Common principles and best practices for engineering microbiomes

An interspecies malate–pyruvate shuttle reconciles redox imbalance in an anaerobic microbial community

(2019) Po-Hsiang Wang et al.   ISME Journal

Metagenomic engineering of the mammalian gut microbiome in situ

(2019) Carlotta Ronda et al.   NATURE METHODS

Biomass segregation between biofilm and flocs improves the control of nitrite-oxidizing bacteria in mainstream partial nitritation and anammox processes

(2019) Michele Laureni et al.   WATER RESEARCH

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

(2019) Kang Soo Lee et al.   Nature Microbiology

Introducing THOR, a Model Microbiome for Genetic Dissection of Community Behavior

(2019) Gabriel L. Lozano et al.   mBio

Harnessing Nature's Anaerobes for Biotechnology and Bioprocessing

(2019) Igor A. Podolsky et al.   Annual Review of Chemical and Biomolecular Engineering

A human gut bacterial genome and culture collection for improved metagenomic analyses

(2019) Samuel C. Forster et al.   NATURE BIOTECHNOLOGY

Metabolic Imaging at the Single-Cell Scale: Recent Advances in Mass Spectrometry Imaging

(2019) Ian S. Gilmore et al.   Annual Review of Analytical Chemistry

Modular Assembly of Polysaccharide-Degrading Marine Microbial Communities

(2019) Tim N. Enke et al.   CURRENT BIOLOGY

Domestication of Industrial Microbes

(2019) Jan Steensels et al.   CURRENT BIOLOGY

Co-cultivation of the anaerobic fungus Anaeromyces robustus with Methanobacterium bryantii enhances transcription of carbohydrate active enzymes

(2019) Candice L. Swift et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Spatial, Temporal, and Phylogenetic Scales of Microbial Ecology

(2019) Joshua Ladau et al.   TRENDS IN MICROBIOLOGY

Application of Machine Learning in Microbiology

(2019) Kaiyang Qu et al.   Frontiers in Microbiology

The Design of FluxML: A Universal Modeling Language for 13C Metabolic Flux Analysis

(2019) Martin Beyß et al.   Frontiers in Microbiology

EcoFABs: advancing microbiome science through standardized fabricated ecosystems

(2019) Karsten Zengler et al.   NATURE METHODS

Massively parallel screening of synthetic microbial communities

(2019) Jared Kehe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Machine and deep learning meet genome-scale metabolic modeling

(2019) Guido Zampieri et al.   PLoS Computational Biology

NanoSIMS for biological applications: Current practices and analyses

(2018) Jamie Nuñez et al.   Biointerphases

Leveraging knowledge engineering and machine learning for microbial bio-manufacturing

(2018) Tolutola Oyetunde et al.   BIOTECHNOLOGY ADVANCES

An integrative review of granular sludge for the biological removal of nutrients and recalcitrant organic matter from wastewater

(2018) Mari-Karoliina Henriikka Winkler et al.   CHEMICAL ENGINEERING JOURNAL

The soil microbiome — from metagenomics to metaphenomics

(2018) Janet K Jansson et al.   CURRENT OPINION IN MICROBIOLOGY

Proteomics and pulse azidohomoalanine labeling of newly synthesized proteins: what are the potential applications?

(2018) Yuanhui Ma et al.   Expert Review of Proteomics

Deciphering microbial interactions in synthetic human gut microbiome communities

(2018) Ophelia S Venturelli et al.   Molecular Systems Biology

Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection

(2018) Rekha Seshadri et al.   NATURE BIOTECHNOLOGY

KBase: The United States Department of Energy Systems Biology Knowledgebase

(2018) Adam P Arkin et al.   NATURE BIOTECHNOLOGY

Next-generation biocontainment systems for engineered organisms

(2018) Jeong Wook Lee et al.   Nature Chemical Biology

CRISPR-based genomic tools for the manipulation of genetically intractable microorganisms

(2018) Rebecca S. Shapiro et al.   NATURE REVIEWS MICROBIOLOGY

Keystone taxa as drivers of microbiome structure and functioning

(2018) Samiran Banerjee et al.   NATURE REVIEWS MICROBIOLOGY

The social network of microorganisms — how auxotrophies shape complex communities

(2018) Karsten Zengler et al.   NATURE REVIEWS MICROBIOLOGY

The microbial nitrogen-cycling network

(2018) Marcel M. M. Kuypers et al.   NATURE REVIEWS MICROBIOLOGY

Gut bacteria selectively promoted by dietary fibers alleviate type 2 diabetes

(2018) Liping Zhao et al.   SCIENCE

Need for Laboratory Ecosystems To Unravel the Structures and Functions of Soil Microbial Communities Mediated by Chemistry

