Marleny; Ghimire, Bandana Frontiers in Plant Science, Vol. 9 https://doi.org/10.3389/fpls.2018.00004	journal	January 2018
Sugars dominate the seagrass rhizosphere Maggie, Sogin, E.; Dolma, Michellod,; Harald, Gruber-Vodicka, ETH Zurich https://doi.org/10.3929/ethz-b-000547211	text	January 2022
Comparative metatranscriptomics of wheat rhizosphere microbiomes in disease suppressive and non-suppressive soils for Rhizoctonia solani AG8. Hayden, Helen; Savin, Keith W.; Wadeson, Jenny figshare https://doi.org/10.6084/m9.figshare.5657215.v1	dataset	January 2018

Cited By (4)

Metatranscriptomics: an approach for retrieving novel eukaryotic genes from polluted and related environments Mukherjee, Arkadeep; Reddy, M. Sudhakara 3 Biotech, Vol. 10, Issue 2 https://doi.org/10.1007/s13205-020-2057-1	journal	January 2020
Perplexity: Evaluating Transcript Abundance Estimation in the Absence of Ground Truth Fan, Jason; Chan, Skylar; Patro, Rob Schloss Dagstuhl - Leibniz-Zentrum für Informatik https://doi.org/10.4230/lipics.wabi.2021.4	text	January 2021
Perplexity: evaluating transcript abundance estimation in the absence of ground truth Fan, Jason; Chan, Skylar; Patro, Rob Algorithms for Molecular Biology, Vol. 17, Issue 1 https://doi.org/10.1186/s13015-022-00214-y	journal	March 2022
Perplexity: evaluating transcript abundance estimation in the absence of ground truth Fan, Jason; Chan, Skylar; Patro, Rob Springer Nature https://doi.org/10.13016/xfag-oldz	text	January 2022

Similar Records

Improved Method for Isolation of Microbial RNA from Biofuel Feedstock for Metatranscriptomics

Journal Article · 2013 · Advances in Microbiology, 3(1):101-107 · OSTI ID:1094933

Piao, Hailan; Markillie, Lye Meng; Culley, David E.; +2 more

Metatranscriptomics and Amplicon Sequencing Reveal Mutualisms in Seagrass Microbiomes

Journal Article · 2018 · Frontiers in Microbiology · OSTI ID:1628164

Crump, Byron C.; Wojahn, John M.; Tomas, Fiona; +1 more

Metaphenomic Responses of a Native Prairie Soil Microbiome to Moisture Perturbations

Journal Article · 2019 · mSystems · OSTI ID:1530883

Roy Chowdhury, Taniya; Lee, Joon-Yong; Bottos, Eric M.; +14 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
RNASeq
microbiome
workflows
gene expression
omics

Title: Advances and Challenges in Metatranscriptomic Analysis

Citation Formats

References (154)

Cited By (4)

Similar Records

Related Subjects