The ecology of wine fermentation: a model for the study of complex microbial ecosystems

Computational Analysis of Microbial Flow Cytometry Data

(2021) Peter Rubbens et al.   mSystems

Effect of a Multistarter Yeast Inoculum on Ethanol Reduction and Population Dynamics in Wine Fermentation

(2021) Xiaolin Zhu et al.   Foods

Bacterial Community Diversity Dynamics Highlight Degrees of Nestedness and Turnover Patterns

(2020) Zishu Liu et al.   CYTOMETRY PART A

Development of Novel Bioreactor Control Systems Based on Smart Sensors and Actuators

(2020) Baowei Wang et al.   Frontiers in Bioengineering and Biotechnology

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

Evolution of mutualistic behaviour between Chlorella sorokiniana and Saccharomyces cerevisiae within a synthetic environment

(2020) J. R. Oosthuizen et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Understanding the evolution of interspecies interactions in microbial communities

(2020) Florien A. Gorter et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Putting science back into microbial ecology: a question of approach

(2020) James I. Prosser   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Conceptual challenges in microbial community ecology

(2020) James I. Prosser et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Community Simulator: A Python package for microbial ecology

(2020) Robert Marsland et al.   PLoS One

Exploring yeast interactions through metabolic profiling

(2020) C. Roullier-Gall et al.   Scientific Reports

Ecological interactions are a primary driver of population dynamics in wine yeast microbiota during fermentation

(2020) Bahareh Bagheri et al.   Scientific Reports

Yeast–Yeast Interactions: Mechanisms, Methodologies and Impact on Composition

(2020) Fanny Bordet et al.   Microorganisms

Synthetic microbial communities of heterotrophs and phototrophs facilitate sustainable growth

(2020) Cristal Zuñiga et al.   Nature Communications

Proteomic characterization of extracellular vesicles produced by several wine yeast species

(2020) Ana Mencher et al.   Microbial Biotechnology

Enforced Mutualism Leads to Improved Cooperative Behavior between Saccharomyces cerevisiae and Lactobacillus plantarum

(2020) S. Christine du Toit et al.   Microorganisms

Dynamics of active potential bacterial and fungal interactions in the assimilation of acidobacterial EPS in soil

(2020) Ohana Y.A. Costa et al.   SOIL BIOLOGY & BIOCHEMISTRY

Modeling microbial cross-feeding at intermediate scale portrays community dynamics and species coexistence

(2020) Chen Liao et al.   PLoS Computational Biology

The Fungal Microbiome Is an Important Component of Vineyard Ecosystems and Correlates with Regional Distinctiveness of Wine

(2020) Di Liu et al.   mSphere

Nutrient Exchange of Carbon and Nitrogen Promotes the Formation of Stable Mutualisms Between Chlorella sorokiniana and Saccharomyces cerevisiae Under Engineered Synthetic Growth Conditions

(2019) René K. Naidoo et al.   Frontiers in Microbiology

De novo origins of multicellularity in response to predation

(2019) Matthew D. Herron et al.   Scientific Reports

Engineering microbial consortia by division of labor

(2019) Garrett W. Roell et al.   Microbial Cell Factories

RNA-seq based transcriptional analysis of Saccharomyces cerevisiae and Lachancea thermotolerans in mixed-culture fermentations under anaerobic conditions

(2019) Kirti Shekhawat et al.   BMC GENOMICS

Emerging strategies for engineering microbial communities

(2019) Ryan Tsoi et al.   BIOTECHNOLOGY ADVANCES

Coculturing bacteria leads to reduced phenotypic heterogeneities

(2019) Jasmine Heyse et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Interactions of Pseudomonas aeruginosa with Acanthamoeba polyphaga Observed by Imaging Flow Cytometry

(2019) Rafik Dey et al.   CYTOMETRY PART A

A flow cytometry method for bacterial quantification and biomass estimates in activated sludge

(2019) M.R. Brown et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Algal-fungal symbiosis leads to photosynthetic mycelium

