Metagenomic tools in microbial ecology research

Taş, Neslihan; de Jong, Anniek EE; Li, Yaoming; Trubl, Gareth; Xue, Yaxin; Dove, Nicholas C.

doi:10.1016/j.copbio.2021.01.019

Metagenomic tools in microbial ecology research

Journal Article · Mon Feb 01 00:00:00 EST 2021 · Current Opinion in Biotechnology

DOI:https://doi.org/10.1016/j.copbio.2021.01.019· OSTI ID:1765899

Taş, Neslihan; ; Li, Yaoming; Trubl, Gareth; Xue, Yaxin; Dove, Nicholas C.

Not Available

View Journal Article

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States); Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: National Natural Science Foundation of China (NNSFC); Netherlands Earth System Science Center (NESSC); USDOE Laboratory Directed Research and Development (LDRD) Program; USDOE National Nuclear Security Administration (NNSA); USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC05-00OR22725; AC52-07NA27344

OSTI ID:: 1765899

Alternate ID(s):: OSTI ID: 1767856
OSTI ID: 1767985
OSTI ID: 1788337

Report Number(s):: LLNL-JRNL--814338; S0958166921000240; PII: S0958166921000240

Journal Information:: Current Opinion in Biotechnology, Journal Name: Current Opinion in Biotechnology Journal Issue: C Vol. 67; ISSN 0958-1669

Publisher:: ElsevierCopyright Statement

Country of Publication:: United Kingdom

Language:: English

References (56)

Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products Handelsman, Jo; Rondon, Michelle R.; Brady, Sean F. Chemistry & Biology, Vol. 5, Issue 10 https://doi.org/10.1016/S1074-5521(98)90108-9	journal	October 1998
Marine DNA Viral Macro- and Microdiversity from Pole to Pole Gregory, Ann C.; Zayed, Ahmed A.; Conceição-Neto, Nádia Cell, Vol. 177, Issue 5 https://doi.org/10.1016/j.cell.2019.03.040	journal	May 2019
Characterization of vesicular stomatitis virus populations by tunable resistive pulse sensing Akpinar, Fulya; Yin, John Journal of Virological Methods, Vol. 218 https://doi.org/10.1016/j.jviromet.2015.02.006	journal	June 2015
Long-Read Sequencing – A Powerful Tool in Viral Transcriptome Research Boldogkői, Zsolt; Moldován, Norbert; Balázs, Zsolt Trends in Microbiology, Vol. 27, Issue 7 https://doi.org/10.1016/j.tim.2019.01.010	journal	July 2019
Host-Associated Quantitative Abundance Profiling Reveals the Microbial Load Variation of Root Microbiome Guo, Xiaoxuan; Zhang, Xiaoning; Qin, Yuan Plant Communications, Vol. 1, Issue 1 https://doi.org/10.1016/j.xplc.2019.100003	journal	January 2020
Translocation of Rigid Rod-Shaped Virus through Various Solid-State Nanopores Wu, Hongwen; Chen, Yuhao; Zhou, Qizhao Analytical Chemistry, Vol. 88, Issue 4 https://doi.org/10.1021/acs.analchem.5b04905	journal	February 2016
Community structure and metabolism through reconstruction of microbial genomes from the environment Tyson, Gene W.; Chapman, Jarrod; Hugenholtz, Philip Nature, Vol. 428, Issue 6978 https://doi.org/10.1038/nature02340	journal	February 2004
Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes Hultman, Jenni; Waldrop, Mark P.; Mackelprang, Rachel Nature, Vol. 521, Issue 7551 https://doi.org/10.1038/nature14238	journal	March 2015
Complex archaea that bridge the gap between prokaryotes and eukaryotes Spang, Anja; Saw, Jimmy H.; Jørgensen, Steffen L. Nature, Vol. 521, Issue 7551 https://doi.org/10.1038/nature14447	journal	May 2015
Unusual biology across a group comprising more than 15% of domain Bacteria Brown, Christopher T.; Hug, Laura A.; Thomas, Brian C. Nature, Vol. 523, Issue 7559 https://doi.org/10.1038/nature14486	journal	June 2015
Complete nitrification by Nitrospira bacteria Daims, Holger; Lebedeva, Elena V.; Pjevac, Petra Nature, Vol. 528, Issue 7583 https://doi.org/10.1038/nature16461	journal	November 2015
New CRISPR–Cas systems from uncultivated microbes Burstein, David; Harrington, Lucas B.; Strutt, Steven C. Nature, Vol. 542, Issue 7640 https://doi.org/10.1038/nature21059	journal	December 2016
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea Bowers, Robert M.; Kyrpides, Nikos C.; Stepanauskas, Ramunas Nature Biotechnology, Vol. 35, Issue 8 https://doi.org/10.1038/nbt.3893	journal	August 2017
KBase: The United States Department of Energy Systems Biology Knowledgebase Arkin, Adam P.; Cottingham, Robert W.; Henry, Christopher S. Nature Biotechnology, Vol. 36, Issue 7 https://doi.org/10.1038/nbt.4163	journal	July 2018
Minimum Information about an Uncultivated Virus Genome (MIUViG) Roux, Simon; Adriaenssens, Evelien M.; Dutilh, Bas E. Nature Biotechnology, Vol. 37, Issue 1 https://doi.org/10.1038/nbt.4306	journal	December 2018
Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs Eloe-Fadrosh, Emiley A.; Paez-Espino, David; Jarett, Jessica Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms10476	journal	January 2016
Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system Anantharaman, Karthik; Brown, Christopher T.; Hug, Laura A. Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms13219	journal	October 2016
Single-virus genomics reveals hidden cosmopolitan and abundant viruses Martinez-Hernandez, Francisco; Fornas, Oscar; Lluesma Gomez, Monica Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/ncomms15892	journal	June 2017
Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota Vanwonterghem, Inka; Evans, Paul N.; Parks, Donovan H. Nature Microbiology, Vol. 1, Issue 12 https://doi.org/10.1038/nmicrobiol.2016.170	journal	October 2016
Genomic and enzymatic evidence for acetogenesis among multiple lineages of the archaeal phylum Bathyarchaeota widespread in marine sediments He, Y.; Li, M.; Perumal, V. Nature Microbiology, Vol. 1, Issue 6 https://doi.org/10.1038/nmicrobiol.2016.35	journal	April 2016
Embracing the unknown: disentangling the complexities of the soil microbiome Fierer, Noah Nature Reviews Microbiology, Vol. 15, Issue 10 https://doi.org/10.1038/nrmicro.2017.87	journal	August 2017
Patterns of protist diversity associated with raw sewage in New York City Maritz, Julia M.; Ten Eyck, Theresa A.; Elizabeth Alter, S. The ISME Journal, Vol. 13, Issue 11 https://doi.org/10.1038/s41396-019-0467-z	journal	July 2019
Landscape topography structures the soil microbiome in arctic polygonal tundra Taş, Neslihan; Prestat, Emmanuel; Wang, Shi Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-03089-z	journal	February 2018
Environmental conditions shape the nature of a minimal bacterial genome Antczak, Magdalena; Michaelis, Martin; Wass, Mark N. Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-10837-2	journal	July 2019
Droplet Tn-Seq combines microfluidics with Tn-Seq for identifying complex single-cell phenotypes Thibault, Derek; Jensen, Paul A.; Wood, Stephen Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-13719-9	journal	December 2019
Integration of absolute multi-omics reveals dynamic protein-to-RNA ratios and metabolic interplay within mixed-domain microbiomes Delogu, F.; Kunath, B. J.; Evans, P. N. Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-18543-0	journal	September 2020
Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life Parks, Donovan H.; Rinke, Christian; Chuvochina, Maria Nature Microbiology, Vol. 2, Issue 11 https://doi.org/10.1038/s41564-017-0012-7	journal	September 2017
Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes Delmont, Tom O.; Quince, Christopher; Shaiber, Alon Nature Microbiology, Vol. 3, Issue 7 https://doi.org/10.1038/s41564-018-0176-9	journal	June 2018