(2018) Kateryna Zhalnina et al.   mBio

Linking soil biology and chemistry in biological soil crust using isolate exometabolomics

(2018) Tami L. Swenson et al.   Nature Communications

NanoSIMS for biological applications: Current practices and analyses

(2018) Jamie Nuñez et al.   Biointerphases

Function and functional redundancy in microbial systems

(2018) Stilianos Louca et al.   Nature Ecology & Evolution

Mutant phenotypes for thousands of bacterial genes of unknown function

(2018) Morgan N. Price et al.   NATURE

Inferring Metabolic Mechanisms of Interaction within a Defined Gut Microbiota

(2018) Gregory L. Medlock et al.   Cell Systems

Engineered integrative and conjugative elements for efficient and inducible DNA transfer to undomesticated bacteria

(2018) Jennifer A. N. Brophy et al.   Nature Microbiology

Can we predict keystones?

(2018) Lisa Röttjers et al.   NATURE REVIEWS MICROBIOLOGY

Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models

(2018) David Heckmann et al.   Nature Communications

Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem

(2018) Lindsey M. Solden et al.   Nature Microbiology

Machine Learning Reveals Missing Edges and Putative Interaction Mechanisms in Microbial Ecosystem Networks

(2018) Demetrius DiMucci et al.   mSystems

Metatranscriptomic and Thermodynamic Insights into Medium-Chain Fatty Acid Production Using an Anaerobic Microbiome

(2018) Matthew J. Scarborough et al.   mSystems

Intermittent Aeration Suppresses Nitrite-Oxidizing Bacteria in Membrane-Aerated Biofilms: A Model-Based Explanation

(2017) Yunjie Ma et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Build your own soil: exploring microfluidics to create microbial habitat structures

(2017) Kristin Aleklett et al.   ISME Journal

DNA-SIP based genome-centric metagenomics identifies key long-chain fatty acid-degrading populations in anaerobic digesters with different feeding frequencies

(2017) Ryan M Ziels et al.   ISME Journal

On-chip integration of droplet microfluidics and nanostructure-initiator mass spectrometry for enzyme screening

(2017) Joshua Heinemann et al.   LAB ON A CHIP

Engineered bacteria can function in the mammalian gut long-term as live diagnostics of inflammation

(2017) David T Riglar et al.   NATURE BIOTECHNOLOGY

Single-cell genome sequencing at ultra-high-throughput with microfluidic droplet barcoding

(2017) Freeman Lan et al.   NATURE BIOTECHNOLOGY

Scaling by shrinking: empowering single-cell 'omics' with microfluidic devices

(2017) Sanjay M. Prakadan et al.   NATURE REVIEWS GENETICS

Printed droplet microfluidics for on demand dispensing of picoliter droplets and cells

(2017) Russell H. Cole et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cas9-mediated genome editing in the methanogenic archaeonMethanosarcina acetivorans

(2017) Dipti D. Nayak et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metabolic network analysis reveals microbial community interactions in anammox granules

(2017) Christopher E. Lawson et al.   Nature Communications

The Experiment Data Depot: A Web-Based Software Tool for Biological Experimental Data Storage, Sharing, and Visualization

(2017) William C. Morrell et al.   ACS Synthetic Biology

3D printing of bacteria into functional complex materials

(2017) Manuel Schaffner et al.   Science Advances

Mass Spectrometry Imaging of Complex Microbial Communities

(2016) Sage J. B. Dunham et al.   ACCOUNTS OF CHEMICAL RESEARCH

Mechanistic modelling of in vitro fermentation and methane production by rumen microbiota

(2016) Rafael Muñoz-Tamayo et al.   ANIMAL FEED SCIENCE AND TECHNOLOGY

High-Throughput Single-Cell Cultivation on Microfluidic Streak Plates

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

Engineering Cellular Metabolism

(2016) Jens Nielsen et al.   CELL

Coupled RNA-SIP and metatranscriptomics of active chemolithoautotrophic communities at a deep-sea hydrothermal vent

(2016) Caroline S Fortunato et al.   ISME Journal

Identification of syntrophic acetate-oxidizing bacteria in anaerobic digesters by combined protein-based stable isotope probing and metagenomics