(2019) Zhi-Yan Du et al.   eLife

A Multicolor Fluorescence in situ Hybridization Approach Using an Extended Set of Fluorophores to Visualize Microorganisms

(2019) Michael Lukumbuzya et al.   Frontiers in Microbiology

Establishment of Coral-Bacteria Symbioses Reveal Changes in the Core Bacterial Community With Host Ontogeny

(2019) Rachele Bernasconi et al.   Frontiers in Microbiology

Hidden Secrets Behind Dots: Improved Phytoplankton Taxonomic Resolution Using High‐Throughput Imaging Flow Cytometry

(2019) Susanne Dunker   CYTOMETRY PART A

Saccharomyces cerevisiae-Starmerella bacillaris strains interaction modulates chemical and volatile profile in red wine mixed fermentations

(2019) Vasileios Englezos et al.   FOOD RESEARCH INTERNATIONAL

Effect of mixed species alcoholic fermentation on growth and malolactic activity of lactic acid bacteria

(2019) Vasileios Englezos et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Peer pressure: evolutionary responses to biotic pressures in wine yeasts

(2019) C G Conacher et al.   FEMS YEAST RESEARCH

Influence of cell-cell contact between L. thermotolerans and S. cerevisiae on yeast interactions and the exo-metabolome

(2019) Clément Petitgonnet et al.   FOOD MICROBIOLOGY

Environmental stimuli drive a transition from cooperation to competition in synthetic phototrophic communities

(2019) Cristal Zuñiga et al.   Nature Microbiology

Biotechnological potential and applications of microbial consortia

(2019) Xiujuan Qian et al.   BIOTECHNOLOGY ADVANCES

Co-evolution as an important component explaining microbial predator-prey interaction

(2019) Veijo Kaitala et al.   JOURNAL OF THEORETICAL BIOLOGY

Organic cultivation of grape affects yeast succession and wine sensory quality during spontaneous fermentation

(2019) Weina Xu et al.   LWT-FOOD SCIENCE AND TECHNOLOGY

High-order interactions distort the functional landscape of microbial consortia

(2019) Alicia Sanchez-Gorostiaga et al.   PLOS BIOLOGY

Defining Higher-Order Interactions in Synthetic Ecology: Lessons from Physics and Quantitative Genetics

(2019) Alvaro Sanchez   Cell Systems

Geographical Origin Has a Greater Impact on Grape Berry Fungal Community than Grape Variety and Maturation State

(2019) Dimitrios Kioroglou et al.   Microorganisms

Small scale fungal community differentiation in a vineyard system

(2019) Sarah J. Knight et al.   FOOD MICROBIOLOGY

Population heterogeneity in microbial bioprocesses: origin, analysis, mechanisms, and future perspectives

(2018) Anna-Lena Heins et al.   BIOPROCESS AND BIOSYSTEMS ENGINEERING

Oxygen availability and strain combination modulate yeast growth dynamics in mixed culture fermentations of grape must with Starmerella bacillaris and Saccharomyces cerevisiae

(2018) Vasileios Englezos et al.   FOOD MICROBIOLOGY

Human gut microbiome: hopes, threats and promises

(2018) Patrice D Cani   GUT

Microbiome dynamics during spontaneous fermentations of sound grapes in comparison with sour rot and Botrytis infected grapes

(2018) Jessica Lleixà et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Adaptation of S. cerevisiae to Fermented Food Environments Reveals Remarkable Genome Plasticity and the Footprints of Domestication

(2018) Jean-Luc Legras et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome dynamics and evolution in yeasts: A long-term yeast-bacteria competition experiment

(2018) Nerve Zhou et al.   PLoS One

Ecological Stability Properties of Microbial Communities Assessed by Flow Cytometry

(2018) Zishu Liu et al.   mSphere

Systems-based approaches enable identification of gene targets which improve the flavour profile of low-ethanol wine yeast strains

(2018) Cristian Varela et al.   METABOLIC ENGINEERING

The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities

(2018) Federico Baldini et al.   BIOINFORMATICS

Cell-to-cell contact mechanism modulates Starmerella bacillaris death in mixed culture fermentations with Saccharomyces cerevisiae

(2018) Vasileios Englezos et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Grape berry surface bacterial microbiome: impact from the varieties and clones in the same vineyard from central China

(2018) J. Zhang et al.   JOURNAL OF APPLIED MICROBIOLOGY

From vineyard to winery: a source map of microbial diversity driving wine fermentation

(2017) Peter Morrison-Whittle et al.   ENVIRONMENTAL MICROBIOLOGY

Monitoring the mycobiota during Greco di Tufo and Aglianico wine fermentation by 18S rRNA gene sequencing

(2017) Francesca De Filippis et al.   FOOD MICROBIOLOGY

Application of flow cytometry to wine microorganisms

(2017) Cédric Longin et al.   FOOD MICROBIOLOGY

Genome Diversity and Evolution in the Budding Yeasts (Saccharomycotina)

(2017) Bernard A. Dujon et al.   GENETICS

Early transcriptional response to biotic stress in mixed starter fermentations involving Saccharomyces cerevisiae and Torulaspora delbrueckii

(2017) Jordi Tronchoni et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Imaging flow cytometry for phytoplankton analysis

(2017) Veronika Dashkova et al.   METHODS

Evolutionary biology through the lens of budding yeast comparative genomics

(2017) Souhir Marsit et al.   NATURE REVIEWS GENETICS

Synthetic Microbial Ecology: Engineering Habitats for Modular Consortia

(2017) Sami Ben Said et al.   Frontiers in Microbiology

Genetic Polymorphism in Wine Yeasts: Mechanisms and Methods for Its Detection

(2017) José M. Guillamón et al.   Frontiers in Microbiology

Different Non-Saccharomyces Yeast Species Stimulate Nutrient Consumption in S. cerevisiae Mixed Cultures

(2017) Jose A. Curiel et al.   Frontiers in Microbiology

The Impact of Saccharomyces cerevisiae on a Wine Yeast Consortium in Natural and Inoculated Fermentations

(2017) Bahareh Bagheri et al.   Frontiers in Microbiology

The Grapevine and Wine Microbiome: Insights from High-Throughput Amplicon Sequencing

(2017) Horatio H. Morgan et al.   Frontiers in Microbiology

Genome Diversity and Evolution in the Budding Yeasts (Saccharomycotina)

(2017) Bernard A. Dujon et al.   GENETICS

Yeast Creates a Niche for Symbiotic Lactic Acid Bacteria through Nitrogen Overflow

(2017) Olga Ponomarova et al.   Cell Systems

Coevolution with bacteria drives the evolution of aerobic fermentation in Lachancea kluyveri

(2017) Nerve Zhou et al.   PLoS One

Ecological interactions among Saccharomyces cerevisiae strains: insight into the dominance phenomenon

(2017) Roberto Pérez-Torrado et al.   Scientific Reports

Principles for designing synthetic microbial communities

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

Bacterial diversity of Grenache and Carignan grape surface from different vineyards at Priorat wine region (Catalonia, Spain)

(2016) Maria del Carmen Portillo et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Engineering microbial consortia for controllable outputs

(2016) Stephen R Lindemann et al.   ISME Journal

Challenges in microbial ecology: building predictive understanding of community function and dynamics

(2016) Stefanie Widder et al.   ISME Journal

Microbial mutualism dynamics governed by dose-dependent toxicity of cross-fed nutrients

(2016) Breah LaSarre et al.   ISME Journal

Synthetic Ecology of Microbes: Mathematical Models and Applications

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

Analysis of microbial diversity and dynamics during wine fermentation of Grenache grape variety by high-throughput barcoding sequencing

(2016) Maria del Carmen Portillo et al.   LWT-FOOD SCIENCE AND TECHNOLOGY

Measuring the biodiversity of microbial communities by flow cytometry

(2016) Ruben Props et al.   Methods in Ecology and Evolution

Pervasive Selection for Cooperative Cross-Feeding in Bacterial Communities

(2016) Sebastian Germerodt et al.   PLoS Computational Biology

The Interaction between Saccharomyces cerevisiae and Non-Saccharomyces Yeast during Alcoholic Fermentation Is Species and Strain Specific

