Editorial Material
Microbiology
Alejandra Rodriguez-Verdugo
Summary: This research aims to understand and predict microbial communities' responses to environmental stressors by studying the influences of eco-evolutionary feedbacks and multiple interacting species on community dynamics. By using experimental evolution, genome sequencing, and mathematical modeling, the goal is to generate general concepts that provide insights into the consequences of evolution on the functioning of whole microbial communities.
Review
Plant Sciences
Geertje M. F. van der Heijden, Ashley D. C. Proctor, Kim Calders, Chris J. Chandler, Richard Field, Giles M. Foody, Sruthi M. Krishna Moorthy, Stefan A. Schnitzer, Catherine E. Waite, Doreen S. Boyd
Summary: This article reviews the application of remote sensing technology in studying the ecology of lianas. Lianas are important components of tropical ecosystems, but little is known about their distribution in forest canopies. Remote sensing technology can help overcome the limitations of traditional field methods and provide important insights into liana ecology.
JOURNAL OF ECOLOGY
(2022)
Article
Engineering, Environmental
Sema Karakurt-Fischer, David R. Johnson, Kathrin Fenner, Jasmin Hafner
Summary: Biodegradation is a promising method for removing synthetic chemical pollutants, but rational engineering in this area remains a challenge. To overcome this, a high-throughput bio-chem-informatics pipeline is proposed to link chemicals with their predicted biotransformation pathways, enzymes, and bacterial strains. This approach can help in the design and study of fit-for-purpose bacterial communities for enhancing pollutant biodegradation.
Article
Ecology
Shuyao Li, Jing Xiao, Tianzheng Sun, Fangjian Yu, Kaihang Zhang, Yuantao Feng, Chenchao Xu, Baojun Wang, Lei Cheng
Summary: This study developed a microbial experimental system that allows for rapidly generating microbial consortia with programmable ecological interactions. By using engineered microbial consortia, the researchers showed different population dynamics under different initial inoculation conditions and controlled the transitions between exploitation, competition, and synergy by tuning the engineered modules. Mathematical models were derived to quantitatively capture the experimentally observed population dynamics of these synthetic microbial consortia.
METHODS IN ECOLOGY AND EVOLUTION
(2022)
Review
Biochemistry & Molecular Biology
Alvaro Sanchez, Djordje Bajic, Juan Diaz-Colunga, Abigail Skwara, Jean C. C. Vila, Seppe Kuehn
Summary: Quantitatively linking the composition and function of microbial communities is challenging. Inspired by genetics, an ecological community-function landscape could be defined to map community composition and function. Exploiting the parallels between both landscapes could improve our ability to engineer and optimize microbial consortia.
Editorial Material
Microbiology
Jimmy H. W. Saw
Summary: Microbial communities are often dominated by a few species, with a long tail of rare biosphere microorganisms that are highly diverse but found in low abundance. They play important roles in maintaining community integrity and resilience, and their phylogenetic diversity is crucial for understanding microbial diversity and evolution. Further efforts should be made to study these poorly understood microbial lineages that hold vast potential for advancing our understanding of microbial diversity, ecology, and evolution on Earth.
Review
Microbiology
Elham Lashani, Mohammad Ali Amoozegar, Raymond J. Turner, Hamid Moghimi
Summary: Microorganisms play a crucial role in reducing metalloid contamination risks through their ability to tolerate and detoxify these elements.
Article
Environmental Sciences
Peipei Chen, Hao Liu, Zhilin Xing, Yongqiong Wang, Xiaoping Zhang, Tiantao Zhao, Yunru Zhang
Summary: The cometabolism mechanism of chlorinated hydrocarbon solvents (CHSs) in mixed consortia was studied for the first time, showing efficient degradation rates with non-fully chlorinated aliphatic hydrocarbons being more easily degraded. Methylocystaceae, Methylomonas, and Methylosarcina were identified as major functional degraders in methanotrophic consortia. Microbial correlation network analysis demonstrated that type I methanotrophs and heterotrophs interacted to determine biodegradability.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2022)
Review
Biochemical Research Methods
Heather S. Deter, Ting Lu
Summary: Synthetic microbial consortia are at the forefront of synthetic biology, promising versatile engineering of cellular functions through coordination of intercellular interactions. Researchers have studied building blocks for intercellular communication, unidirectional positive and negative interactions, and have developed bidirectional interactions towards complex communities.
