Microorganisms do not exist in isolation in the environment.
Instead, they form complex communities among themselves
as well as with their hosts. Different forms of interactions not
only shape the composition of these communities but also define
how these communities are established and maintained.
The kinds of interaction a bacterium can employ are largely
encoded in its genome. This allows us to deploy a genomescale
modeling approach to understand, and ultimately predict,
the complex and intertwined relationships in which microorganisms
engage. So far, most studies on microbial communities
have been focused on synthetic co-cultures and simple
communities. However, recent advances in molecular
and computational biology now enable bottom up methods
to be deployed for complex microbial communities from the
environment to provide insight into the intricate and dynamic
interactions in which microorganisms are engaged.
These methods will be applicable for a wide range of microbial
communities involved in industrial processes, as well as
understanding, preserving and reconditioning natural microbial
communities present in soil, water, and the human
microbiome.
Citations
Citations to this article as recorded by
Synthetic model ecosystem of 12 cryopreservable microbial species allowing for a noninvasive approach Kazufumi Hosoda, Shigeto Seno, Naomi Murakami, Hideo Matsuda, Yutaka Osada, Rikuto Kamiura, Michio Kondoh BioSystems.2024; 235: 105087. CrossRef
Synthetic microbial communities: A gateway to understanding resistance, resilience, and functionality in spontaneously fermented food microbiomes Olga Nikoloudaki, Francis Aheto, Raffaella Di Cagno, Marco Gobbetti Food Research International.2024; 192: 114780. CrossRef
Volatile compounds for biotechnological applications produced during competitive interactions between yeasts and fungi Luciana Silva Ribeiro, Mariana Lino de Souza, Jean Marcel Sousa Lira, Rosane Freitas Schwan, Luís Roberto Batista, Cristina Ferreira Silva Journal of Basic Microbiology.2023; 63(6): 658. CrossRef
A thermophilic chemolithoautotrophic bacterial consortium suggests a mutual relationship between bacteria in extreme oligotrophic environments Yuri Pinheiro, Fabio Faria da Mota, Raquel S. Peixoto, Jan Dirk van Elsas, Ulysses Lins, Jorge L. Mazza Rodrigues, Alexandre Soares Rosado Communications Biology.2023;[Epub] CrossRef
Area Rate Efficiency in Multi-Link Molecular Communications Lukas Brand, Sebastian Lotter, Vahid Jamali, Robert Schober, Maximilian Schäfer IEEE Transactions on Molecular, Biological and Multi-Scale Communications.2023; 9(4): 391. CrossRef
Construction of stable microbial consortia for effective biochemical synthesis Yujia Jiang, Ruofan Wu, Wenming Zhang, Fengxue Xin, Min Jiang Trends in Biotechnology.2023; 41(11): 1430. CrossRef
What on earth? The impact of digestates and composts from farm effluent management on fluxes of foodborne pathogens in agricultural lands Pascal Piveteau, Céline Druilhe, Lynda Aissani Science of The Total Environment.2022; 840: 156693. CrossRef
The effect of ultrasound treatment in combination with nisin on the inactivation of Listeria innocua and Escherichia coli Katherine M. Costello, Eirini Velliou, Jorge Gutierrez-Merino, Cindy Smet, Hani El Kadri, Jan F. Van Impe, Madeleine Bussemaker Ultrasonics Sonochemistry.2021; 79: 105776. CrossRef
Polarization of microbial communities between competitive and cooperative metabolism Daniel Machado, Oleksandr M. Maistrenko, Sergej Andrejev, Yongkyu Kim, Peer Bork, Kaustubh R. Patil, Kiran R. Patil Nature Ecology & Evolution.2021; 5(2): 195. CrossRef
The antimicrobial efficacy of remote cold atmospheric plasma effluent against single and mixed bacterial biofilms of varying age Hani El Kadri, Katherine M. Costello, Phillip Thomas, Thomas Wantock, Gavin Sandison, Thomas Harle, Andrea Lucca Fabris, Jorge Gutierrez-Merino, Eirini G. Velliou Food Research International.2021; 141: 110126. CrossRef
Formation, characterization and modeling of emergent synthetic microbial communities Jia Wang, Dana L. Carper, Leah H. Burdick, Him K. Shrestha, Manasa R. Appidi, Paul E. Abraham, Collin M. Timm, Robert L. Hettich, Dale A. Pelletier, Mitchel J. Doktycz Computational and Structural Biotechnology Journal.2021; 19: 1917. CrossRef
Molecular Screening and Analysis Reveal Novel Oral Site-Specific Locations for the Cariogenic Pathogen Scardovia wiggsiae Steven McDaniel, Jaydene McDaniel, Katherine M. Howard, Karl Kingsley Dentistry Journal.2021; 9(6): 73. CrossRef
Kinetic, metabolic, and statistical analytics: addressing metabolic transport limitations among organelles and microbial communities Cristal Zuniga, Juan D Tibocha-Bonilla, Michael J Betenbaugh Current Opinion in Biotechnology.2021; 71: 91. CrossRef
The sum is greater than the parts: exploiting microbial communities to achieve complex functions Livia S Zaramela, Oriane Moyne, Manish Kumar, Cristal Zuniga, Juan D Tibocha-Bonilla, Karsten Zengler Current Opinion in Biotechnology.2021; 67: 149. CrossRef
Non‐steroidal anti‐inflammatory pharmaceutical wastewater treatment using a two‐chambered microbial fuel cell Samar Amari, Mohammad Boshrouyeh Ghandashtani Water and Environment Journal.2020; 34(3): 413. CrossRef
Synthetic microbial communities of heterotrophs and phototrophs facilitate sustainable growth Cristal Zuñiga, Tingting Li, Michael T. Guarnieri, Jackson P. Jenkins, Chien-Ting Li, Kerem Bingol, Young-Mo Kim, Michael J. Betenbaugh, Karsten Zengler Nature Communications.2020;[Epub] CrossRef
Engineering the metabolic pathways of lipid biosynthesis to develop robust microalgal strains for biodiesel production Ayesha Shahid, Abd ur Rehman, Muhammad Usman, Muhammad Umer Farooq Ashraf, Muhammad Rizwan Javed, Aqib Zafar Khan, Saba Shahid Gill, Muhammad Aamer Mehmood Biotechnology and Applied Biochemistry.2020; 67(1): 41. CrossRef
Composition and Metabolic Functions of the Microbiome in Fermented Grain during Light-Flavor Baijiu Fermentation Xiaoning Huang, Yi Fan, Ting Lu, Jiamu Kang, Xiaona Pang, Beizhong Han, Jingyu Chen Microorganisms.2020; 8(9): 1281. CrossRef
Biotransformation of 2,4‐dinitrotoluene in a phototrophic co‐culture of engineered Synechococcus elongatus and Pseudomonas putida Derek T. Fedeson, Pia Saake, Patricia Calero, Pablo Iván Nikel, Daniel C. Ducat Microbial Biotechnology.2020; 13(4): 997. CrossRef
Short-range interactions govern the dynamics and functions of microbial communities Alma Dal Co, Simon van Vliet, Daniel Johannes Kiviet, Susan Schlegel, Martin Ackermann Nature Ecology & Evolution.2020; 4(3): 366. CrossRef
Dynamic resource allocation drives growth under nitrogen starvation in eukaryotes Juan D. Tibocha-Bonilla, Manish Kumar, Anne Richelle, Rubén D. Godoy-Silva, Karsten Zengler, Cristal Zuñiga npj Systems Biology and Applications.2020;[Epub] CrossRef
An interspecies malate–pyruvate shuttle reconciles redox imbalance in an anaerobic microbial community Po-Hsiang Wang, Kevin Correia, Han-Chen Ho, Naveen Venayak, Kayla Nemr, Robert Flick, Radhakrishnan Mahadevan, Elizabeth A Edwards The ISME Journal.2019; 13(4): 1042. CrossRef
Production of Biosurfactant Produced from Used Cooking Oil by Bacillus sp. HIP3 for Heavy Metals Removal Nurul Hanisah Md Badrul Hisham, Mohamad Faizal Ibrahim, Norhayati Ramli, Suraini Abd-Aziz Molecules.2019; 24(14): 2617. CrossRef
Gut bacteria responding to dietary change encode sialidases that exhibit preference for red meat-associated carbohydrates Livia S. Zaramela, Cameron Martino, Frederico Alisson-Silva, Steven D. Rees, Sandra L. Diaz, Léa Chuzel, Mehul B. Ganatra, Christopher H. Taron, Patrick Secrest, Cristal Zuñiga, Jianbo Huang, Dionicio Siegel, Geoffrey Chang, Ajit Varki, Karsten Zengler Nature Microbiology.2019; 4(12): 2082. CrossRef
Exploring the effects of operational mode and microbial interactions on bacterial community assembly in a one-stage partial-nitritation anammox reactor using integrated multi-omics Yulin Wang, Qigui Niu, Xu Zhang, Lei Liu, Yubo Wang, Yiqiang Chen, Mishty Negi, Daniel Figeys, Yu-You Li, Tong Zhang Microbiome.2019;[Epub] CrossRef
Finding Functional Differences Between Species in a Microbial Community: Case Studies in Wine Fermentation and Kefir Culture Chrats Melkonian, Willi Gottstein, Sonja Blasche, Yongkyu Kim, Martin Abel-Kistrup, Hentie Swiegers, Sofie Saerens, Nathalia Edwards, Kiran R. Patil, Bas Teusink, Douwe Molenaar Frontiers in Microbiology.2019;[Epub] CrossRef
