Cargando…

A pipeline for targeted metagenomics of environmental bacteria

BACKGROUND: Metagenomics and single cell genomics provide a window into the genetic repertoire of yet uncultivated microorganisms, but both methods are usually taxonomically untargeted. The combination of fluorescence in situ hybridization (FISH) and fluorescence activated cell sorting (FACS) has th...

Descripción completa

Detalles Bibliográficos
Autores principales:	Grieb, Anissa, Bowers, Robert M., Oggerin, Monike, Goudeau, Danielle, Lee, Janey, Malmstrom, Rex R., Woyke, Tanja, Fuchs, Bernhard M.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2020
Materias:	Research
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7024552/ https://www.ncbi.nlm.nih.gov/pubmed/32061258 http://dx.doi.org/10.1186/s40168-020-0790-7

Ejemplares similares

Dissecting the dominant hot spring microbial populations based on community-wide sampling at single-cell genomic resolution
por: Bowers, Robert M., et al.
Publicado: (2021)

Hidden diversity of soil giant viruses
por: Schulz, Frederik, et al.
Publicado: (2018)

Active microbial biofilms in deep poor porous continental subsurface rocks
por: Escudero, Cristina, et al.
Publicado: (2018)

Complementary Metagenomic Approaches Improve Reconstruction of Microbial Diversity in a Forest Soil
por: Alteio, L. V., et al.
Publicado: (2020)

Metagenomes and Metagenome-Assembled Genomes from Substrate-Amended Hot Spring Sediment Incubations from Yellowstone National Park
por: Reichart, Nicholas J., et al.
Publicado: (2022)

High Potential for Biomass-Degrading Enzymes Revealed by Hot Spring Metagenomics
por: Reichart, Nicholas J., et al.
Publicado: (2021)

Decontamination of MDA Reagents for Single Cell Whole Genome Amplification
por: Woyke, Tanja, et al.
Publicado: (2011)

Subsurface hydrocarbon degradation strategies in low- and high-sulfate coal seam communities identified with activity-based metagenomics
por: Schweitzer, Hannah D., et al.
Publicado: (2022)

Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs
por: Eloe-Fadrosh, Emiley A., et al.
Publicado: (2016)

Analysis of single-cell genome sequences of bacteria and archaea
por: Bowers, Robert M., et al.
Publicado: (2017)

Advantages and Limits of Metagenomic Assembly and Binning of a Giant Virus
por: Schulz, Frederik, et al.
Publicado: (2020)

Hybridization breaks species barriers in long-term coevolution of a cyanobacterial population
por: Birzu, Gabriel, et al.
Publicado: (2023)

Advancing Genome-Resolved Metagenomics beyond the Shotgun
por: Malmstrom, Rex R., et al.
Publicado: (2019)

Optimizing de novo genome assembly from PCR-amplified metagenomes
por: Roux, Simon, et al.
Publicado: (2019)

Assessment of Common and Emerging Bioinformatics Pipelines for Targeted Metagenomics
por: Siegwald, Léa, et al.
Publicado: (2017)

Host population diversity as a driver of viral infection cycle in wild populations of green sulfur bacteria with long standing virus-host interactions
por: Berg, Maureen, et al.
Publicado: (2021)

Physiological potential and evolutionary trajectories of syntrophic sulfate-reducing bacterial partners of anaerobic methanotrophic archaea
por: Murali, Ranjani, et al.
Publicado: (2023)

BONCAT-FACS-Seq reveals the active fraction of a biocrust community undergoing a wet-up event
por: Trexler, Ryan V., et al.
Publicado: (2023)

Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples
por: Yu, Feiqiao Brian, et al.
Publicado: (2017)

An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs
por: Dong, Xiaoli, et al.
Publicado: (2019)

UMGAP: the Unipept MetaGenomics Analysis Pipeline
por: Van der Jeugt, Felix, et al.
Publicado: (2022)

A single-cell genomics pipeline for environmental microbial eukaryotes
por: Ciobanu, Doina, et al.
Publicado: (2021)

Metapangenomics reveals depth-dependent shifts in metabolic potential for the ubiquitous marine bacterial SAR324 lineage
por: Boeuf, Dominique, et al.
Publicado: (2021)

Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community
por: Bowers, Robert M., et al.
Publicado: (2015)

Unlocking Short Read Sequencing for Metagenomics
por: Rodrigue, Sébastien, et al.
Publicado: (2010)

Metabolic Effects of Sucralose on Environmental Bacteria
por: Omran, Arthur, et al.
Publicado: (2013)

Probing the active fraction of soil microbiomes using BONCAT-FACS
por: Couradeau, Estelle, et al.
Publicado: (2019)

MetCap: a bioinformatics probe design pipeline for large-scale targeted metagenomics
por: Kushwaha, Sandeep K, et al.
Publicado: (2015)

TAR-VIR: a pipeline for TARgeted VIRal strain reconstruction from metagenomic data
por: Chen, Jiao, et al.
Publicado: (2019)

STATR: A simple analysis pipeline of Ribo-Seq in bacteria
por: Choe, Donghui, et al.
Publicado: (2020)

VIP: an integrated pipeline for metagenomics of virus identification and discovery
por: Li, Yang, et al.
Publicado: (2016)

Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments
por: Clarke, Erik L., et al.
Publicado: (2019)

Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea
por: Chadwick, Grayson L., et al.
Publicado: (2022)

MeCorS: Metagenome-enabled error correction of single cell sequencing reads
por: Bremges, Andreas, et al.
Publicado: (2016)

Erratum to: MetCap: A bioinformatics probe design pipeline for large-scale targeted metagenomics
por: Kushwaha, Sandeep K., et al.
Publicado: (2016)

Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics
por: Roux, Simon, et al.
Publicado: (2017)

MetAMOS: a metagenomic assembly and analysis pipeline for AMOS
por: Treangen, Todd J, et al.
Publicado: (2011)

MetaCRAM: an integrated pipeline for metagenomic taxonomy identification and compression
por: Kim, Minji, et al.
Publicado: (2016)

FMAP: Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies
por: Kim, Jiwoong, et al.
Publicado: (2016)

SAR11 bacteria linked to ocean anoxia and nitrogen loss
por: Tsementzi, Despina, et al.
Publicado: (2016)

Cannot write session to /tmp/vufind_sessions/sess_1d55po1d1tdndpr2l0qpt5vdqu