Measurement Techniques to Resolve and Control Population Dynamics of Mixed-Culture Processes

Development and characterization of Escherichia coli triple reporter strains for investigation of population heterogeneity in bioprocesses

(2020) Anna-Lena Heins et al.   Microbial Cell Factories

Inducible cell-to-cell signaling for tunable dynamics in microbial communities

(2020) Arianna Miano et al.   Nature Communications

Development of a Quorum-Sensing Based Circuit for Control of Coculture Population Composition in a Naringenin Production System

(2020) Christina V. Dinh et al.   ACS Synthetic Biology

Real-time monitoring of population dynamics and physical interactions in a synthetic yeast ecosystem by use of multicolour flow cytometry

(2020) C. G. Conacher et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Deep reinforcement learning for the control of microbial co-cultures in bioreactors

(2020) Neythen J. Treloar et al.   PLoS Computational Biology

A heterogeneous microbial consortium producing short-chain fatty acids from lignocellulose

(2020) Robert L. Shahab et al.   SCIENCE

FlopR: An Open Source Software Package for Calibration and Normalization of Plate Reader and Flow Cytometry Data

(2020) Alex J. H. Fedorec et al.   ACS Synthetic Biology

Consolidated bioprocessing of cellulose to itaconic acid by a co-culture of Trichoderma reesei and Ustilago maydis

(2020) Ivan Schlembach et al.   Biotechnology for Biofuels

Synchrotron infrared spectral regions as signatures for foodborne bacterial typing

(2019) Ya-Di Wang et al.   Nuclear Science and Techniques

EXPRESS: Mid-Infrared Spectroscopy and Multivariate Analysis to Characterize Lactobacillus acidophilus Fermentation Processes

(2019) Sumana Narayana et al.   APPLIED SPECTROSCOPY

Using autofluorescence to detect bacterial contamination in root fractures

(2019) Hye-min Ku et al.   JOURNAL OF DENTISTRY

A guide to the application of Hill numbers to DNA‐based diversity analyses

(2019) Antton Alberdi et al.   Molecular Ecology Resources

Segregostat: a novel concept to control phenotypic diversification dynamics on the example of Gram‐negative bacteria

(2019) Hosni Sassi et al.   Microbial Biotechnology

A split fluorescent reporter with rapid and reversible complementation

(2019) Alison G. Tebo et al.   Nature Communications

Effect of the oxygen transfer rate on oxygen-limited production of plasmid DNA by Escherichia coli

(2019) Alvaro R. Lara et al.   BIOCHEMICAL ENGINEERING JOURNAL

Bacterial co-culture with cell signaling translator and growth controller modules for autonomously regulated culture composition

(2019) Kristina Stephens et al.   Nature Communications

Probeless non-invasive near-infrared spectroscopic bioprocess monitoring using microspectrometer technology

(2019) Robert Zimmerleiter et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Noninvasive tool for optical online monitoring of individual biomass concentrations in a defined coculture

(2019) Bertram Geinitz et al.   BIOTECHNOLOGY AND BIOENGINEERING

Robust blind spectral unmixing for fluorescence microscopy using unsupervised learning

(2019) Tristan D. McRae et al.   PLoS One

Exploring thematic structure and predicted functionality of 16S rRNA amplicon data

(2019) Stephen Woloszynek et al.   PLoS One

Consolidated bioprocessing of lignocellulosic biomass to lactic acid by a synthetic fungal-bacterial consortium

(2018) Robert L. Shahab et al.   BIOTECHNOLOGY AND BIOENGINEERING

Mixed culture fermentation using Torulaspora delbrueckii and Saccharomyces cerevisiae with direct and indirect contact: impact of anaerobic growth factors

(2018) Paul Brou et al.   EUROPEAN FOOD RESEARCH AND TECHNOLOGY

Engineered monoculture and co-culture of methylotrophic yeast for de novo production of monacolin J and lovastatin from methanol

(2018) Yiqi Liu et al.   METABOLIC ENGINEERING

Personalized microbiome dynamics – Cytometric fingerprints for routine diagnostics

(2018) Christin Koch et al.   MOLECULAR ASPECTS OF MEDICINE

Confocal autofluorescence identification of bacteria, fungi, and acanthamoeba in infected porcine cornea models

(2018) Shu-Han Wen et al.   OPTIK

Synergistic activity of cosecreted natural products from amoebae-associated bacteria

(2018) Johannes Arp et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A hand-held fluorescent sensor platform for selectively estimating green algae and cyanobacteria biomass

(2018) Young-Ho Shin et al.   SENSORS AND ACTUATORS B-CHEMICAL

Ecological Stability Properties of Microbial Communities Assessed by Flow Cytometry

(2018) Zishu Liu et al.   mSphere

Consolidated bioprocessing of lignocellulosic biomass to itaconic acid by metabolically engineering Neurospora crassa

(2018) Chen Zhao et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Inter-Kingdom beach warfare: Microbial chemical communication activates natural chemical defences

(2018) Zeinab G. Khalil et al.   ISME Journal

Publisher Correction: Detection of antibiotics synthetized in microfluidic picolitre-droplets by various actinobacteria

(2018) Lisa Mahler et al.   Scientific Reports

Neutral mechanisms and niche differentiation in steady-state insular microbial communities revealed by single cell analysis

(2018) Zishu Liu et al.   ENVIRONMENTAL MICROBIOLOGY

High-throughput microfluidic imaging flow cytometry

(2018) Stavros Stavrakis et al.   CURRENT OPINION IN BIOTECHNOLOGY

The Berkeleylactones, Antibiotic Macrolides from Fungal Coculture

(2017) Andrea A. Stierle et al.   JOURNAL OF NATURAL PRODUCTS

Flow cytometric quantification, sorting and sequencing of methanogenic archaea based on F420 autofluorescence

(2017) Johannes Lambrecht et al.   Microbial Cell Factories

Symbiosis-inspired approaches to antibiotic discovery

(2017) Navid Adnani et al.   NATURAL PRODUCT REPORTS

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

(2017) Freeman Lan et al.   NATURE BIOTECHNOLOGY

Microfluidic droplet platform for ultrahigh-throughput single-cell screening of biodiversity

(2017) Stanislav S. Terekhov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Effects of growth rate and promoter activity on single-cell protein expression

(2017) Niclas Nordholt et al.   Scientific Reports

A Review on the Applications of Next Generation Sequencing Technologies as Applied to Food-Related Microbiome Studies

(2017) Yu Cao et al.   Frontiers in Microbiology

A stabilized microbial ecosystem of self-limiting bacteria using synthetic quorum-regulated lysis

(2017) Spencer R. Scott et al.   Nature Microbiology

Expression of fluorescent proteins in Lactobacillus rhamnosus to study host-microbe and microbe-microbe interactions

(2017) Irina Spacova et al.   Microbial Biotechnology

Flow Cytometric Single-Cell Identification of Populations in Synthetic Bacterial Communities

(2017) Peter Rubbens et al.   PLoS One

Spectroscopic sensors for in-line bioprocess monitoring in research and pharmaceutical industrial application

(2016) Jens Claßen et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Impact of oxygenation on the performance of three non-Saccharomyces yeasts in co-fermentation with Saccharomyces cerevisiae

(2016) Kirti Shekhawat et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Parallel online multi-wavelength (2D) fluorescence spectroscopy in each well of a continuously shaken microtiter plate

(2016) Tobias Ladner et al.   Biotechnology Journal

Principles for designing synthetic microbial communities

(2016) Nathan I Johns et al.   CURRENT OPINION IN MICROBIOLOGY

Parallel online multi-wavelength (2D) fluorescence spectroscopy in each well of a continuously shaken microtiter plate

(2016) Tobias Ladner et al.   Biotechnology Journal

Online flow cytometry reveals microbial dynamics influenced by concurrent natural and operational events in groundwater used for drinking water treatment

(2016) Michael D. Besmer et al.   Scientific Reports

Bioreactor control improves bioprocess performance

(2015) Rimvydas Simutis et al.   Biotechnology Journal

A synthetic growth switch based on controlled expression of RNA polymerase

(2015) J. Izard et al.   Molecular Systems Biology

Fluorescence Spectroscopy and Chemometric Modeling for Bioprocess Monitoring

(2015) Saskia Faassen et al.   SENSORS

A palette of fluorescent proteins optimized for diverse cellular environments

(2015) Lindsey M. Costantini et al.   Nature Communications

Bioreactor control improves bioprocess performance

(2015) Rimvydas Simutis et al.   Biotechnology Journal

Spectrophotometric Analysis of Pigments: A Critical Assessment of a High-Throughput Method for Analysis of Algal Pigment Mixtures by Spectral Deconvolution

(2015) Jan-Erik Thrane et al.   PLoS One

Interactions of Nitrosomonas europaea and Nitrobacter winogradskyi grown in co-culture

(2014) José Pérez et al.   ARCHIVES OF MICROBIOLOGY

Metabolite induction via microorganism co-culture: A potential way to enhance chemical diversity for drug discovery

(2014) Samuel Bertrand et al.   BIOTECHNOLOGY ADVANCES

Unmixing of fluorescence spectra to resolve quantitative time-series measurements of gene expression in plate readers

(2014) Catherine A Lichten et al.   BMC BIOTECHNOLOGY

Species-specific viability analysis of Pseudomonas aeruginosa, Burkholderia cepacia and Staphylococcus aureus in mixed culture by flow cytometry

(2014) Marc Rüger et al.   BMC MICROBIOLOGY

Impact of Next Generation Sequencing Techniques in Food Microbiology

(2014) Baltasar Mayo et al.   CURRENT GENOMICS

Consolidated bioprocessing of lignocellulose by a microbial consortium

(2014) Simone Brethauer et al.   Energy & Environmental Science

An evaluation of genetically encoded FRET-based biosensors for quantitative metabolite analyses in vivo

(2014) Roland Moussa et al.   JOURNAL OF BIOTECHNOLOGY

Photosynthetic mixed culture polyhydroxyalkanoate (PHA) production from individual and mixed volatile fatty acids (VFAs): Substrate preferences and co-substrate uptake

(2014) J.C. Fradinho et al.   JOURNAL OF BIOTECHNOLOGY

Co-culture systems and technologies: taking synthetic biology to the next level

(2014) L. Goers et al.   Journal of the Royal Society Interface

Real time monitoring of population dynamics in concurrent bacterial growth using SIFT-MS quantification of volatile metabolites

(2013) Kristýna Sovová et al.   ANALYST

Multi-analyte quantification in bioprocesses by Fourier-transform-infrared spectroscopy by partial least squares regression and multivariate curve resolution

(2013) Cosima Koch et al.   ANALYTICA CHIMICA ACTA

Genetic Techniques for the Archaea

(2013) Joel A. Farkas et al.   Annual Review of Genetics

Consortia-mediated bioprocessing of cellulose to ethanol with a symbiotic Clostridium phytofermentans/yeast co-culture

(2013) Trevor R Zuroff et al.   Biotechnology for Biofuels

Monitoring of Lactic Acid Fermentation Process Using Fourier Transform near Infrared Spectroscopy

(2013) Silvia Grassi et al.   JOURNAL OF NEAR INFRARED SPECTROSCOPY

Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass

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

Identification and discrimination of bacteria using Fourier transform infrared spectroscopy

(2013) Jyoti Prakash Maity et al.   SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY

Short-chain fluorescent tryptophan tags for on-line detection of functional recombinant proteins

(2012) Eva-Maria Siepert et al.   BMC BIOTECHNOLOGY

Towards synthetic microbial consortia for bioprocessing

(2012) Jasmine Shong et al.   CURRENT OPINION IN BIOTECHNOLOGY

A flow cytometric method for viability assessment ofStaphylococcus aureusandBurkholderia cepaciain mixed culture

(2012) Marc Rüger et al.   CYTOMETRY PART A

A Programmable Escherichia coli Consortium via Tunable Symbiosis

(2012) Alissa Kerner et al.   PLoS One

In situ sensor techniques in modern bioprocess monitoring

(2011) Sascha Beutel et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

A novel concept combining experimental and mathematical analysis for the identification of unknown interspecies effects in a mixed culture

(2011) Julia K. Schmidt et al.   BIOTECHNOLOGY AND BIOENGINEERING

Designing biological systems: Systems Engineering meets Synthetic Biology

(2011) Sascha Rollié et al.   CHEMICAL ENGINEERING SCIENCE

RNA-seq reveals cooperative metabolic interactions between two termite-gut spirochete species in co-culture

(2011) Adam Z Rosenthal et al.   ISME Journal

Evaluation of FT-IR spectroscopy as a tool to quantify bacteria in binary mixed cultures

(2011) Robert Schäwe et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Flavin Mononucleotide-Based Fluorescent Reporter Proteins Outperform Green Fluorescent Protein-Like Proteins as Quantitative In Vivo Real-Time Reporters

(2010) T. Drepper et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Biosystems analysis and engineering of microbial consortia for industrial biotechnology

(2010) Wael Sabra et al.   ENGINEERING IN LIFE SCIENCES

Application of flow cytometry to industrial microbial bioprocesses

(2009) Mario Díaz et al.   BIOCHEMICAL ENGINEERING JOURNAL

Engineering microbial consortia: a new frontier in synthetic biology

(2008) Katie Brenner et al.   TRENDS IN BIOTECHNOLOGY

The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing

(2008) Les Dethlefsen et al.   PLOS BIOLOGY