Analysis of the bacteria community in wild
Cordyceps cicadae
and its influence on the production of HEA and nucleosides in
Cordyceps cicadae
Q.S. Qu, F. Yang, C.Y. Zhao, X.Y. Shi Journal of Applied Microbiology.2019; 127(6): 1759. CrossRef
Constraint-based modeling in microbial food biotechnology Martin H. Rau, Ahmad A. Zeidan Biochemical Society Transactions.2018; 46(2): 249. CrossRef
Advances in metabolic modeling of oleaginous microalgae Juan D. Tibocha-Bonilla, Cristal Zuñiga, Rubén D. Godoy-Silva, Karsten Zengler Biotechnology for Biofuels.2018;[Epub] CrossRef
A mapping framework of competition–cooperation QTLs that drive community dynamics Libo Jiang, Xiaoqing He, Yi Jin, Meixia Ye, Mengmeng Sang, Nan Chen, Jing Zhu, Zuoran Zhang, Jinting Li, Rongling Wu Nature Communications.2018;[Epub] CrossRef
New azaphilones and tremulane sesquiterpene from endophytic Nigrospora oryzae cocultured with Irpex lacteus Qing-Yan Zhou, Xue-Qiong Yang, Zhuo-Xi Zhang, Bang-Yan Wang, Ming Hu, Ya-Bin Yang, Hao Zhou, Zhong-Tao Ding Fitoterapia.2018; 130: 26. CrossRef
Biotechnological potential of microbial consortia and future perspectives Shashi Kant Bhatia, Ravi Kant Bhatia, Yong-Keun Choi, Eunsung Kan, Yun-Gon Kim, Yung-Hun Yang Critical Reviews in Biotechnology.2018; 38(8): 1209. CrossRef
Genome-scale biological models for industrial microbial systems Nan Xu, Chao Ye, Liming Liu Applied Microbiology and Biotechnology.2018; 102(8): 3439. CrossRef
The social network of microorganisms — how auxotrophies shape complex communities Karsten Zengler, Livia S. Zaramela Nature Reviews Microbiology.2018; 16(6): 383. CrossRef
From Genes to Ecosystems in Microbiology: Modeling Approaches and the Importance of Individuality Jan-Ulrich Kreft, Caroline M. Plugge, Clara Prats, Johan H. J. Leveau, Weiwen Zhang, Ferdi L. Hellweger Frontiers in Microbiology.2017;[Epub] CrossRef
Microbiome and metabolome data integration provides insight into health and disease Michael Shaffer, Abigail J.S. Armstrong, Vanessa V. Phelan, Nichole Reisdorph, Catherine A. Lozupone Translational Research.2017; 189: 51. CrossRef
Experimental design and quantitative analysis of microbial community multiomics Himel Mallick, Siyuan Ma, Eric A. Franzosa, Tommi Vatanen, Xochitl C. Morgan, Curtis Huttenhower Genome Biology.2017;[Epub] CrossRef
Temporal dynamics in microbial soil communities at anthrax carcass sites Karoline Valseth, Camilla L. Nesbø, W. Ryan Easterday, Wendy C. Turner, Jaran S. Olsen, Nils Chr. Stenseth, Thomas H. A. Haverkamp BMC Microbiology.2017;[Epub] CrossRef
Elucidation of complexity and prediction of interactions in microbial communities Cristal Zuñiga, Livia Zaramela, Karsten Zengler Microbial Biotechnology.2017; 10(6): 1500. CrossRef
Transitioning from Microbiome Composition to Microbial Community Interactions: The Potential of the Metaorganism Hydra as an Experimental Model Peter Deines, Thomas C. G. Bosch Frontiers in Microbiology.2016;[Epub] CrossRef
Metabolic Complementation in Bacterial Communities: Necessary Conditions and Optimality Matteo Mori, Miguel Ponce-de-León, Juli Peretó, Francisco Montero Frontiers in Microbiology.2016;[Epub] CrossRef
Microbial Metagenomics Reveals Climate-Relevant Subsurface Biogeochemical Processes Philip E. Long, Kenneth H. Williams, Susan S. Hubbard, Jillian F. Banfield Trends in Microbiology.2016; 24(8): 600. CrossRef
INVITED: Microbial Communication via Quorum Sensing James Boedicker, Kenneth Nealson IEEE Transactions on Molecular, Biological and Multi-Scale Communications.2016; : 1. CrossRef
Engineering of oleaginous organisms for lipid production Jennifer Levering, Jared Broddrick, Karsten Zengler Current Opinion in Biotechnology.2015; 36: 32. CrossRef
The evolution of mutualism from reciprocal parasitism: more ecological clothes for the Prisoner’s Dilemma Janis Antonovics, Joana Bergmann, Stefan Hempel, Erik Verbruggen, Stavros Veresoglou, Matthias Rillig Evolutionary Ecology.2015; 29(5): 627. CrossRef