From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems

Decoding the jargon of bottom-up metabolic systems biology

(2015) Óttar Rolfsson et al.   BIOESSAYS

Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species

(2015) Sharon Greenblum et al.   CELL

Biogeography of the Intestinal Mucosal and Lumenal Microbiome in the Rhesus Macaque

(2015) Koji Yasuda et al.   Cell Host & Microbe

Metagenomics meets time series analysis: unraveling microbial community dynamics

(2015) Karoline Faust et al.   CURRENT OPINION IN MICROBIOLOGY

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

(2015) Christopher T. Brown et al.   NATURE

A new antibiotic kills pathogens without detectable resistance

(2015) Losee L. Ling et al.   NATURE

Complex archaea that bridge the gap between prokaryotes and eukaryotes

(2015) Anja Spang et al.   NATURE

Metabolic dependencies drive species co-occurrence in diverse microbial communities

(2015) Aleksej Zelezniak et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Application of a Neutral Community Model To Assess Structuring of the Human Lung Microbiome

(2015) Arvind Venkataraman et al.   mBio

High-Throughput Metagenomic Technologies for Complex Microbial Community Analysis: Open and Closed Formats

(2015) Jizhong Zhou et al.   mBio

Genomes of Planktonic Acidimicrobiales : Widening Horizons for Marine Actinobacteria by Metagenomics

(2015) Carolina Megumi Mizuno et al.   mBio

Microbial taxonomy in the post-genomic era: Rebuilding from scratch?

(2014) Cristiane C. Thompson et al.   ARCHIVES OF MICROBIOLOGY

The Unculturables: targeted isolation of bacterial species associated with canine periodontal health or disease from dental plaque

(2014) Ian J Davis et al.   BMC MICROBIOLOGY

Ammonia oxidation-dependent growth of group I.1bThaumarchaeotain acidic red soil microcosms

(2014) Yucheng Wu et al.   FEMS MICROBIOLOGY ECOLOGY

Taxonomical and functional microbial community selection in soybean rhizosphere

(2014) Lucas W Mendes et al.   ISME Journal

Estimation method for serial dilution experiments

(2014) Avishai Ben-David et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

(2014) H Bjørn Nielsen et al.   NATURE BIOTECHNOLOGY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses

(2014) B. L. Hurwitz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ten years of next-generation sequencing technology

(2014) Erwin L. van Dijk et al.   TRENDS IN GENETICS

Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics

(2014) William R. Harcombe et al.   Cell Reports

Species-Level Deconvolution of Metagenome Assemblies with Hi-C–Based Contact Probability Maps

(2014) Joshua N. Burton et al.   G3-Genes Genomes Genetics

Emergent Biosynthetic Capacity in Simple Microbial Communities

(2014) Hsuan-Chao Chiu et al.   PLoS Computational Biology

Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms

(2014) Martial Marbouty et al.   eLife

Recoding of the stop codon UGA to glycine by a BD1-5/SN-2 bacterium and niche partitioning between Alpha- and Gammaproteobacteria in a tidal sediment microbial community naturally selected in a laboratory chemostat

(2014) Anna Hanke et al.   Frontiers in Microbiology

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares

(2014) Genivaldo Gueiros Z. Silva et al.   PeerJ

Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products

(2014) Christopher W. Beitel et al.   PeerJ

Methods for integration of transcriptomic data in genome-scale metabolic models

(2014) Min Kyung Kim et al.   Computational and Structural Biotechnology Journal

Explaining microbial phenotypes on a genomic scale: GWAS for microbes

(2013) B. E. Dutilh et al.   Briefings in Functional Genomics

Combining “Omics” Strategies to Analyze the Biotechnological Potential of Complex Microbial Environments

(2013) Alinne Castro et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

The ecology of differences: assessing community assembly with trait and evolutionary distances

(2013) Marc Cadotte et al.   ECOLOGY LETTERS

Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform

(2013) J. S. McLean et al.   GENOME RESEARCH

Changes in assembly processes in soil bacterial communities following a wildfire disturbance

