Opportunities and challenges of using metagenomic data to bring uncultured microbes into cultivation

High-throughput cultivation and identification of bacteria from the plant root microbiota

(2021) Jingying Zhang et al.   Nature Protocols

Imaging Commensal Microbiota and Pathogenic Bacteria in the Gut

(2021) Liyuan Lin et al.   ACCOUNTS OF CHEMICAL RESEARCH

Metagenomic Data Assembly – The Way of Decoding Unknown Microorganisms

(2021) Alla L. Lapidus et al.   Frontiers in Microbiology

Species- and site-specific genome editing in complex bacterial communities

(2021) Benjamin E. Rubin et al.   Nature Microbiology

Raman‐activated sorting of antibiotic‐resistant bacteria in human gut microbiota

(2020) Yi Wang et al.   ENVIRONMENTAL MICROBIOLOGY

Complete, closed bacterial genomes from microbiomes using nanopore sequencing

(2020) Eli L. Moss et al.   NATURE BIOTECHNOLOGY

Single-cell genomics of uncultured bacteria reveals dietary fiber responders in the mouse gut microbiota

(2020) Rieka Chijiiwa et al.   Microbiome

Connections and Feedback: Aquatic, Plant, and Soil Microbiomes in Heterogeneous and Changing Environments

(2020) Walter K Dodds et al.   BIOSCIENCE

Accurate and complete genomes from metagenomes

(2020) Lin-Xing Chen et al.   GENOME RESEARCH

Functional and Genomic Variation between Human-Derived Isolates of Lachnospiraceae Reveals Inter- and Intra-Species Diversity

(2020) Matthew T. Sorbara et al.   Cell Host & Microbe

Epichloë endophytes of a wild grass promote mycorrhizal colonization of neighbor grasses

(2020) M. Victoria Vignale et al.   Fungal Ecology

Complete Genome Sequencing and Transcriptome Analysis of Nitrogen Metabolism of Succinivibrio dextrinosolvens Strain Z6 Isolated From Dairy Cow Rumen

(2020) Samson Hailemariam et al.   Frontiers in Microbiology

Roadmap for naming uncultivated Archaea and Bacteria

(2020) Alison E. Murray et al.   Nature Microbiology

Virus-Receptor Interactions of Glycosylated SARS-CoV-2 Spike and Human ACE2 Receptor

(2020) Peng Zhao et al.   Cell Host & Microbe

Targeted isolation based on metagenome‐assembled genomes reveals a phylogenetically distinct group of thermophilic spirochetes from deep biosphere

(2020) Olga V. Karnachuk et al.   ENVIRONMENTAL MICROBIOLOGY

Estimate of the sequenced proportion of the global prokaryotic genome

(2020) Zheng Zhang et al.   Microbiome

Metagenomic analysis reveals antibiotic resistance genes in the bovine rumen

(2020) Ruoxi Jing et al.   MICROBIAL PATHOGENESIS

Comparison of long-read methods for sequencing and assembly of a plant genome

(2020) Valentine Murigneux et al.   GigaScience

An automated Raman-based platform for the sorting of live cells by functional properties

(2019) Kang Soo Lee et al.   Nature Microbiology

A census-based estimate of Earth's bacterial and archaeal diversity

(2019) Stilianos Louca et al.   PLOS BIOLOGY

Natural C. elegans Microbiota Protects against Infection via Production of a Cyclic Lipopeptide of the Viscosin Group

(2019) Kohar A.B. Kissoyan et al.   CURRENT BIOLOGY

Predicting the optimal growth temperatures of prokaryotes using only genome derived features

(2019) David B Sauer et al.   BIOINFORMATICS

Metagenomic characterization of antibiotic resistance genes in Antarctic soils

(2019) Ke Yuan et al.   ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY

Primer-free FISH probes from metagenomics/metatranscriptomics data permit the study of uncharacterised taxa in complex microbial communities

(2019) Shi Ming Tan et al.   npj Biofilms and Microbiomes

Targeted isolation and cultivation of uncultivated bacteria by reverse genomics

(2019) Karissa L. Cross et al.   NATURE BIOTECHNOLOGY

Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery

(2019) Robert D. Stewart et al.   NATURE BIOTECHNOLOGY

Metagenomic and culturomic analysis of gut microbiota dysbiosis during Clostridium difficile infection

(2019) Sophie Amrane et al.   Scientific Reports

An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs

(2019) Xiaoli Dong et al.   Frontiers in Genetics

Fluorescence in situ hybridization (FISH) and cell sorting of living bacteria

(2019) Giampiero Batani et al.   Scientific Reports

LPSN – List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on

(2018) Aidan C. Parte   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Detoxifying symbiosis: microbe-mediated detoxification of phytotoxins and pesticides in insects

(2018) Hideomi Itoh et al.   NATURAL PRODUCT REPORTS

The social network of microorganisms — how auxotrophies shape complex communities

(2018) Karsten Zengler et al.   NATURE REVIEWS MICROBIOLOGY

A primordial and reversible TCA cycle in a facultatively chemolithoautotrophic thermophile

(2018) Takuro Nunoura et al.   SCIENCE

The contribution of culturomics to the repertoire of isolated human bacterial and archaeal species

(2018) Melhem Bilen et al.   Microbiome

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

Phylogenetically Novel Uncultured Microbial Cells Dominate Earth Microbiomes

(2018) Karen G. Lloyd et al.   mSystems

BRENDA in 2019: a European ELIXIR core data resource

(2018) Lisa Jeske et al.   NUCLEIC ACIDS RESEARCH

Transmission modes of the mammalian gut microbiota

(2018) Andrew H. Moeller et al.   SCIENCE

Recent Advances in Function-based Metagenomic Screening

(2018) Tanyaradzwa Rodgers Ngara et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Illuminating microbial diversity

(2017) Samuel C. Forster   NATURE REVIEWS MICROBIOLOGY

Embracing the unknown: disentangling the complexities of the soil microbiome

(2017) Noah Fierer   NATURE REVIEWS MICROBIOLOGY

The MetaCyc database of metabolic pathways and enzymes

(2017) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

High-Throughput Single-Cell Cultivation on Microfluidic Streak Plates

(2016) Cheng-Ying Jiang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

Reply to Willis: Powerful predictions of biodiversity from ecological models and scaling laws

(2016) Kenneth J. Locey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Scaling laws predict global microbial diversity

(2016) Kenneth J. Locey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Status of the Archaeal and Bacterial Census: an Update

(2016) Patrick D. Schloss et al.   mBio

Reply to “The Underestimation of Global Microbial Diversity”

(2016) Rudolf Amann et al.   mBio

Genomics-informed isolation and characterization of a symbiotic Nanoarchaeota system from a terrestrial geothermal environment

(2016) Louie Wurch et al.   Nature Communications

The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation

(2016) Amy Langdon et al.   Genome Medicine

Moleculo Long-Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil Metagenomes

(2016) Richard Allen White et al.   mSystems

Single-cell genomics based on Raman sorting reveals novel carotenoid-containing bacteria in the Red Sea

(2016) Yizhi Song et al.   Microbial Biotechnology

Current and Past Strategies for Bacterial Culture in Clinical Microbiology

(2015) Jean-Christophe Lagier et al.   CLINICAL MICROBIOLOGY REVIEWS

Technologies for Single-Cell Isolation

(2015) Andre Gross et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Defensive symbioses of animals with prokaryotic and eukaryotic microorganisms

(2015) Laura V. Flórez et al.   NATURAL PRODUCT REPORTS

Unusual biology across a group comprising more than 15% of domain Bacteria

(2015) Christopher T. Brown et al.   NATURE

Complete nitrification by Nitrospira bacteria

(2015) Holger Daims et al.   NATURE

Assembly and diploid architecture of an individual human genome via single-molecule technologies

(2015) Matthew Pendleton et al.   NATURE METHODS

Marine microbial community dynamics and their ecological interpretation

(2015) Jed A. Fuhrman et al.   NATURE REVIEWS MICROBIOLOGY

Ecology and exploration of the rare biosphere

(2015) Michael D. J. Lynch et al.   NATURE REVIEWS MICROBIOLOGY

Enhanced and homogeneous oxygen availability during incubation of microfluidic droplets

(2015) Lisa Mahler et al.   RSC Advances

Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences

(2014) Pablo Yarza et al.   NATURE REVIEWS MICROBIOLOGY

Gene-targeted microfluidic cultivation validated by isolation of a gut bacterium listed in Human Microbiome Project's Most Wanted taxa

(2014) Liang Ma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cultivation-based multiplex phenotyping of human gut microbiota allows targeted recovery of previously uncultured bacteria

(2014) Elizabeth A. Rettedal et al.   Nature Communications

Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis

(2014) Agata Wesolowska-Andersen et al.   Microbiome

Raman Activated Cell Ejection for Isolation of Single Cells

(2013) Yun Wang et al.   ANALYTICAL CHEMISTRY

Implementing sponge physiological and genomic information to enhance the diversity of its culturable associated bacteria

(2013) Adi Lavy et al.   FEMS MICROBIOLOGY ECOLOGY

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

Microbial life under extreme energy limitation

(2013) Tori M. Hoehler et al.   NATURE REVIEWS MICROBIOLOGY

Animals in a bacterial world, a new imperative for the life sciences

(2013) Margaret McFall-Ngai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Condensing the omics fog of microbial communities

(2013) Emilie E.L. Muller et al.   TRENDS IN MICROBIOLOGY

Microbial culturomics: paradigm shift in the human gut microbiome study

(2012) J.-C. Lagier et al.   CLINICAL MICROBIOLOGY AND INFECTION

Zero-valent sulphur is a key intermediate in marine methane oxidation

(2012) Jana Milucka et al.   NATURE

Microbial life in the phyllosphere

(2012) Julia A. Vorholt   NATURE REVIEWS MICROBIOLOGY

dbCAN: a web resource for automated carbohydrate-active enzyme annotation

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

Functional equivalence and evolutionary convergence in complex communities of microbial sponge symbionts

(2012) L. Fan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Isolation of Succinivibrionaceae Implicated in Low Methane Emissions from Tammar Wallabies

(2011) P. B. Pope et al.   SCIENCE

Use of Ichip for High-Throughput In Situ Cultivation of "Uncultivable" Microbial Species

(2010) D. Nichols et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges

(2010) Alexander Siegl et al.   ISME Journal

An in situ method for cultivating microorganisms using a double encapsulation technique

(2009) Eitan Ben-Dov et al.   FEMS MICROBIOLOGY ECOLOGY

Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies

(2009) Alexandra M. Schnoes et al.   PLoS Computational Biology

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

A Bioinformatician's Guide to Metagenomics

(2008) V. Kunin et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS