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Correction: Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Robert M Bowers
Nikos C Kyrpides
Tanja Woyke
Amendments and Corrections06 Feb 2018
Nature Biotechnology

Volume: 36, P: 196
Correction: Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Robert M Bowers
Nikos C Kyrpides
Tanja Woyke
Amendments and Corrections06 Jul 2018
Nature Biotechnology

Volume: 36, P: 660
The microbiome of a bacterivorous marine choanoflagellate contains a resource-demanding obligate bacterial associate

Choanoflagellates are the closest living unicellular relatives of animals and are important bacterivorous predators in the ocean. Here the authors show that the microbiome of this predator includes an obligate, host resource-dependent bacterial associate.

David M. Needham
Camille Poirier
Alexandra Z. Worden
ResearchOpen Access15 Aug 2022
Nature Microbiology

Volume: 7, P: 1466-1479
Probing the active fraction of soil microbiomes using BONCAT-FACS

Standard DNA-based analyses of microbial communities cannot distinguish between active microbes and dead or dormant cells. Here, Couradeau et al. use BONCAT (bioorthogonal non-canonical amino acid tagging), flow cytometry, and 16S rRNA gene amplicon sequencing to identify active microbial cells in soils.

Estelle Couradeau
Joelle Sasse
Trent R. Northen
ResearchOpen Access24 Jun 2019
Nature Communications

Volume: 10, P: 1-10
Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs

The analysis of existing metagenomic data can lead to discovery of new microorganisms. Here, Eloe-Fadrosh et al. perform a large-scale analysis of global metagenomic data, followed by genome reconstruction and single-cell genomics, to describe a new bacterial phylum that inhabits geothermal springs.

Emiley A. Eloe-Fadrosh
David Paez-Espino
Natalia N. Ivanova
ResearchOpen Access27 Jan 2016
Nature Communications

Volume: 7, P: 1-10
SAR11 bacteria linked to ocean anoxia and nitrogen loss

Bacteria of the SAR11 clade constitute up to one half of all marine microbes and are thought to require oxygen for growth; here, a subgroup of SAR11 bacteria are shown to thrive in ocean oxygen minimum zones and to encode abundant respiratory nitrate reductases.

Despina Tsementzi
Jieying Wu
Frank J. Stewart
Research03 Aug 2016
Nature

Volume: 536, P: 179-183
Hidden diversity of soil giant viruses

Current knowledge of giant virus diversity is largely based on samples from aquatic environments. Here the authors employ cultivation-independent metagenomics and mini-metagenomics on forest soil and identify 16 novel giant virus genomes, some of which representing novel lineages, including the so far largest genome in Mimiviridae.

Frederik Schulz
Lauren Alteio
Tanja Woyke
ResearchOpen Access19 Nov 2018
Nature Communications

Volume: 9, P: 1-9
Spatial co-transcriptomics reveals discrete stages of the arbuscular mycorrhizal symbiosis

Using a combination of single-cell and spatial transcriptomic analysis, Serrano et al. uncover transcriptional dynamics during the establishment of arbuscular mycorrhizal symbiosis.

Karen Serrano
Margaret Bezrutczyk
Benjamin Cole
ResearchOpen Access08 Apr 2024
Nature Plants

Volume: 10, P: 673-688
Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface

Analysis of a CO₂-driven geyser over a complete eruption cycle showed temporal changes in microbial community composition and function, associated with eruption phase and aquifer water depth, and revealed a putative archaeal symbiosis.

Alexander J. Probst
Bethany Ladd
Jillian F. Banfield
ResearchOpen Access29 Jan 2018
Nature Microbiology

Volume: 3, P: 328-336
Temporal dynamics of Prochlorococcus ecotypes in the Atlantic and Pacific oceans

Rex R Malmstrom
Allison Coe
Sallie W Chisholm
Research13 May 2010
The ISME Journal

Volume: 4, P: 1252-1264
Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics

Virophages are recently-identified small viruses that infect larger viruses, yet their diversity and ecological roles are poorly understood. Here, Roux and colleagues present time series metagenomics data revealing new virophage genera and their putative ecological interactions in two freshwater lakes.

Simon Roux
Leong-Keat Chan
Matthew B. Sullivan
ResearchOpen Access11 Oct 2017
Nature Communications

Volume: 8, P: 1-12
Quality MAGnified

This Genome Watch highlights different tools and strategies used to enhance the quality of metagenome-assembled genomes (MAGs) generated in microbiome studies.

Rex R. Malmstrom
News03 Oct 2023
Nature Reviews Microbiology

Volume: 21, P: 771
Ecology of uncultured Prochlorococcus clades revealed through single-cell genomics and biogeographic analysis

Rex R Malmstrom
Sébastien Rodrigue
Sallie W Chisholm
Research16 Aug 2012
The ISME Journal

Volume: 7, P: 184-198
Minimum Information about an Uncultivated Virus Genome (MIUViG)

This paper presents standards and best practices for reporting genome sequences of uncultivated viruses.