(2016) Chunxiao Wang et al.   Frontiers in Microbiology

Microbial communities for bioprocessing: lessons learned from nature

(2016) Xuefeng “Nick” Peng et al.   Current Opinion in Chemical Engineering

Photosymbiosis and the expansion of shallow-water corals

(2016) K. Frankowiak et al.   Science Advances

Wine microbiology is driven by vineyard and winery anthropogenic factors

(2016) Cédric Grangeteau et al.   Microbial Biotechnology

Characterization of Fluorescent Proteins for Three- and Four-Color Live-Cell Imaging in S. cerevisiae

(2016) Ryo Higuchi-Sanabria et al.   PLoS One

Are Epiphytic Microbial Communities in the Carposphere of Ripening Grape Clusters (Vitis vinifera L.) Different between Conventional, Organic, and Biodynamic Grapes?

(2016) Elizabeth Kecskeméti et al.   PLoS One

Wine microbiome: A dynamic world of microbial interactions

(2015) Youzhong Liu et al.   CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION

Deciphering microbial community robustness through synthetic ecology and molecular systems synecology

(2015) Ben Stenuit et al.   CURRENT OPINION IN BIOTECHNOLOGY

Better together: engineering and application of microbial symbioses

(2015) Stephanie G Hays et al.   CURRENT OPINION IN BIOTECHNOLOGY

Interaction between Hanseniaspora uvarum and Saccharomyces cerevisiae during alcoholic fermentation

(2015) Chunxiao Wang et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

In vivo imaging and tracking of host–microbiota interactions via metabolic labeling of gut anaerobic bacteria

(2015) Naama Geva-Zatorsky et al.   NATURE MEDICINE

Imaging flow cytometry enhances particle detection sensitivity for extracellular vesicle analysis

(2015) Robin T Clark   NATURE METHODS

Fluorescence Spectroscopy and Chemometric Modeling for Bioprocess Monitoring

(2015) Saskia Faassen et al.   SENSORS

The Soil Microbiome Influences Grapevine-Associated Microbiota

(2015) Iratxe Zarraonaindia et al.   mBio

Regional microbial signatures positively correlate with differential wine phenotypes: evidence for a microbial aspect to terroir

(2015) Sarah Knight et al.   Scientific Reports

Fungal diversity in grape must and wine fermentation assessed by massive sequencing, quantitative PCR and DGGE

(2015) Chunxiao Wang et al.   Frontiers in Microbiology

Sequence-based Analysis of the Vitis vinifera L. cv Cabernet Sauvignon Grape Must Mycobiome in Three South African Vineyards Employing Distinct Agronomic Systems

(2015) Mathabatha E. Setati et al.   Frontiers in Microbiology

Wine fermentation microbiome: a landscape from different Portuguese wine appellations

(2015) Cátia Pinto et al.   Frontiers in Microbiology

Yeast interactions in multi-starter wine fermentation

(2015) Maurizio Ciani et al.   Current Opinion in Food Science

Sulfur Dioxide Treatment Alters Wine Microbial Diversity and Fermentation Progression in a Dose-Dependent Fashion

(2014) Nicholas A. Bokulich et al.   AMERICAN JOURNAL OF ENOLOGY AND VITICULTURE

Pyrosequencing reveals regional differences in fruit-associated fungal communities

(2014) Michael W. Taylor et al.   ENVIRONMENTAL MICROBIOLOGY

Monitoring of Saccharomyces cerevisiae, Hanseniaspora uvarum, and Starmerella bacillaris (synonym Candida zemplinina) populations during alcoholic fermentation by fluorescence in situ hybridization

(2014) Chunxiao Wang et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Evolution of species interactions determines microbial community productivity in new environments

(2014) Francesca Fiegna et al.   ISME Journal

Quantifying separation and similarity in a Saccharomyces cerevisiae metapopulation

(2014) Sarah Knight et al.   ISME Journal

High-throughput sequencing of amplicons for monitoring yeast biodiversity in must and during alcoholic fermentation

(2014) Vanessa David et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Winemaking and Bioprocesses Strongly Shaped the Genetic Diversity of the Ubiquitous Yeast Torulaspora delbrueckii

(2014) Warren Albertin et al.   PLoS One

Niche engineering demonstrates a latent capacity for fungal-algal mutualism

(2014) E. F. Y. Hom et al.   SCIENCE

Interactions between Kluyveromyces marxianus and Saccharomyces cerevisiae in tequila must type medium fermentation

(2014) Claudia Lorena Fernandez Lopez et al.   WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY

Interactions between Torulaspora delbrueckii and Saccharomyces cerevisiae in wine fermentation: influence of inoculation and nitrogen content

(2014) Patricia Taillandier et al.   WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY

Divining the Essence of Symbiosis: Insights from the Squid-Vibrio Model

(2014) Margaret McFall-Ngai   PLOS BIOLOGY

An innovative tool reveals interaction mechanisms among yeast populations under oenological conditions

(2013) P. E. Renault et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Synthetic microbial ecosystems: an exciting tool to understand and apply microbial communities

(2013) Karen De Roy et al.   ENVIRONMENTAL MICROBIOLOGY

Improved Blue, Green, and Red Fluorescent Protein Tagging Vectors for S. cerevisiae

(2013) Sidae Lee et al.   PLoS One

PNAS Plus: From the Cover: Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate

(2013) N. A. Bokulich et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Strong inter-population cooperation leads to partner intermixing in microbial communities

(2013) Babak Momeni et al.   eLife

Bioreactor monitoring with spectroscopy and chemometrics: a review

(2012) N. D. Lourenço et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Mutualistic interactions between vitamin B12-dependent algae and heterotrophic bacteria exhibit regulation

(2012) Elena Kazamia et al.   ENVIRONMENTAL MICROBIOLOGY

Synthetic ecology – A way forward for sustainable algal biofuel production?

(2012) Elena Kazamia et al.   JOURNAL OF BIOTECHNOLOGY

Effect of mixed culture fermentations on yeast populations and aroma profile

(2012) Imma Andorrà et al.   LWT-FOOD SCIENCE AND TECHNOLOGY

Next-Generation Sequencing Reveals Significant Bacterial Diversity of Botrytized Wine

(2012) Nicholas A. Bokulich et al.   PLoS One

Species Interactions Alter Evolutionary Responses to a Novel Environment

(2012) Diane Lawrence et al.   PLOS BIOLOGY

Multistarter from Organic Viticulture for Red Wine Montepulciano d’Abruzzo Production

(2012) Suzzi Giovanna et al.   Frontiers in Microbiology

MICROBIAL CONSORTIA ENGINEERING FOR CELLULAR FACTORIES: IN VITRO TO IN SILICO SYSTEMS

(2012) Hans C Bernstein et al.   Computational and Structural Biotechnology Journal

Selected non-Saccharomyces wine yeasts in controlled multistarter fermentations with Saccharomyces cerevisiae

(2010) Francesca Comitini et al.   FOOD MICROBIOLOGY

Fluorescent Proteins and Their Applications in Imaging Living Cells and Tissues

(2010) Dmitriy M. Chudakov et al.   PHYSIOLOGICAL REVIEWS

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

Application of microbioreactors in fermentation process development: a review

(2009) Daniel Schäpper et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Controlled mixed culture fermentation: a new perspective on the use of non-Saccharomyces  yeasts in winemaking

(2009) Maurizio Ciani et al.   FEMS YEAST RESEARCH

Rules of Engagement: Interspecies Interactions that Regulate Microbial Communities

(2008) Ainslie E.F. Little et al.   Annual Review of Microbiology

FISH glossary: an overview of the fluorescence in situ hybridization technique

(2008) Emanuela V. Volpi et al.   BIOTECHNIQUES

Availability of prey resources drives evolution of predator-prey interaction

(2008) V.-P. Friman et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Engineering microbial consortia: a new frontier in synthetic biology

(2008) Katie Brenner et al.   TRENDS IN BIOTECHNOLOGY