Stochasticity in microbiology: managing unpredictability to reach the Sustainable Development Goals

Understanding antimicrobial discovery and resistance from a metagenomic and metatranscriptomic perspective: Advances and applications

(2019) Jonathan Asante et al.   Environmental Microbiology Reports

Nontuberculous mycobacteria in drinking water systems – the challenges of characterization and risk mitigation

(2019) Katherine Dowdell et al.   CURRENT OPINION IN BIOTECHNOLOGY

Bacterial assembly in the bio-cake of membrane bioreactors: Stochastic vs. deterministic processes

(2019) Ronghua Xu et al.   WATER RESEARCH

A Rapid and Accurate MinION-Based Workflow for Tracking Species Biodiversity in the Field

(2019) Maestri et al.   Genes

Understanding microbial community dynamics to improve optimal microbiome selection

(2019) Robyn J. Wright et al.   Microbiome

Metagenomic and metatranscriptomic analyses reveal activity and hosts of antibiotic resistance genes in activated sludge

(2019) Zongbao Liu et al.   ENVIRONMENT INTERNATIONAL

Unveiling hákarl: A study of the microbiota of the traditional Icelandic fermented fish

(2019) Andrea Osimani et al.   FOOD MICROBIOLOGY

Is the cell really a machine?

(2019) Daniel J. Nicholson   JOURNAL OF THEORETICAL BIOLOGY

A general framework for quantitatively assessing ecological stochasticity

(2019) Daliang Ning et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Urine nitrification with a synthetic microbial community

(2019) Marlies E.R. Christiaens et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Anaerobic digestion of agricultural manure and biomass – Critical indicators of risk and knowledge gaps

(2019) Rajat Nag et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Quantifying the contribution of microbial immigration in engineered water systems

(2019) Ran Mei et al.   Microbiome

Review and perspective on mathematical modeling of microbial ecosystems

(2018) Antonella Succurro et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Metabolic heterogeneity in clonal microbial populations

(2018) Vakil Takhaveev et al.   CURRENT OPINION IN MICROBIOLOGY

Metagenomic Characterization of Antibiotic Resistance Genes in Full-Scale Reclaimed Water Distribution Systems and Corresponding Potable Systems

(2018) Emily Garner et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Bacterial community in naturally fermented milk products of Arunachal Pradesh and Sikkim of India analysed by high-throughput amplicon sequencing

(2018) H. Nakibapher Jones Shangpliang et al.   Scientific Reports

Protozoan Parasites in Drinking Water: A System Approach for Improved Water, Sanitation and Hygiene in Developing Countries

(2018) Alua Omarova et al.   International Journal of Environmental Research and Public Health

Special Issue: Microbial Community Modeling: Prediction of Microbial Interactions and Community Dynamics

(2018) Hyun-Seob Song   Processes

Function and functional redundancy in microbial systems

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

A vegetable fermentation facility hosts distinct microbiomes reflecting the production environment

(2018) Jonah E. Einson et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Redundancy in Anaerobic Digestion Microbiomes during Disturbances by the Antibiotic Monensin

(2018) Catherine M. Spirito et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

In vitro community synergy between bacterial soil isolates can be facilitated by pH stabilisation of the environment

(2018) Jakob Herschend et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Niche and fitness differences determine invasion success and impact in laboratory bacterial communities

(2018) Shao-peng Li et al.   ISME Journal

Terminal restriction fragment length polymorphism is an “old school” reliable technique for swift microbial community screening in anaerobic digestion

(2018) Jo De Vrieze et al.   Scientific Reports

Integrated culturing, modeling and transcriptomics uncovers complex interactions and emergent behavior in a three-species synthetic gut community

(2018) Kevin D'hoe et al.   eLife

Flow cytometric monitoring of bacterioplankton phenotypic diversity predicts high population-specific feeding rates by invasive dreissenid mussels

(2017) Ruben Props et al.   ENVIRONMENTAL MICROBIOLOGY

Global Cryptosporidium Loads from Livestock Manure

(2017) Lucie C. Vermeulen et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Application of next generation sequencing in clinical microbiology and infection prevention

(2017) Ruud H. Deurenberg et al.   JOURNAL OF BIOTECHNOLOGY

Strain-level characterization of cold-stressed Listeria monocytogenes using maldi-tof mass fingerprinting

(2017) Han Zhao et al.   JOURNAL OF FOOD SAFETY

Characterization of microbial mixtures by mass spectrometry

(2017) Todd R. Sandrin et al.   MASS SPECTROMETRY REVIEWS

Stochastic Community Assembly: Does It Matter in Microbial Ecology?