Simon Roux
Evelien M Adriaenssens
Emiley A Eloe-Fadrosh
ReviewsOpen Access17 Dec 2018
Nature Biotechnology

Volume: 37, P: 29-37
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Standards for sequencing the microbial 'uncultivated majority', namely bacterial and archaeal single-cell genome sequences, and genome sequences from metagenomic datasets, are proposed.

Robert M Bowers
Nikos C Kyrpides
Tanja Woyke
ReviewsOpen Access01 Aug 2017
Nature Biotechnology

Volume: 35, P: 725-731
Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations

Matthew L Bendall
Sarah LR Stevens
Rex R Malmstrom
ResearchOpen Access08 Jan 2016
The ISME Journal

Volume: 10, P: 1589-1601
Host population diversity as a driver of viral infection cycle in wild populations of green sulfur bacteria with long standing virus-host interactions

Maureen Berg
Danielle Goudeau
Simon Roux
ResearchOpen Access15 Jan 2021
The ISME Journal

Volume: 15, P: 1569-1584
Dissecting the dominant hot spring microbial populations based on community-wide sampling at single-cell genomic resolution

Robert M. Bowers
Stephen Nayfach
Tanja Woyke
ResearchOpen Access30 Dec 2021
The ISME Journal

Volume: 16, P: 1337-1347
Niche differentiation is spatially and temporally regulated in the rhizosphere

Erin E. Nuccio
Evan Starr
Jennifer Pett-Ridge
Research17 Jan 2020
The ISME Journal

Volume: 14, P: 999-1014
Obtaining genomes from uncultivated environmental microorganisms using FACS–based single-cell genomics

Christian Rinke
Janey Lee
Tanja Woyke
Protocols10 Apr 2014
Nature Protocols

Volume: 9, P: 1038-1048
Single cell genomic and transcriptomic evidence for the use of alternative nitrogen substrates by anammox bacteria

Sangita Ganesh
Anthony D. Bertagnolli
Frank J. Stewart
Research10 Jul 2018
The ISME Journal

Volume: 12, P: 2706-2722
Subsurface hydrocarbon degradation strategies in low- and high-sulfate coal seam communities identified with activity-based metagenomics

Hannah D. Schweitzer
Heidi J. Smith
Matthew W. Fields
ResearchOpen Access17 Feb 2022
npj Biofilms and Microbiomes

Volume: 8, P: 1-10
Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations

Sarahi L. Garcia
Sarah L. R. Stevens
Katherine D. McMahon
ResearchOpen Access08 Dec 2017
The ISME Journal

Volume: 12, P: 742-755
Novel copper-containing membrane monooxygenases (CuMMOs) encoded by alkane-utilizing Betaproteobacteria

Fauziah F. Rochman
Miye Kwon
Tobin J. Verbeke
Research03 Dec 2019
The ISME Journal

Volume: 14, P: 714-726
Activity-based, genome-resolved metagenomics uncovers key populations and pathways involved in subsurface conversions of coal to methane

Luke J. McKay
Heidi J. Smith
Matthew W. Fields
Research23 Oct 2021
The ISME Journal

Volume: 16, P: 915-926
A compendium of bacterial and archaeal single-cell amplified genomes from oxygen deficient marine waters

Julia Anstett
Alvaro M. Plominsky
Steven J. Hallam
ResearchOpen Access27 May 2023
Scientific Data

Volume: 10, P: 1-13

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Correction: Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Correction: Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

The microbiome of a bacterivorous marine choanoflagellate contains a resource-demanding obligate bacterial associate

Probing the active fraction of soil microbiomes using BONCAT-FACS

Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs

SAR11 bacteria linked to ocean anoxia and nitrogen loss

Hidden diversity of soil giant viruses

Spatial co-transcriptomics reveals discrete stages of the arbuscular mycorrhizal symbiosis

Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface

Temporal dynamics of Prochlorococcus ecotypes in the Atlantic and Pacific oceans

Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics

Quality MAGnified

Ecology of uncultured Prochlorococcus clades revealed through single-cell genomics and biogeographic analysis

Minimum Information about an Uncultivated Virus Genome (MIUViG)

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations

Host population diversity as a driver of viral infection cycle in wild populations of green sulfur bacteria with long standing virus-host interactions

Dissecting the dominant hot spring microbial populations based on community-wide sampling at single-cell genomic resolution

Niche differentiation is spatially and temporally regulated in the rhizosphere

Obtaining genomes from uncultivated environmental microorganisms using FACS–based single-cell genomics

Single cell genomic and transcriptomic evidence for the use of alternative nitrogen substrates by anammox bacteria

Subsurface hydrocarbon degradation strategies in low- and high-sulfate coal seam communities identified with activity-based metagenomics

Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations

Novel copper-containing membrane monooxygenases (CuMMOs) encoded by alkane-utilizing Betaproteobacteria

Activity-based, genome-resolved metagenomics uncovers key populations and pathways involved in subsurface conversions of coal to methane

A compendium of bacterial and archaeal single-cell amplified genomes from oxygen deficient marine waters

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