CURRENT OPINION IN BIOTECHNOLOGY
(2022)
Article
Microbiology
Xinhua Qi, Yuan Ma, Hanchen Chang, Bingzhi Li, Mingzhu Ding, Yingjin Yuan
Summary: This study constructed an artificial microbial consortium to degrade PET, which gradually increased the weight loss rate to 23.2% by adding different microorganisms step by step, demonstrating the potential of artificial microbial consortia in utilizing complex substrates.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Alex J. H. Fedorec, Behzad D. Karkaria, Michael Sulu, Chris P. Barnes
Summary: The scope of bioengineering is expanding to include the design of microbial communities, and researchers have shown that a stable two-strain community can be achieved by engineering a strain of Escherichia coli to secrete a toxin in response to competition. Experimental and mathematical evidence demonstrates that this system can produce stable populations with tunable compositions controlled by easily adjustable parameters. This approach allows for the creation of tunable, stable two-strain consortia with the potential to interface with natural microbiomes.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Ziqi Deng, Jorge Botas, Carlos P. Cantalapiedra, Ana Hernandez-Plaza, Jordi Burguet-Castell, Jaime Huerta-Cepas
Summary: PhyloCloud is an online platform designed to host and index large collections of phylogenetic trees, providing seamless access to analyses and operations, as well as custom annotations and multiple sequence alignments.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Microbiology
Ashley E. Beck, Kathryn Pintar, Diana Schepens, Ashley Schrammeck, Timothy Johnson, Alissa Bleem, Martina Du, William R. Harcombe, Hans C. Bernstein, Jeffrey J. Heys, Tomas Gedeon, Ross P. Carlson
Summary: This study investigates how different cellular interaction motifs influence performance properties of microbial consortia, with environmental context ultimately controlling the division of labor performance. Shifts from weakly buffered to highly buffered conditions negate the benefits of the strategy.
Review
Biotechnology & Applied Microbiology
Katherine E. Duncker, Zachary A. Holmes, Lingchong You
Summary: Applications of microbial synthetic biology are becoming more complex, and engineering microbial consortia has shown progress in distributing tasks, preventing overgrowth, and reducing competition among populations.
MICROBIAL CELL FACTORIES
(2021)
Article
Multidisciplinary Sciences
Lin Wang, Xi Zhang, Chenwang Tang, Pengcheng Li, Runtao Zhu, Jing Sun, Yunfeng Zhang, Hua Cui, Jiajia Ma, Xinyu Song, Weiwen Zhang, Xiang Gao, Xiaozhou Luo, Lingchong You, Ye Chen, Zhuojun Dai
Summary: The study presents a microbial swarmbot mediated spatial segregation method to assemble stable synthetic microbial consortia with flexibility and precision. This approach allows for the control over subpopulations, enabling modulation of division of labor and communication, which can serve as a foundation for various applications in synthetic biology.
NATURE COMMUNICATIONS
(2022)
Article
Ecology
Konstanze T. Schiessl, Adin Ross-Gillespie, Daniel M. Cornforth, Michael Weigert, Colette Bigosch, Sam P. Brown, Martin Ackermann, Rolf Kummerli
Article
Ecology
Sheyda Azimi, Aled E. L. Roberts, Shengyun Peng, Joshua S. Weitz, Alan McNally, Samuel P. Brown, Stephen P. Diggle
Article
Multidisciplinary Sciences
Yifei Wang, Jennifer B. Rattray, Stephen A. Thomas, James Gurney, Sam P. Brown
SCIENTIFIC REPORTS
(2020)
Article
Microbiology
James Gurney, Sheyda Azimi, Sam P. Brown, Stephen P. Diggle
Correction
Multidisciplinary Sciences
Yifei Wang, Jennifer B. Rattray, Stephen A. Thomas, James Gurney, Sam P. Brown
SCIENTIFIC REPORTS
(2020)
Article
Ecology
Antonio M. M. Rodrigues, Sylvie Estrela, Sam P. Brown
Summary: Microbes in dense and diverse communities exhibit various traits that promote growth and survival while also competing for resources. The evolution of mutualistic interactions in such dynamic communities is still poorly understood. A model was developed to explore how different forms of helping affect community growth and the evolution of mutualisms, with focus on yield-enhancing traits such as niche expansion. The study suggests that yield-enhancing mutualisms are more prevalent in stable habitats with high population densities.
JOURNAL OF EVOLUTIONARY BIOLOGY
(2021)
Article
Immunology
Conan Y. Zhao, Yiqi Hao, Yifei Wang, John J. Varga, Arlene A. Stecenko, Joanna B. Goldberg, Sam P. Brown
Summary: The study found that models trained on whole-microbiome quantitation outperformed models trained only on pathogen quantitation in lung infections in people with cystic fibrosis. The most accurate models retained key pathogens and nonpathogen taxa as important predictors of lung health.
JOURNAL OF INFECTIOUS DISEASES
(2021)
Article
Microbiology
Jennifer M. Farrell, Conan Y. Zhao, Keiko M. Tarquinio, Sam P. Brown
Summary: The COVID-19 literature suggests that bacterial infections are more common in fatal cases than in recovered cases, but it is unclear if they significantly contribute to mortality. More data is needed to determine the relative importance of bacterial infections in COVID-19 mortality. Additionally, potential long-term consequences of SARS-CoV-2 infection are also summarized.
FRONTIERS IN MICROBIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
James Gurney, Camille Simonet, Kristofer Wollein Waldetoft, Sam P. Brown
Summary: The article discusses how bacterial pathogens communicate and cooperate within groups to make us sick, and introduces two cheat therapy methods. These methods, including genetic engineering and chemical induction, can reduce pathogen burden and disease severity, but also face challenges of instability in efficacy.
NATURAL PRODUCT REPORTS
(2022)
Editorial Material
Biochemistry & Molecular Biology
Tatiana Dimitriu, Dusan Misevic, Ariel B. Lindner, Francois Taddei, Sam P. Brown
Article
Microbiology
Jennifer B. Rattray, Stephen A. Thomas, Yifei Wang, Evgeniya Molotkova, James Gurney, John J. Varga, Sam P. Brown
Summary: Quorum sensing is a cell-cell communication mechanism that connects gene expression to environmental conditions. In this study, it was found that Pseudomonas aeruginosa can generate graded behavioral responses to fine-scale variation in population density. These results indicate that quorum sensing can adjust gene expression to graded environmental change, and there is no hard threshold separating attack mode from stealth mode in an infection context.
Article
Microbiology
John J. Varga, Conan Y. Zhao, Jacob D. Davis, Yiqi Hao, Jennifer M. Farrell, James R. Gurney, Eberhard Voit, Sam P. Brown
Summary: We research and analyze the impacts of antibiotic exposures on chronic, polymicrobial infections by developing and clinically benchmarking an experimental model of the cystic fibrosis (CF) lung infection microbiome. We find that a single experimental model, defined by metacommunity data, can partially replicate the diversity of individual microbiome states observed in CF patients. In the absence of antibiotics, the community structures are highly repeatable and dominated by oral microbes. However, under clinically relevant antibiotic exposures, diverse and frequently pathogen-dominated communities are observed, along with an enrichment of antimicrobial resistance on the community scale, mediated by competitive release. These findings highlight the potential importance of nonevolutionary (community-ecological) processes in driving the growing global crisis of increasing antibiotic resistance.
Editorial Material
Multidisciplinary Sciences
Kristofer Wollein Waldetoft, Sam P. Brown
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Microbiology
Kristofer Wollein Waldetoft, Sarah Sundius, Rachel Kuske, Sam P. Brown
Summary: Antibiotic resistance is a major challenge in medical and public health, but resistance in commensal bacteria can have benefits during antibiotic treatment by suppressing pathogens.
Article
Microbiology
Jennifer B. Rattray, Patrick J. Kramer, James Gurney, Stephen Thomas, Sam P. Brown
Summary: Quorum sensing is a widespread mechanism used by bacteria to sense their environment and coordinate their behavior. It is based on the production, sensing, and response to small signaling molecules. This study investigates how genetic and signal perturbations affect the graded responses to density in Pseudomonas aeruginosa. The results show that density-dependent control of gene expression is robust to genetic deletions and density-independent signal supplementation.
