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Improved metagenome binning and assembly using deep variational autoencoders

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Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community

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Global Constraints within the Developmental Program of the Drosophila Wing

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Next-generation physiology approaches to study microbiome function at single cell level

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A universal trade-off between growth and lag in fluctuating environments

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Trophic Interactions and the Drivers of Microbial Community Assembly

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Correlation between autochthonous microbial communities and key odorants during the fermentation of red pepper (Capsicum annuum L.)

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A comprehensive quantification of global nitrous oxide sources and sinks

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Evolutionary dynamics of bacteria in the gut microbiome within and across hosts

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A high-bias, low-variance introduction to Machine Learning for physicists

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Correlation between volatile profiles and microbial communities: A metabonomic approach to study Jiang-flavor liquor Daqu

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Modular Assembly of Polysaccharide-Degrading Marine Microbial Communities

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Microbial biospherics: The experimental study of ecosystem function and evolution

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More Than the Sum of Its Parts: Microbiome Biodiversity as a Driver of Plant Growth and Soil Health

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Substrate cross-feeding affects the speed and trajectory of molecular evolution within a synthetic microbial assemblage

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Tracking the precession of single nuclear spins by weak measurements

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The Plastisphere – Uncovering tightly attached plastic “specific” microorganisms

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Host selection and stochastic effects influence bacterial community assembly on the microalgal phycosphere

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A sparse covarying unit that describes healthy and impaired human gut microbiota development

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Cooperation and spatial self-organization determine rate and efficiency of particulate organic matter degradation in marine bacteria

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The role of multiple global change factors in driving soil functions and microbial biodiversity

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The characteristics and correlation of the microbial communities and flavors in traditionally pickled radishes

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High-order interactions distort the functional landscape of microbial consortia

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Higher-Order Interaction between Species Inhibits Bacterial Invasion of a Phototroph-Predator Microbial Community

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Evidence of niche partitioning among bacteria living on plastics, organic particles and surrounding seawaters

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Oxygen minimum zone cryptic sulfur cycling sustained by offshore transport of key sulfur oxidizing bacteria

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Impact of Microbial Composition of Cambodian Traditional Dried Starters (Dombea) on Flavor Compounds of Rice Wine: Combining Amplicon Sequencing With HP-SPME-GCMS

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Linear Regression Links Transcriptomic Data and Cellular Raman Spectra

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Metagenomics reveals niche partitioning within the phototrophic zone of a microbial mat

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Ultrahigh-throughput functional profiling of microbiota communities

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Microbial communities and volatile metabolites in different traditional fermentation starters used for Hong Qu glutinous rice wine

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Review of recent developments in GC–MS approaches to metabolomics-based research

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Synthetic multispecies microbial communities reveals shifts in secondary metabolism and facilitates cryptic natural product discovery

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Assembly of microbial communities in replicate nutrient-cycling model ecosystems follows divergent trajectories, leading to alternate stable states

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Metabolite toxicity slows local diversity loss during expansion of a microbial cross-feeding community

(2017) Felix Goldschmidt et al.   ISME Journal

Phenotypic and genotypic richness of denitrifiers revealed by a novel isolation strategy

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Subsurface Microbial Ecosystems: A Photon Flux and a Metabolic Cascade

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Embracing the unknown: disentangling the complexities of the soil microbiome

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Antagonistic bacteria disrupt calcium homeostasis and immobilize algal cells

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Anaerobic microsites have an unaccounted role in soil carbon stabilization

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A phylogenetic transform enhances analysis of compositional microbiota data

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Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing

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Microbiome Datasets Are Compositional: And This Is Not Optional

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Learning Microbial Community Structures with Supervised and Unsupervised Non-negative Matrix Factorization

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Community structure follows simple assembly rules in microbial microcosms

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Characterization of bacterial community associated with phytoplankton bloom in a eutrophic lake in South Norway using 16S rRNA gene amplicon sequence analysis

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Towards Process Spectroscopy in Complex Fermentation Samples and Mixtures

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Segregating metabolic processes into different microbial cells accelerates the consumption of inhibitory substrates

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Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation

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DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Global biogeography of microbial nitrogen-cycling traits in soil

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Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children

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The identification of carbamazepine biodegrading phylotypes and phylotypes sensitive to carbamazepine exposure in two soil microbial communities

(2016) Jean-Rene Thelusmond et al.   SCIENCE OF THE TOTAL ENVIRONMENT

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Microbial interactions lead to rapid micro-scale successions on model marine particles

(2016) Manoshi S. Datta et al.   Nature Communications

Microbial community structure and dynamics in thermophilic composting viewed through metagenomics and metatranscriptomics

(2016) Luciana Principal Antunes et al.   Scientific Reports

Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes?