(2013) Scott Ferrenberg et al.   ISME Journal

Multifactorial diversity sustains microbial community stability

(2013) Oylum Erkus et al.   ISME Journal

The microbial gene diversity along an elevation gradient of the Tibetan grassland

(2013) Yunfeng Yang et al.   ISME Journal

High throughput sequencing methods and analysis for microbiome research

(2013) Julia M. Di Bella et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome

(2013) Sheetal R. Modi et al.   NATURE

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

IMG 4 version of the integrated microbial genomes comparative analysis system

(2013) Victor M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

Identification of a Novel Human Papillomavirus by Metagenomic Analysis of Samples from Patients with Febrile Respiratory Illness

(2013) John L. Mokili et al.   PLoS One

Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean

(2013) B. K. Swan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments

(2013) J. M. Monk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomes from Metagenomics

(2013) I. Sharon et al.   SCIENCE

Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla

(2013) R. S. Kantor et al.   mBio

Can You Sequence Ecology? Metagenomics of Adaptive Diversification

(2013) Christopher J. Marx   PLOS BIOLOGY

Estimation of viral richness from shotgun metagenomes using a frequency count approach

(2013) Heather K Allen et al.   Microbiome

Reference-independent comparative metagenomics using cross-assembly: crAss

(2012) Bas E. Dutilh et al.   BIOINFORMATICS

Classification of metagenomic sequences: methods and challenges

(2012) S. S. Mande et al.   BRIEFINGS IN BIOINFORMATICS

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

Microbial metaproteomics: identifying the repertoire of proteins that microorganisms use to compete and cooperate in complex environmental communities

(2012) Robert L. Hettich et al.   CURRENT OPINION IN MICROBIOLOGY

CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome

(2012) A. Stern et al.   GENOME RESEARCH

Multi-scale structure and geographic drivers of cross-infection within marine bacteria and phages

(2012) Cesar O Flores et al.   ISME Journal

Growing Unculturable Bacteria

(2012) E. J. Stewart   JOURNAL OF BACTERIOLOGY

Mathematical optimization applications in metabolic networks

(2012) Ali R. Zomorrodi et al.   METABOLIC ENGINEERING

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Predicting bacterial community assemblages using an artificial neural network approach

(2012) Peter E Larsen et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Genomic sequencing of uncultured microorganisms from single cells

(2012) Roger S. Lasken   NATURE REVIEWS MICROBIOLOGY

Phylogenomics of Prokaryotic Ribosomal Proteins

(2012) Natalya Yutin et al.   PLoS One

Taxonomic and Functional Microbial Signatures of the Endemic Marine Sponge Arenosclera brasiliensis

(2012) Amaro E. Trindade-Silva et al.   PLoS One

MultiMetEval: Comparative and Multi-Objective Analysis of Genome-Scale Metabolic Models

(2012) Piotr Zakrzewski et al.   PLoS One

Cross-biome metagenomic analyses of soil microbial communities and their functional attributes

(2012) N. Fierer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla

(2012) K. C. Wrighton et al.   SCIENCE

Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota

(2012) V. Iverson et al.   SCIENCE

Phage–bacteria infection networks

(2012) Joshua S. Weitz et al.   TRENDS IN MICROBIOLOGY

Metagenomics and future perspectives in virus discovery

(2012) John L Mokili et al.   Current Opinion in Virology

OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities

(2012) Ali R. Zomorrodi et al.   PLoS Computational Biology

Marine Viruses: Truth or Dare

(2011) Mya Breitbart   Annual Review of Marine Science

Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates

(2011) Li C Xia et al.   BMC Systems Biology

Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis

(2011) Matthew B. Scholz et al.   CURRENT OPINION IN BIOTECHNOLOGY

The human gut virome: Inter-individual variation and dynamic response to diet

(2011) S. Minot et al.   GENOME RESEARCH

De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities

(2011) Priya Narasingarao et al.   ISME Journal

Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage

(2011) Chris L Dupont et al.   ISME Journal

Stochastic and deterministic processes interact in the assembly of desert microbial communities on a global scale