(2016) Freya Mosbæk et al.   ISME Journal

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

(2016) Elin E Lilja et al.   ISME Journal

Rapid evolution of microbe-mediated protection against pathogens in a worm host

(2016) Kayla C King et al.   ISME Journal

Synthetic Ecology of Microbes: Mathematical Models and Applications

(2016) Ali R. Zomorrodi et al.   JOURNAL OF MOLECULAR BIOLOGY

Towards Engineering Biological Systems in a Broader Context

(2016) Ophelia S. Venturelli et al.   JOURNAL OF MOLECULAR BIOLOGY

Droplet microfluidics for microbiology: techniques, applications and challenges

(2016) Tomasz S. Kaminski et al.   LAB ON A CHIP

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

(2016) Hilary P. Browne et al.   NATURE

Spatial structure, cooperation and competition in biofilms

(2016) Carey D. Nadell et al.   NATURE REVIEWS MICROBIOLOGY

Quorum sensing signal–response systems in Gram-negative bacteria

(2016) Kai Papenfort et al.   NATURE REVIEWS MICROBIOLOGY

Advancing microbial sciences by individual-based modelling

(2016) Ferdi L. Hellweger et al.   NATURE REVIEWS MICROBIOLOGY

Visualizing in situ translational activity for identifying and sorting slow-growing archaeal−bacterial consortia

(2016) Roland Hatzenpichler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Biogeography of a human oral microbiome at the micron scale

(2016) Jessica L. Mark Welch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Artificial electron acceptors decouple archaeal methane oxidation from sulfate reduction

(2016) S. Scheller et al.   SCIENCE

Manipulating Bacterial Communities by in situ Microbiome Engineering

(2016) Ravi U. Sheth et al.   TRENDS IN GENETICS

Impact of cell cluster size on apparent half-saturation coefficients for oxygen in nitrifying sludge and biofilms

(2016) Cristian Picioreanu et al.   WATER RESEARCH

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

(2016) Karthik Anantharaman et al.   Nature Communications

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

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

A microfluidics-based in vitro model of the gastrointestinal human–microbe interface

(2016) Pranjul Shah et al.   Nature Communications

A Droplet Microfluidic Platform for Automating Genetic Engineering

(2016) Philip C. Gach et al.   ACS Synthetic Biology

Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution

(2016) Jose Utrilla et al.   Cell Systems

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

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

Metabolism Links Bacterial Biofilms and Colon Carcinogenesis

(2015) Caroline H. Johnson et al.   Cell Metabolism

Linking metabolite production to taxonomic identity in environmental samples by (MA)LDI-FISH

(2015) Martin Kaltenpoth et al.   ISME Journal

Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor

(2015) Masaru K Nobu et al.   ISME Journal

13 C-metabolic flux analysis of co-cultures: A novel approach

(2015) Nikodimos A. Gebreselassie et al.   METABOLIC ENGINEERING

Microbiology: Create a global microbiome effort

(2015) Nicole Dubilier et al.   NATURE

Intercellular wiring enables electron transfer between methanotrophic archaea and bacteria

(2015) Gunter Wegener et al.   NATURE

Single cell activity reveals direct electron transfer in methanotrophic consortia

(2015) Shawn E. McGlynn et al.   NATURE

Distributing a metabolic pathway among a microbial consortium enhances production of natural products

(2015) Kang Zhou et al.   NATURE BIOTECHNOLOGY

Novel pathways for fuels and lubricants from biomass optimized using life-cycle greenhouse gas assessment

(2015) Madhesan Balakrishnan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mathematical modelling of anaerobic digestion processes: applications and future needs

(2015) Damien J. Batstone et al.   REVIEWS IN ENVIRONMENTAL SCIENCE AND BIO-TECHNOLOGY

A unified initiative to harness Earth's microbiomes

(2015) A. P. Alivisatos et al.   SCIENCE

Engineering Microbiomes to Improve Plant and Animal Health

(2015) U.G. Mueller et al.   TRENDS IN MICROBIOLOGY

MiDAS: the field guide to the microbes of activated sludge

(2015) Simon Jon McIlroy et al.   Database-The Journal of Biological Databases and Curation

A Versatile Microfluidic Device for Automating Synthetic Biology

(2015) Steve C. C. Shih et al.   ACS Synthetic Biology

Manipulation of the Quorum Sensing Signal AI-2 Affects the Antibiotic-Treated Gut Microbiota

(2015) Jessica Ann Thompson et al.   Cell Reports

An Integrated Approach to Reconstructing Genome-Scale Transcriptional Regulatory Networks

(2015) Saheed Imam et al.   PLoS Computational Biology

Mathematical modelling of anaerobic digestion processes: applications and future needs

(2015) Damien J. Batstone et al.   REVIEWS IN ENVIRONMENTAL SCIENCE AND BIO-TECHNOLOGY

Engineering Modular Viral Scaffolds for Targeted Bacterial Population Editing

(2015) Hiroki Ando et al.   Cell Systems

In situvisualization of newly synthesized proteins in environmental microbes using amino acid tagging and click chemistry

(2014) Roland Hatzenpichler et al.   ENVIRONMENTAL MICROBIOLOGY

Navigating Wastewater Energy Recovery Strategies: A Life Cycle Comparison of Anaerobic Membrane Bioreactor and Conventional Treatment Systems with Anaerobic Digestion

(2014) Adam L. Smith et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Functionally relevant diversity of closely related Nitrospira in activated sludge

(2014) Christiane Gruber-Dorninger et al.   ISME Journal

Dynamics in microbial communities: unraveling mechanisms to identify principles

(2014) Allan Konopka et al.   ISME Journal

Selection on soil microbiomes reveals reproducible impacts on plant function

(2014) Kevin Panke-Buisse et al.   ISME Journal

Programmable bacteria detect and record an environmental signal in the mammalian gut

(2014) Jonathan W. Kotula et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Syntrophic exchange in synthetic microbial communities

(2014) M. T. Mee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes

(2014) A. K. Hawley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-Efficiency Multiplex Genome Editing of Streptomyces Species Using an Engineered CRISPR/Cas System

(2014) Ryan E. Cobb et al.   ACS Synthetic Biology

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

Connecting the dots: linking nitrogen cycle gene expression to nitrogen fluxes in marine sediment mesocosms

(2014) Jennifer L. Bowen et al.   Frontiers in Microbiology

“Replica-Extraction-Transfer” Nanostructure-Initiator Mass Spectrometry Imaging of Acoustically Printed Bacteria

(2013) Katherine B. Louie et al.   ANALYTICAL CHEMISTRY

A new model for electron flow during anaerobic digestion: direct interspecies electron transfer to Methanosaeta for the reduction of carbon dioxide to methane

(2013) Amelia-Elena Rotaru et al.   Energy & Environmental Science

The nature of laboratory domestication changes in freshly isolatedEscherichia colistrains

(2013) Gustavo Eydallin et al.   ENVIRONMENTAL MICROBIOLOGY

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

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

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

3D printing of microscopic bacterial communities

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

Microbial interactions: from networks to models

(2012) Karoline Faust et al.   NATURE REVIEWS MICROBIOLOGY

Fundamentals of Microbial Community Resistance and Resilience

(2012) Ashley Shade et al.   Frontiers in Microbiology

Microbial community engineering for biopolymer production from glycerol

(2011) Helena Moralejo-Gárate et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Microbial communities involved in enhanced biological phosphorus removal from wastewater—a model system in environmental biotechnology

(2011) Per Halkjær Nielsen et al.   CURRENT OPINION IN BIOTECHNOLOGY

Segregation of Biomass in Cyclic Anaerobic/Aerobic Granular Sludge Allows the Enrichment of Anaerobic Ammonium Oxidizing Bacteria at Low Temperatures

(2011) Mari K. H. Winkler et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Domestic Wastewater Treatment as a Net Energy Producer–Can This be Achieved?

(2011) Perry L. McCarty et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Microbial metabolic exchange—the chemotype-to-phenotype link

(2011) Vanessa V Phelan et al.   Nature Chemical Biology

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

(2011) J. J. Werner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments

(2010) Kai Zhuang et al.   ISME Journal

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

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

(2010) Ines Thiele et al.   Nature Protocols

Rapid evolution of stability and productivity at the origin of a microbial mutualism

(2010) K. L. Hillesland et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A conceptual ecosystem model of microbial communities in enhanced biological phosphorus removal plants

(2010) Per Halkjær Nielsen et al.   WATER RESEARCH

Robo-Lector – a novel platform for automated high-throughput cultivations in microtiter plates with high information content

(2009) Robert Huber et al.   Microbial Cell Factories

Genome evolution and adaptation in a long-term experiment with Escherichia coli

(2009) Jeffrey E. Barrick et al.   NATURE

Ensemble Modeling of Metabolic Networks

(2008) Linh M. Tran et al.   BIOPHYSICAL JOURNAL

A synthetic Escherichia coli predator–prey ecosystem

(2008) Frederick K Balagaddé et al.   Molecular Systems Biology

Defined spatial structure stabilizes a synthetic multispecies bacterial community

(2008) H. J. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Large-scale reconstruction and phylogenetic analysis of metabolic environments

(2008) E. Borenstein et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Microbial Engines That Drive Earth's Biogeochemical Cycles

(2008) P. G. Falkowski et al.   SCIENCE

Granular biomass capable of partial nitritation and anammox

(2008) S. E. Vlaeminck et al.   WATER SCIENCE AND TECHNOLOGY