Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems
Published 2021 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems
Authors
Keywords
-
Journal
Nature Microbiology
Volume -, Issue -, Pages -
Publisher
Springer Science and Business Media LLC
Online
2021-01-26
DOI
10.1038/s41564-020-00840-5
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Consistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species Boundaries
- (2020) Matthew R. Olm et al. mSystems
- Lipid analysis of CO2-rich subsurface aquifers suggests an autotrophy-based deep biosphere with lysolipids enriched in CPR bacteria
- (2020) Alexander J. Probst et al. ISME Journal
- Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity
- (2020) Renmao Tian et al. Microbiome
- The influence of spaceflight on the astronaut salivary microbiome and the search for a microbiome biomarker for viral reactivation
- (2020) Camilla Urbaniak et al. Microbiome
- Acquisition and Adaptation of Ultra-small Parasitic Reduced Genome Bacteria to Mammalian Hosts
- (2020) Jeffrey S. McLean et al. Cell Reports
- Ancestral Absence of Electron Transport Chains in Patescibacteria and DPANN
- (2020) Jacob P. Beam et al. Frontiers in Microbiology
- Mediterranean grassland soil C–N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms
- (2019) Spencer Diamond et al. Nature Microbiology
- Unexpected host dependency of Antarctic Nanohaloarchaeota
- (2019) Joshua N. Hamm et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Establishing microbial composition measurement standards with reference frames
- (2019) James T. Morton et al. Nature Communications
- Predominance of Cand. Patescibacteria in Groundwater Is Caused by Their Preferential Mobilization From Soils and Flourishing Under Oligotrophic Conditions
- (2019) Martina Herrmann et al. Frontiers in Microbiology
- Targeted isolation and cultivation of uncultivated bacteria by reverse genomics
- (2019) Karissa L. Cross et al. NATURE BIOTECHNOLOGY
- Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life
- (2018) Cindy J. Castelle et al. CELL
- The biomass distribution on Earth
- (2018) Yinon M. Bar-On et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy
- (2018) Christian M. K. Sieber et al. Nature Microbiology
- Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface
- (2018) Alexander J. Probst et al. Nature Microbiology
- The biomass and biodiversity of the continental subsurface
- (2018) C. Magnabosco et al. Nature Geoscience
- Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations
- (2018) Cindy J. Castelle et al. NATURE REVIEWS MICROBIOLOGY
- A new symbiotic nanoarchaeote (Candidatus Nanoclepta minutus) and its host (Zestosphaera tikiterensis gen. nov., sp. nov.) from a New Zealand hot spring
- (2018) Emily St. John et al. SYSTEMATIC AND APPLIED MICROBIOLOGY
- dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication
- (2017) Matthew R Olm et al. ISME Journal
- Automated tilt series alignment and tomographic reconstruction in IMOD
- (2017) David N. Mastronarde et al. JOURNAL OF STRUCTURAL BIOLOGY
- Numerous uncharacterized and highly divergent microbes which colonize humans are revealed by circulating cell-free DNA
- (2017) Mark Kowarsky et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life
- (2017) Anja Spang et al. SCIENCE
- First Insights into the Diverse Human Archaeome: Specific Detection of Archaea in the Gastrointestinal Tract, Lung, and Nose and on Skin
- (2017) Kaisa Koskinen et al. mBio
- ‘ARMAN’ archaea depend on association with euryarchaeal host in culture and in situ
- (2017) Olga V. Golyshina et al. Nature Communications
- Exploring the under-investigated “microbial dark matter” of drinking water treatment plants
- (2017) Antonia Bruno et al. Scientific Reports
- Members of the Candidate Phyla Radiation are functionally differentiated by carbon- and nitrogen-cycling capabilities
- (2017) R. E. Danczak et al. Microbiome
- Assessing biosynthetic potential of agricultural groundwater through metagenomic sequencing: A diverse anammox community dominates nitrate-rich groundwater
- (2017) William B. Ludington et al. PLoS One
- Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO2concentrations
- (2016) Alexander J. Probst et al. ENVIRONMENTAL MICROBIOLOGY
- Measurement of bacterial replication rates in microbial communities
- (2016) Christopher T Brown et al. NATURE BIOTECHNOLOGY
- UniProt: the universal protein knowledgebase
- (2016) NUCLEIC ACIDS RESEARCH
- Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system
- (2016) Karthik Anantharaman et al. Nature Communications
- Genomics-informed isolation and characterization of a symbiotic Nanoarchaeota system from a terrestrial geothermal environment
- (2016) Louie Wurch et al. Nature Communications
- Emerging investigators series: microbial communities in full-scale drinking water distribution systems – a meta-analysis
- (2016) Quyen M. Bautista-de los Santos et al. Environmental Science-Water Research & Technology
- A new view of the tree of life
- (2016) Laura A. Hug et al. Nature Microbiology
- Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition
- (2016) Berith E. Knudsen et al. mSystems
- MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets
- (2015) Yu-Wei Wu et al. BIOINFORMATICS
- MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
- (2015) Dinghua Li et al. BIOINFORMATICS
- Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling
- (2015) Cindy J. Castelle et al. CURRENT BIOLOGY
- Metagenomic analysis of a high carbon dioxide subsurface microbial community populated by chemolithoautotrophs and bacteria and archaea from candidate phyla
- (2015) Joanne B. Emerson et al. ENVIRONMENTAL MICROBIOLOGY
- CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
- (2015) Donovan H. Parks et al. GENOME RESEARCH
- Unusual biology across a group comprising more than 15% of domain Bacteria
- (2015) Christopher T. Brown et al. NATURE
- KEGG as a reference resource for gene and protein annotation
- (2015) Minoru Kanehisa et al. NUCLEIC ACIDS RESEARCH
- Diverse uncultivated ultra-small bacterial cells in groundwater
- (2015) Birgit Luef et al. Nature Communications
- Groundwater Isolation Governs Chemistry and Microbial Community Structure along Hydrologic Flowpaths
- (2015) Sarah Ben Maamar et al. Frontiers in Microbiology
- The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle
- (2015) William C. Nelson et al. Frontiers in Microbiology
- Polyploidy in Archaea and Bacteria: About Desiccation Resistance, Giant Cell Size, Long-Term Survival, Enforcement by a Eukaryotic Host and Additional Aspects
- (2015) Jörg Soppa JOURNAL OF MOLECULAR MICROBIOLOGY AND BIOTECHNOLOGY
- FactoMineR: AnRPackage for Multivariate Analysis
- (2015) Sébastien Lê et al. Journal of Statistical Software
- UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches
- (2014) B. E. Suzek et al. BIOINFORMATICS
- RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
- (2014) Alexandros Stamatakis BIOINFORMATICS
- Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer
- (2014) Kelly C Wrighton et al. ISME Journal
- Binning metagenomic contigs by coverage and composition
- (2014) Johannes Alneberg et al. NATURE METHODS
- Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences
- (2014) Pablo Yarza et al. NATURE REVIEWS MICROBIOLOGY
- Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle
- (2014) Xuesong He et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Groundwater geochemistry and microbial community structure in the aquifer transition from volcanic to alluvial areas
- (2014) S. Amalfitano et al. WATER RESEARCH
- Spatial-Temporal Survey and Occupancy-Abundance Modeling To Predict Bacterial Community Dynamics in the Drinking Water Microbiome
- (2014) A. J. Pinto et al. mBio
- Insights into the phylogeny and coding potential of microbial dark matter
- (2013) Christian Rinke et al. NATURE
- “Candidatus Sonnebornia yantaiensis”, a member of candidate division OD1, as intracellular bacteria of the ciliated protist Paramecium bursaria (Ciliophora, Oligohymenophorea)
- (2013) Jun Gong et al. SYSTEMATIC AND APPLIED MICROBIOLOGY
- Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla
- (2013) R. S. Kantor et al. mBio
- IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
- (2012) Y. Peng et al. BIOINFORMATICS
- Fast gapped-read alignment with Bowtie 2
- (2012) Ben Langmead et al. NATURE METHODS
- The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
- (2012) Christian Quast et al. NUCLEIC ACIDS RESEARCH
- Deep Sequencing of the Oral Microbiome Reveals Signatures of Periodontal Disease
- (2012) Bo Liu et al. PLoS One
- Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla
- (2012) K. C. Wrighton et al. SCIENCE
- A portable cryo-plunger for on-site intact cryogenic microscopy sample preparation in natural environments
- (2011) Luis R. Comolli et al. MICROSCOPY RESEARCH AND TECHNIQUE
- HMMER web server: interactive sequence similarity searching
- (2011) R. D. Finn et al. NUCLEIC ACIDS RESEARCH
- Search and clustering orders of magnitude faster than BLAST
- (2010) Robert C. Edgar BIOINFORMATICS
- Prodigal: prokaryotic gene recognition and translation initiation site identification
- (2010) Doug Hyatt et al. BMC BIOINFORMATICS
- The Human Oral Microbiome
- (2010) F. E. Dewhirst et al. JOURNAL OF BACTERIOLOGY
- Enigmatic, ultrasmall, uncultivated Archaea
- (2010) B. J. Baker et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
- (2009) S. Capella-Gutierrez et al. BIOINFORMATICS
- Recent developments in the MAFFT multiple sequence alignment program
- (2008) K. Katoh et al. BRIEFINGS IN BIOINFORMATICS
- Intestinal TM7 bacterial phylogenies in active inflammatory bowel disease
- (2008) T. Kuehbacher et al. JOURNAL OF MEDICAL MICROBIOLOGY
- A Bioinformatician's Guide to Metagenomics
- (2008) V. Kunin et al. MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreAsk a Question. Answer a Question.
Quickly pose questions to the entire community. Debate answers and get clarity on the most important issues facing researchers.
Get Started