Genome scale metabolic models and analysis for evaluating probiotic potentials

MEMOTE for standardized genome-scale metabolic model testing

(2020) Christian Lieven et al.   NATURE BIOTECHNOLOGY

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

(2019) Laurent Heirendt et al.   Nature Protocols

A genome-scale metabolic network of the aroma bacterium Leuconostoc mesenteroides subsp. cremoris

(2019) Emrah Özcan et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Integrated In Vitro and In Silico Modeling Delineates the Molecular Effects of a Synbiotic Regimen on Colorectal-Cancer-Derived Cells

(2019) Kacy Greenhalgh et al.   Cell Reports

Probiotics in health and disease: fooling Mother Nature?

(2019) Muhammad Bilal Abid et al.   INFECTION

Baseline human gut microbiota profile in healthy people and standard reporting template

(2019) Charles H. King et al.   PLoS One

A metabolic reconstruction of Lactobacillus reuteri JCM 1112 and analysis of its potential as a cell factory

(2019) Thordis Kristjansdottir et al.   Microbial Cell Factories

Deciphering the metabolic capabilities of Bifidobacteria using genome-scale metabolic models

(2019) N. T. Devika et al.   Scientific Reports

Manually curated genome-scale reconstruction of the metabolic network of Bacillus megaterium DSM319

(2019) Javad Aminian-Dehkordi et al.   Scientific Reports

Paraprobiotics and postbiotics: concepts and potential applications in dairy products

(2019) Cássia P Barros et al.   Current Opinion in Food Science

Constraint-based modeling in microbial food biotechnology

(2018) Martin H. Rau et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Shared mechanisms among probiotic taxa: implications for general probiotic claims

(2018) Mary Ellen Sanders et al.   CURRENT OPINION IN BIOTECHNOLOGY

Fast automated reconstruction of genome-scale metabolic models for microbial species and communities

(2018) Daniel Machado et al.   NUCLEIC ACIDS RESEARCH

Postbiotics: An evolving term within the functional foods field

(2018) J.E. Aguilar-Toalá et al.   TRENDS IN FOOD SCIENCE & TECHNOLOGY

Mapping the Physiological Response of Oenococcus oeni to Ethanol Stress Using an Extended Genome-Scale Metabolic Model

(2018) Angela Contreras et al.   Frontiers in Microbiology

How to select a probiotic? A review and update of methods and criteria

(2018) Gilberto Vinícius de Melo Pereira et al.   BIOTECHNOLOGY ADVANCES

Gut microbiota dysbiosis is associated with malnutrition and reduced plasma amino acid levels: Lessons from genome-scale metabolic modeling

(2018) Manish Kumar et al.   METABOLIC ENGINEERING

The Genus Enterococcus: Between Probiotic Potential and Safety Concerns—An Update

(2018) Hasna Hanchi et al.   Frontiers in Microbiology

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

(2018) Federico Baldini et al.   BIOINFORMATICS

Probiotic supplements might not be universally-effective and safe: A review

(2018) Damini Kothari et al.   BIOMEDICINE & PHARMACOTHERAPY

Quantitative microbiome profiling links gut community variation to microbial load

(2017) Doris Vandeputte et al.   NATURE

Strain-specific probiotic properties of lactic acid bacteria and their interference with human intestinal pathogens invasion

(2017) Raffaella Campana et al.   Gut Pathogens

Genome-scale modeling and transcriptome analysis of Leuconostoc mesenteroides unravel the redox governed metabolic states in obligate heterofermentative lactic acid bacteria

(2017) Lokanand Koduru et al.   Scientific Reports

BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities

(2017) Eugen Bauer et al.   PLoS Computational Biology

Genome-Scale Reconstruction of the Metabolic Network in Oenococcus oeni to Assess Wine Malolactic Fermentation

(2017) Sebastián N. Mendoza et al.   Frontiers in Microbiology

Next-generation probiotics: the spectrum from probiotics to live biotherapeutics

(2017) Paul W. O’Toole et al.   Nature Microbiology

Systematic development and optimization of chemically defined medium supporting high cell density growth of Bacillus coagulans

(2016) Yu Chen et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Exopolysaccharides produced by lactic acid bacteria: from health-promoting benefits to stress tolerance mechanisms