(2011) Tancredi Caruso et al.   ISME Journal

Statistical structure of host-phage interactions

(2011) C. O. Flores et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacterial community assembly based on functional genes rather than species

(2011) C. Burke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen

(2011) M. Hess et al.   SCIENCE

The Unified Neutral Theory of Biodiversity and Biogeography at Age Ten

(2011) James Rosindell et al.   TRENDS IN ECOLOGY & EVOLUTION

The Human Gut Microbiome: Ecology and Recent Evolutionary Changes

(2010) Jens Walter et al.   Annual Review of Microbiology

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

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

Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model

(2010) K. Yizhak et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Predicting conserved protein motifs with Sub-HMMs

(2010) Kevin Horan et al.   BMC BIOINFORMATICS

Siderophores from Neighboring Organisms Promote the Growth of Uncultured Bacteria

(2010) Anthony D'Onofrio et al.   CHEMISTRY & BIOLOGY

Analysis of streptococcal CRISPRs from human saliva reveals substantial sequence diversity within and between subjects over time

(2010) D. T. Pride et al.   GENOME RESEARCH

Viral and microbial community dynamics in four aquatic environments

(2010) Beltran Rodriguez-Brito et al.   ISME Journal

Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism

(2010) R.M.T. Fleming et al.   JOURNAL OF THEORETICAL BIOLOGY

Species abundance distributions and richness estimations in fungal metagenomics - lessons learned from community ecology

(2010) MARTIN UNTERSEHER et al.   MOLECULAR ECOLOGY

Genomic and functional adaptation in surface ocean planktonic prokaryotes

(2010) Shibu Yooseph et al.   NATURE

High-throughput generation, optimization and analysis of genome-scale metabolic models

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

A protocol for generating a high-quality genome-scale metabolic reconstruction

(2010) Ines Thiele et al.   Nature Protocols

Environments that Induce Synthetic Microbial Ecosystems

(2010) Niels Klitgord et al.   PLoS Computational Biology

Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly

(2009) Bas E. Dutilh et al.   BIOINFORMATICS

Metabolic modelling of syntrophic-like growth of a 1,3-propanediol producer, Clostridium butyricum, and a methanogenic archeon, Methanosarcina mazei, under anaerobic conditions

(2009) Marcin Bizukojc et al.   BIOPROCESS AND BIOSYSTEMS ENGINEERING

The merging of community ecology and phylogenetic biology

(2009) Jeannine Cavender-Bares et al.   ECOLOGY LETTERS

Relative roles of niche and neutral processes in structuring a soil microbial community

(2009) Alex J Dumbrell et al.   ISME Journal

Initial community evenness favours functionality under selective stress

(2009) Lieven Wittebolle et al.   NATURE

Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models

(2009) Arthur Brady et al.   NATURE METHODS

Explaining microbial population genomics through phage predation

(2009) Francisco Rodriguez-Valera et al.   NATURE REVIEWS MICROBIOLOGY

Assembling the Marine Metagenome, One Cell at a Time

(2009) Tanja Woyke et al.   PLoS One

Host cell-free growth of the Q fever bacterium Coxiella burnetii

(2009) A. Omsland et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Community-wide analysis of microbial genome sequence signatures

(2009) Gregory J Dick et al.   GENOME BIOLOGY

Short Peptide Induces an "Uncultivable" Microorganism To Grow In Vitro

(2008) D. Nichols et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

Binning sequences using very sparse labels within a metagenome

(2008) Chon-Kit Chan et al.   BMC BIOINFORMATICS

Functional metagenomic profiling of nine biomes

(2008) Elizabeth A. Dinsdale et al.   NATURE

SAR11 marine bacteria require exogenous reduced sulphur for growth

(2008) H. James Tripp et al.   NATURE

Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota

(2008) Céline Brochier-Armanet et al.   NATURE REVIEWS MICROBIOLOGY