(2017) Jizhong Zhou et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Effect of water flow and chemical environment on microbiota growth and composition in the human colon

(2017) Jonas Cremer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Occurrence and genetic diversity of Cryptosporidium and Giardia in urban wastewater treatment plants in north-eastern Spain

(2017) Ana Ramo et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Microbial community redundancy in anaerobic digestion drives process recovery after salinity exposure

(2017) Jo De Vrieze et al.   WATER RESEARCH

Emerging Challenges and Opportunities for Education and Research in Weed Science

(2017) Bhagirath S. Chauhan et al.   Frontiers in Plant Science

Characterization of Multidrug Resistant E. faecalis Strains from Pigs of Local Origin by ADSRRS-Fingerprinting and MALDI -TOF MS; Evaluation of the Compatibility of Methods Employed for Multidrug Resistance Analysis

(2017) Aneta Nowakiewicz et al.   PLoS One

Population cycles and species diversity in dynamic Kill-the-Winner model of microbial ecosystems

(2017) Sergei Maslov et al.   Scientific Reports

The impact of immigration on microbial community composition in full-scale anaerobic digesters

(2017) Rasmus H. Kirkegaard et al.   Scientific Reports

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

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

Diversity, Productivity, and Stability of an Industrial Microbial Ecosystem

(2016) Doruk Beyter et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A novel high-throughput multi-parameter flow cytometry based method for monitoring and rapid characterization of microbiome dynamics in anaerobic systems

(2016) Abhishek S. Dhoble et al.   BIORESOURCE TECHNOLOGY

Microbial community diversity, structure and assembly across oxygen gradients in meromictic marine lakes, Palau

(2016) Matthew S. Meyerhof et al.   ENVIRONMENTAL MICROBIOLOGY

Use of matrix-assisted laser desorption/ionization–time of flight (MALDI–TOF) mass spectrometry for bacterial monitoring in routine analysis at a drinking water treatment plant

(2016) Laura Sala-Comorera et al.   INTERNATIONAL JOURNAL OF HYGIENE AND ENVIRONMENTAL HEALTH

Effects of dispersal and selection on stochastic assembly in microbial communities

(2016) Sarah Evans et al.   ISME Journal

A conceptual framework for invasion in microbial communities

(2016) Marta Kinnunen et al.   ISME Journal

Diversity is the question, not the answer

(2016) Ashley Shade   ISME Journal

Regional synchrony in full-scale activated sludge bioreactors due to deterministic microbial community assembly

(2016) James S Griffin et al.   ISME Journal

Molecular Detection ofLegionellaspp. and their associations withMycobacteriumspp.,Pseudomonas aeruginosaand amoeba hosts in a drinking water distribution system

(2016) J. Lu et al.   JOURNAL OF APPLIED MICROBIOLOGY

The full-scale anaerobic digestion microbiome is represented by specific marker populations

(2016) Jo De Vrieze et al.   WATER RESEARCH

High-rate activated sludge communities have a distinctly different structure compared to low-rate sludge communities, and are less sensitive towards environmental and operational variables

(2016) Francis A. Meerburg et al.   WATER RESEARCH

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

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

Disturbance opens recruitment sites for bacterial colonization in activated sludge

(2015) David C. Vuono et al.   ENVIRONMENTAL MICROBIOLOGY

Methane as a Resource: Can the Methanotrophs Add Value?

(2015) P. J. Strong et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Bacterial diversity in typical Italian salami at different ripening stages as revealed by high-throughput sequencing of 16S rRNA amplicons

(2015) Justyna Połka et al.   FOOD MICROBIOLOGY

Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes

(2015) Bing Li et al.   ISME Journal

A functional perspective on phenotypic heterogeneity in microorganisms

(2015) Martin Ackermann   NATURE REVIEWS MICROBIOLOGY

The unseen world: reflections on Leeuwenhoek (1677) 'Concerning little animals'

(2015) N. Lane   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Microbial Invasions: The Process, Patterns, and Mechanisms

(2015) Cyrus Alexander Mallon et al.   TRENDS IN MICROBIOLOGY

Functionally redundant but dissimilar microbial communities within biogas reactors treating maize silage in co-fermentation with sugar beet silage

(2015) Susanne G. Langer et al.   Microbial Biotechnology

Dynamic variation of the microbial community structure during the long-time mono-fermentation of maize and sugar beet silage

(2015) Johanna Klang et al.   Microbial Biotechnology

Song, H.-S., et al. Mathematical Modeling of Microbial Community Dynamics: A Methodological Review. Processes 2014, 2, 711–752

(2015) Hyun-Seob Song et al.   Processes

Modelling the emergent dynamics and major metabolites of the human colonic microbiota

(2014) Helen Kettle et al.   ENVIRONMENTAL MICROBIOLOGY

Community fingerprinting in a sequencing world

(2014) Josie van Dorst et al.   FEMS MICROBIOLOGY ECOLOGY

Traditional cheeses: Rich and diverse microbiota with associated benefits

(2014) Marie-Christine Montel et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

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

(2014) Inka Vanwonterghem et al.   ISME Journal

Bacterial assembly and temporal dynamics in activated sludge of a full-scale municipal wastewater treatment plant

(2014) Feng Ju et al.   ISME Journal

The Microbial Diversity of Traditional Spontaneously Fermented Lambic Beer

(2014) Freek Spitaels et al.   PLoS One

Strengths and Limitations of 16S rRNA Gene Amplicon Sequencing in Revealing Temporal Microbial Community Dynamics

(2014) Rachel Poretsky et al.   PLoS One

Stochasticity, succession, and environmental perturbations in a fluidic ecosystem

(2014) Jizhong Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evaluation of five antibiotic resistance genes in wastewater treatment systems of swine farms by real-time PCR

(2014) Chi-Wei Tao et al.   SCIENCE OF THE TOTAL ENVIRONMENT

A hundred years of activated sludge: time for a rethink

(2014) Abdul R. Sheik et al.   Frontiers in Microbiology

A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer

(2014) Joshua Quick et al.   GigaScience

Ecological coherence of diversity patterns derived from classical fingerprinting and Next Generation Sequencing techniques

(2013) Angélique Gobet et al.   ENVIRONMENTAL MICROBIOLOGY

Comparing the anterior nare bacterial community of two discrete human populations using Illumina amplicon sequencing

(2013) Amélia Camarinha-Silva et al.   ENVIRONMENTAL MICROBIOLOGY

Bacterial invasion potential in water is determined by nutrient availability and the indigenous community

(2013) Sam Van Nevel et al.   FEMS MICROBIOLOGY ECOLOGY

Quantifying community assembly processes and identifying features that impose them

(2013) James C Stegen et al.   ISME Journal

Phylogenetic beta diversity in bacterial assemblages across ecosystems: deterministic versus stochastic processes

(2013) Jianjun Wang et al.   ISME Journal

Biodiversity decreases disease through predictable changes in host community competence

(2013) Pieter T. J. Johnson et al.   NATURE

Hygienization of sludge through anaerobic digestion at 35, 55 and 60 °C

(2013) H. Kjerstadius et al.   WATER SCIENCE AND TECHNOLOGY

Random Sampling Process Leads to Overestimation of  -Diversity of Microbial Communities

(2013) J. Zhou et al.   mBio

Stochastic Assembly Leads to Alternative Communities with Distinct Functions in a Bioreactor Microbial Community

(2013) J. Zhou et al.   mBio

Environmental conditions and community evenness determine the outcome of biological invasion

(2013) Karen De Roy et al.   Nature Communications

Bacterial colonization and extinction on marine aggregates: stochastic model of species presence and abundance

(2013) Andrew M. Kramer et al.   Ecology and Evolution

Repeated pulse feeding induces functional stability in anaerobic digestion

(2013) Jo De Vrieze et al.   Microbial Biotechnology

Increasing antagonistic interactions cause bacterial communities to collapse at high diversity

(2012) Joachim Becker et al.   ECOLOGY LETTERS

Land Application of Manure and Class B Biosolids: An Occupational and Public Quantitative Microbial Risk Assessment

(2012) John P. Brooks et al.   JOURNAL OF ENVIRONMENTAL QUALITY

Metabolic versatility of Gram-positive microbial isolates from contaminated river sediments