(2016) Graziano Caggianiello et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

(2016) Stefanía Magnúsdóttir et al.   NATURE BIOTECHNOLOGY

Construction and analysis of a genome-scale metabolic network for Bacillus licheniformis WX-02

(2016) Jing Guo et al.   RESEARCH IN MICROBIOLOGY

Applications of Genome-Scale Metabolic Models in Biotechnology and Systems Medicine

(2016) Cheng Zhang et al.   Frontiers in Physiology

Functional genomic and metagenomic approaches to understanding gut microbiota–animal mutualism

(2015) Sang Sun Yoon et al.   CURRENT OPINION IN MICROBIOLOGY

Reconstruction and analysis of the genome-scale metabolic model of Lactobacillus casei LC2W

(2015) Nan Xu et al.   GENE

Multi -omics and metabolic modelling pipelines: Challenges and tools for systems microbiology

(2015) Marco Fondi et al.   MICROBIOLOGICAL RESEARCH

Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction

(2014) Ibrahim E El-Semman et al.   BMC Systems Biology

The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic

(2014) Colin Hill et al.   Nature Reviews Gastroenterology & Hepatology

Genome –Scale Reconstruction of Metabolic Networks of Lactobacillus casei ATCC 334 and 12A

(2014) Elena Vinay-Lara et al.   PLoS One

Personalized therapy with probiotics from the host by TripleA

(2014) Remco Kort   TRENDS IN BIOTECHNOLOGY

Genome-scale metabolic model for Lactococcus lactis MG1363 and its application to the analysis of flavor formation

(2013) Nicolas A. L. Flahaut et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Sources, isolation, characterisation and evaluation of probiotics

(2013) Luis Fontana et al.   BRITISH JOURNAL OF NUTRITION

Predicting the impact of diet and enzymopathies on human small intestinal epithelial cells

(2013) Swagatika Sahoo et al.   HUMAN MOLECULAR GENETICS

Establishment, in silico analysis, and experimental verification of a large-scale metabolic network of the xanthan producing Xanthomonas campestris pv. campestris strain B100

(2013) Sarah Schatschneider et al.   JOURNAL OF BIOTECHNOLOGY

Reconstruction and analysis of the industrial strain Bacillus megaterium WSH002 genome-scale in silico metabolic model

(2013) Wei Zou et al.   JOURNAL OF BIOTECHNOLOGY

Probiotics, gut microbiota and health

(2013) M.-J. Butel   MEDECINE ET MALADIES INFECTIEUSES

In silico metabolic engineering of Bacillus subtilis for improved production of riboflavin, Egl-237, (R,R)-2,3-butanediol and isobutanol

(2013) Tong Hao et al.   Molecular BioSystems

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules

(2013) R. Levy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Environmental factors influencing the efficacy of probiotic bacteria

(2012) Maria L Marco et al.   CURRENT OPINION IN BIOTECHNOLOGY

Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model

(2012) Kosei Tanaka et al.   NUCLEIC ACIDS RESEARCH

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

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

Effects of probiotics on gut microbiota: mechanisms of intestinal immunomodulation and neuromodulation

(2012) Peera Hemarajata et al.   Therapeutic Advances in Gastroenterology

Exploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstruction

(2011) Kechi Fang et al.   BMC Systems Biology

Recent advances in reconstruction and applications of genome-scale metabolic models

(2011) Tae Yong Kim et al.   CURRENT OPINION IN BIOTECHNOLOGY

Exploring Metabolic Pathway Reconstruction and Genome-Wide Expression Profiling in Lactobacillus reuteri to Define Functional Probiotic Features

(2011) Delphine M. Saulnier et al.   PLoS One

Competitive and cooperative metabolic interactions in bacterial communities

(2011) Shiri Freilich et al.   Nature Communications

BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

(2010) Chen Li et al.   BMC Systems Biology

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Genome-Scale Model of Streptococcus thermophilus LMG18311 for Metabolic Comparison of Lactic Acid Bacteria

(2009) M. I. Pastink et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations

(2009) Christopher S Henry et al.   GENOME BIOLOGY

Reconstruction and analysis of the genetic and metabolic regulatory networks of the central metabolism of Bacillus subtilis

(2008) Anne Goelzer et al.   BMC Systems Biology