(2016) Emily B. Graham et al.   Frontiers in Microbiology

Culture of previously uncultured members of the human gut microbiota by culturomics

(2016) Jean-Christophe Lagier et al.   Nature Microbiology

From sample treatment to biomarker discovery: A tutorial for untargeted metabolomics based on GC-(EI)-Q-MS

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Networks of energetic and metabolic interactions define dynamics in microbial communities

(2015) Mallory Embree et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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(2015) M. J. Rosen et al.   SCIENCE

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

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Relating methanogen community structure and anaerobic digester function

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NMR and MALDI-TOF MS based characterization of exopolysaccharides in anaerobic microbial aggregates from full-scale reactors

(2015) Graciela Gonzalez-Gil et al.   Scientific Reports

Phycosphere bacterial diversity in green algae reveals an apparent similarity across habitats

(2015) Rishiram Ramanan et al.   Algal Research-Biomass Biofuels and Bioproducts

Structural Diversity of Bacterial Communities Associated with Bloom-Forming Freshwater Cyanobacteria Differs According to the Cyanobacterial Genus

(2015) Imen Louati et al.   PLoS One

Cheese Rind Communities Provide Tractable Systems for In Situ and In Vitro Studies of Microbial Diversity

(2014) Benjamin E. Wolfe et al.   CELL

Microscale sulfur cycling in the phototrophic pink berry consortia of the Sippewissett Salt Marsh

(2014) Elizabeth G. Wilbanks et al.   ENVIRONMENTAL MICROBIOLOGY

Inference of interactions in cyanobacterial–heterotrophic co-cultures via transcriptome sequencing

(2014) Alexander S Beliaev et al.   ISME Journal

Deterministic processes guide long-term synchronised population dynamics in replicate anaerobic digesters

(2014) Inka Vanwonterghem et al.   ISME Journal

A Winogradsky-based culture system shows an association between microbial fermentation and cystic fibrosis exacerbation

(2014) Robert A Quinn et al.   ISME Journal

Relationships between protein-encoding gene abundance and corresponding process are commonly assumed yet rarely observed

(2014) Jennifer D Rocca et al.   ISME Journal

Mapping the stereotyped behaviour of freely moving fruit flies

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Master recyclers: features and functions of bacteria associated with phytoplankton blooms

(2014) Alison Buchan et al.   NATURE REVIEWS MICROBIOLOGY

Niche engineering demonstrates a latent capacity for fungal-algal mutualism

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

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

A Peptide-Based Method for 13C Metabolic Flux Analysis in Microbial Communities

(2014) Amit Ghosh et al.   PLoS Computational Biology

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

Corrosion of Iron by Sulfate-Reducing Bacteria: New Views of an Old Problem

(2013) Dennis Enning et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Community history affects the predictability of microbial ecosystem development

(2013) Eulyn Pagaling et al.   ISME Journal

Eco-evolutionary feedbacks drive species interactions

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Metabolic flux analysis using13C peptide label measurements

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Behavioral diversity in microbes and low-dimensional phenotypic spaces

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Community Structure and Function of High-Temperature Chlorophototrophic Microbial Mats Inhabiting Diverse Geothermal Environments

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Contingency and Statistical Laws in Replicate Microbial Closed Ecosystems

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Competition, Not Cooperation, Dominates Interactions among Culturable Microbial Species

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Evolutionary Trade-Offs, Pareto Optimality, and the Geometry of Phenotype Space

(2012) O. Shoval et al.   SCIENCE

Substrate-Controlled Succession of Marine Bacterioplankton Populations Induced by a Phytoplankton Bloom

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Targeted Restoration of the Intestinal Microbiota with a Simple, Defined Bacteriotherapy Resolves Relapsing Clostridium difficile Disease in Mice

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Subpopulation-Specific Metabolic Pathway Usage in Mixed Cultures as Revealed by Reporter Protein-Based13C Analysis

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How the 1D-NOESY suppresses solvent signal in metabonomics NMR spectroscopy: An examination of the pulse sequence components and evolution

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Direct-coupling analysis of residue coevolution captures native contacts across many protein families

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Bacterial community structures are unique and resilient in full-scale bioenergy systems

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Correction: Structure and Evolution of Streptomyces Interaction Networks in Soil and In Silico

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Fourier transform infrared spectroscopy as a metabolite fingerprinting tool for monitoring the phenotypic changes in complex bacterial communities capable of degrading phenol

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New monitoring approach for metabolic dynamics in microbial ecosystems using stable-isotope-labeling technologies

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Dynamic Omics Approach Identifies Nutrition-Mediated Microbial Interactions

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Emergent cooperation in microbial metabolism

(2010) Edwin H Wintermute et al.   Molecular Systems Biology

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Soil-carbon response to warming dependent on microbial physiology

(2010) Steven D. Allison et al.   Nature Geoscience

Protein-based stable isotope probing

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A Cryptic Sulfur Cycle in Oxygen-Minimum-Zone Waters off the Chilean Coast

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Investigation of the microbial degradation of phenazone-type drugs and their metabolites by natural biofilms derived from river water using liquid chromatography/tandem mass spectrometry (LC-MS/MS)

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Community metabolism of aquatic Closed Ecological Systems: Effects of nitrogen sources

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High-throughput serum NMR metabonomics for cost-effective holistic studies on systemic metabolism

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Hollow-Fiber Membrane Chamber as a Device for In Situ Environmental Cultivation

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Protein Sectors: Evolutionary Units of Three-Dimensional Structure

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Ongoing Revolution in Bacteriology: Routine Identification of Bacteria by Matrix‐Assisted Laser Desorption Ionization Time‐of‐Flight Mass Spectrometry

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Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli

(2009) Bryson D Bennett et al.   Nature Chemical Biology

13C-based metabolic flux analysis

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Kinetic flux profiling for quantitation of cellular metabolic fluxes

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