Host-linked soil viral ecology along a permafrost thaw gradient Emerson, Joanne B.; Roux, Simon; Brum, Jennifer R. Nature Microbiology, Vol. 3, Issue 8 https://doi.org/10.1038/s41564-018-0190-y	journal	July 2018
Bacterial fermentation and respiration processes are uncoupled in anoxic permeable sediments Kessler, Adam J.; Chen, Ya-Jou; Waite, David W. Nature Microbiology, Vol. 4, Issue 6 https://doi.org/10.1038/s41564-019-0391-z	journal	March 2019
Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes Roux, Simon; Krupovic, Mart; Daly, Rebecca A. Nature Microbiology https://doi.org/10.1038/s41564-019-0510-x	journal	July 2019
Genome-centric view of carbon processing in thawing permafrost Woodcroft, Ben J.; Singleton, Caitlin M.; Boyd, Joel A. Nature, Vol. 560, Issue 7716 https://doi.org/10.1038/s41586-018-0338-1	journal	July 2018
Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks Bin Jang, Ho; Bolduc, Benjamin; Zablocki, Olivier Nature Biotechnology, Vol. 37, Issue 6 https://doi.org/10.1038/s41587-019-0100-8	journal	May 2019
Genomic features of bacterial adaptation to plants Levy, Asaf; Salas Gonzalez, Isai; Mittelviefhaus, Maximilian Nature Genetics, Vol. 50, Issue 1 https://doi.org/10.1038/s41588-017-0012-9	journal	December 2017
Functional metagenomic analysis of dust-associated microbiomes above the Red Sea Aalismail, Nojood A.; Ngugi, David K.; Díaz-Rúa, Rubén Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-50194-0	journal	September 2019
Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil Starr, Evan P.; Nuccio, Erin E.; Pett-Ridge, Jennifer Proceedings of the National Academy of Sciences, Vol. 116, Issue 51 https://doi.org/10.1073/pnas.1908291116	journal	November 2019
MG-RAST version 4—lessons learned from a decade of low-budget ultra-high-throughput metagenome analysis Meyer, Folker; Bagchi, Saurabh; Chaterji, Somali Briefings in Bioinformatics, Vol. 20, Issue 4 https://doi.org/10.1093/bib/bbx105	journal	September 2017
Ultra-deep, long-read nanopore sequencing of mock microbial community standards Nicholls, Samuel M.; Quick, Joshua C.; Tang, Shuiquan GigaScience, Vol. 8, Issue 5 https://doi.org/10.1093/gigascience/giz043	journal	May 2019
EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies Mitchell, Alex L.; Scheremetjew, Maxim; Denise, Hubert Nucleic Acids Research, Vol. 46, Issue D1 https://doi.org/10.1093/nar/gkx967	journal	October 2017
IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes Chen, I-Min A.; Chu, Ken; Palaniappan, Krishna Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky901	journal	October 2018
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes Parks, Donovan H.; Imelfort, Michael; Skennerton, Connor T. Genome Research, Vol. 25, Issue 7 https://doi.org/10.1101/gr.186072.114	journal	May 2015
Interrogating marine virus-host interactions and elemental transfer with BONCAT and nanoSIMS-based methods: BONCAT and nanoSIMS measurements of viruses Pasulka, Alexis L.; Thamatrakoln, Kimberlee; Kopf, Sebastian H. Environmental Microbiology, Vol. 20, Issue 2 https://doi.org/10.1111/1462-2920.13996	journal	December 2017
‘Metagenomics 2.0’ McMahon, Katherine Environmental Microbiology Reports, Vol. 7, Issue 1 https://doi.org/10.1111/1758-2229.12253	journal	February 2015
Comparative Metagenomics of Microbial Communities Tringe, S. G. Science, Vol. 308, Issue 5721 https://doi.org/10.1126/science.1107851	journal	April 2005
Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla Wrighton, K. C.; Thomas, B. C.; Sharon, I. Science, Vol. 337, Issue 6102 https://doi.org/10.1126/science.1224041	journal	September 2012
Reconstructing the Microbial Diversity and Function of Pre-Agricultural Tallgrass Prairie Soils in the United States Fierer, N.; Ladau, J.; Clemente, J. C. Science, Vol. 342, Issue 6158 https://doi.org/10.1126/science.1243768	journal	October 2013
Structure and function of the global ocean microbiome Sunagawa, S.; Coelho, L. P.; Chaffron, S. Science, Vol. 348, Issue 6237 https://doi.org/10.1126/science.1261359	journal	May 2015
Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics Evans, P. N.; Parks, D. H.; Chadwick, G. L. Science, Vol. 350, Issue 6259 https://doi.org/10.1126/science.aac7745	journal	October 2015
Functional Metagenomics Reveals an Overlooked Diversity and Novel Features of Soil-Derived Bacterial Phosphatases and Phytases Castillo Villamizar, Genis Andrés; Nacke, Heiko; Boehning, Marc mBio, Vol. 10, Issue 1 https://doi.org/10.1128/mBio.01966-18	journal	January 2019
Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing Trubl, Gareth; Jang, Ho Bin; Roux, Simon mSystems, Vol. 3, Issue 5 https://doi.org/10.1128/mSystems.00076-18	journal	October 2018
NanoSIMS: Microscale Quantification of Biogeochemical Activity with Large-Scale Impacts Mayali, Xavier Annual Review of Marine Science, Vol. 12, Issue 1 https://doi.org/10.1146/annurev-marine-010419-010714	journal	January 2020
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
bin3C: exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes DeMaere, Matthew Z.; Darling, Aaron E. Genome Biology, Vol. 20, Issue 1 https://doi.org/10.1186/s13059-019-1643-1	journal	February 2019
The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families Yooseph, Shibu; Sutton, Granger; Rusch, Douglas B. PLoS Biology, Vol. 5, Issue 3 https://doi.org/10.1371/journal.pbio.0050016	journal	March 2007
Coming-of-Age Characterization of Soil Viruses: A User’s Guide to Virus Isolation, Detection within Metagenomes, and Viromics Trubl, Gareth; Hyman, Paul; Roux, Simon Soil Systems, Vol. 4, Issue 2 https://doi.org/10.3390/soilsystems4020023	journal	April 2020
Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands Warwick-Dugdale, Joanna; Solonenko, Natalie; Moore, Karen PeerJ, Vol. 7 https://doi.org/10.7717/peerj.6800	journal	January 2019

Similar Records

Related Subjects

54 ENVIRONMENTAL SCIENCES
59 BASIC BIOLOGICAL SCIENCES
77 NANOSCIENCE AND NANOTECHNOLOGY
97 MATHEMATICS AND COMPUTING

Metagenomic tools in microbial ecology research

Citation Formats

References (56)

Similar Records

Related Subjects