(2012) Tanja Narancic et al.   JOURNAL OF HAZARDOUS MATERIALS

Performance comparison of benchtop high-throughput sequencing platforms

(2012) Nicholas J Loman et al.   NATURE BIOTECHNOLOGY

Testing the Limits of 454 Pyrotag Sequencing: Reproducibility, Quantitative Assessment and Comparison to T-RFLP Fingerprinting of Aquifer Microbes

(2012) Giovanni Pilloni et al.   PLoS One

Microbial diversity determines the invasion of soil by a bacterial pathogen

(2012) J. D. van Elsas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Population dynamics of filamentous bacteria in Danish wastewater treatment plants with nutrient removal

(2012) Artur Tomasz Mielczarek et al.   WATER RESEARCH

Population dynamics of bacteria involved in enhanced biological phosphorus removal in Danish wastewater treatment plants

(2012) Artur Tomasz Mielczarek et al.   WATER RESEARCH

Genetic drift

(2011) Joanna Masel   CURRENT BIOLOGY

Community assembly: alternative stable states or alternative transient states?

(2011) Tadashi Fukami et al.   ECOLOGY LETTERS

Correlation of Community Dynamics and Process Parameters As a Tool for the Prediction of the Stability of Wastewater Treatment

(2011) Susanne Günther et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Reproducibility and quantitation of amplicon sequencing-based detection

(2011) Jizhong Zhou et al.   ISME Journal

Prey bacteria shape the community structure of their predators

(2011) Huan Chen et al.   ISME Journal

Drivers of bacterial  -diversity depend on spatial scale

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

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

Flow cytometry for fast microbial community fingerprinting

(2011) Karen De Roy et al.   WATER RESEARCH

A time-course analysis of four full-scale anaerobic digesters in relation to the dynamics of change of their microbial communities

(2011) B. F. G. Pycke et al.   WATER SCIENCE AND TECHNOLOGY

Methanotrophy: From the environment to industry and back

(2010) Geoffrey Hamer   CHEMICAL ENGINEERING JOURNAL

Origin and analysis of microbial population heterogeneity in bioprocesses

(2010) Susann Müller et al.   CURRENT OPINION IN BIOTECHNOLOGY

Ironing out the wrinkles in the rare biosphere through improved OTU clustering

(2010) Susan M. Huse et al.   ENVIRONMENTAL MICROBIOLOGY

Bacterial community dynamics in two full-scale wastewater treatment systems with functional stability

(2010) X. Wang et al.   JOURNAL OF APPLIED MICROBIOLOGY

Phenotypic plasticity in development and evolution: facts and concepts

(2010) G. Fusco et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Combined niche and neutral effects in a microbial wastewater treatment community

(2010) I. D. Ofiteru et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Succession of microbial consortia in the developing infant gut microbiome

(2010) J. E. Koenig et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates

(2009) Victor Kunin et al.   ENVIRONMENTAL MICROBIOLOGY

The consequences of genetic drift for bacterial genome complexity

(2009) C.-H. Kuo et al.   GENOME RESEARCH

Initial community evenness favours functionality under selective stress

(2009) Lieven Wittebolle et al.   NATURE

Bacterial competition: surviving and thriving in the microbial jungle

(2009) Michael E. Hibbing et al.   NATURE REVIEWS MICROBIOLOGY

Survey of Wastewater Indicators and Human Pathogen Genomes in Biosolids Produced by Class A and Class B Stabilization Treatments

(2008) E. Viau et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Quantitative PCR Monitoring of Antibiotic Resistance Genes and Bacterial Pathogens in Three European Artificial Groundwater Recharge Systems

(2008) U. Bockelmann et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences

(2008) Arjun Raj et al.   CELL

How to get more out of molecular fingerprints: practical tools for microbial ecology

(2008) Massimo Marzorati et al.   ENVIRONMENTAL MICROBIOLOGY

Temporal scaling of bacterial taxa is influenced by both stochastic and deterministic ecological factors

(2008) Christopher J. Van Der Gast et al.   ENVIRONMENTAL MICROBIOLOGY

Microbes orchestrate life on Earth

(2008) George A Kowalchuk et al.   ISME Journal

The tragedy of the uncommon: understanding limitations in the analysis of microbial diversity

(2008) Stephen J Bent et al.   ISME Journal

Resistance, resilience, and redundancy in microbial communities

(2008) S. D. Allison et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA