Review
Biochemistry & Molecular Biology
Maziya Ibrahim, Lavanya Raajaraam, Karthik Raman
Summary: Studying and engineering microbial communities offer significant advantages over single strains, such as division of labour and improved substrate utilization. By utilizing constraint-based modeling methods and approaches based on graph theory, we can gain insights into microbial interactions and enhance community productivity. Advanced omics technologies are paving the way for rapid expansion of microbial community engineering, with a promising impact on biotechnological processes.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Microbiology
Kuanguan Huang, Jie Wang, Junhao Huang, Shouke Zhang, Alfried P. Vogler, Quanquan Liu, Yongchun Li, Maowei Yang, You Li, Xuguo Zhou
Summary: In this study, gut microbiota of bamboo-feeding insects were examined to understand their convergent adaptation to extreme diet specialization. Results showed that while both phylogeny and diet can influence the gut microbiome composition, phylogeny primarily drives the convergent adaptation to a highly specialized diet in insects feeding on bamboo.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Minsuk Kim, Jaeyun Sung, Nicholas Chia
Summary: Predictive modeling tools are important for assessing microbial communities in various fields. Constraint-based community-scale metabolic modeling has the potential to predict both the structure and function of microbial communities. This study investigates the implications of resource-allocation constraints in community-scale metabolic modeling and shows that they are indispensable for predicting the structure and function of microbial communities.
METABOLIC ENGINEERING
(2022)
Article
Multidisciplinary Sciences
Gabriele Micali, Alyson M. Hockenberry, Alma Dal Co, Martin Ackermann, Dianne Newman
Summary: Microbial communities are essential for life on Earth, but their metabolic dependencies can be detrimental when external conditions change rapidly. We found that the spatial arrangement of a microbial community plays a crucial role in maintaining metabolic interactions and growth after an environmental shift.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Kristopher D. Parker, Akhilendra K. Maurya, Hend Ibrahim, Sangeeta Rao, Petronella R. Hove, Dileep Kumar, Rama Kant, Bupinder Raina, Rajesh Agarwal, Kristine A. Kuhn, Komal Raina, Elizabeth P. Ryan
Summary: The study demonstrates that modified gut microbiota from humans consuming rice bran can protect mice from colon carcinogenesis, with specific microbial communities associated with colon health. The findings suggest that integrated dietary-FMT intervention strategies could be effective for colorectal cancer control, treatment, and prevention.
Editorial Material
Oncology
Chi Chun Wong, Winnie Fong, Jun Yu
Summary: This study tracked gut bacteria and metabolites in rectal cancer patients undergoing neoadjuvant chemoradiotherapy and identified Bacteroides vulgatus as a driver bacterium of therapeutic resistance by supplying tumors with nucleotides.
Review
Nutrition & Dietetics
Jinliang Hou, Jianguo Xiang, Deliang Li, Xinhua Liu, Wangcheng Pan
Summary: There is an important relationship between gut microbes and host metabolic phenotypes, as they participate in host metabolism, physiology, and immunity through mechanisms such as metabolite differences and gene expression. Understanding this relationship can lead to new ways to prevent and treat metabolic diseases.
FRONTIERS IN NUTRITION
(2022)
Article
Multidisciplinary Sciences
Sammy Pontrelli, Rachel Szabo, Shaul Pollak, Julia Schwartzman, Daniela Ledezma-Tejeida, Otto X. Cordero, Uwe Sauer
Summary: A study on a model marine microbial community that degrades chitin reveals that chitinases secreted by the degraders produce specific chain length oligomers, which select for specialized consumers and influence the metabolites secreted by these consumers. Each species in the breakdown cascade exhibits unique hierarchical preferences for substrates, leading to sequential colonization of metabolically distinct groups over time. This study uncovers a hierarchical cross-feeding structure that allows biopolymer degraders to shape the dynamics of community assembly.
Article
Genetics & Heredity
Long H. Nguyen, Daniel Okin, David A. Drew, Vincent M. Battista, Sirus J. Jesudasen, Thomas M. Kuntz, Amrisha Bhosle, Kelsey N. Thompson, Trenton Reinicke, Chun-Han Lo, Jacqueline E. Woo, Alexander Caraballo, Lorenzo Berra, Jacob Vieira, Ching-Ying Huang, Upasana Das Adhikari, Minsik Kim, Hui-Yu Sui, Marina Magicheva-Gupta, Lauren McIver, Marcia B. Goldberg, Douglas S. Kwon, Curtis Huttenhower, Andrew T. Chan, Peggy S. Lai
Summary: The gut microbiome is linked to the severity of COVID-19, with specific microbial taxa and metabolites associated with severe disease. These findings suggest the potential of using the gut microbiome as a biomarker for disease severity and as a target for therapeutic intervention in COVID-19.
Article
Multidisciplinary Sciences
Akshit Goyal, Tong Wang, Veronika Dubinkina, Sergei Maslov
Summary: Combining ecology-based computational methods and optimization techniques, GutCP predicts a large number of experimentally untested cross-feeding interactions in the human gut microbiome. It has the potential to improve microbial community models and predict the metabolic profile of the gut.
NATURE COMMUNICATIONS
(2021)
Review
Environmental Sciences
Lvjing Wang, Xiaoyu Wang, Hao Wu, Haixia Wang, Yihan Wang, Zhenmei Lu
Summary: The genome-scale metabolic model (GEM) is a mathematical representation of whole-cell metabolism that allows for in silico simulations of metabolic flux distribution. GEMs have been extensively used in studying microbial interactions and guiding the design of synthetic microbial communities for bioremediation. This review summarizes the various types of microbial interactions, the process of GEM reconstruction, automatic reconstruction programs, and knowledge databases. It also discusses the exciting combination of metabolic models, omics, and machine learning approaches in recent application studies. However, further work is needed to fully understand and utilize GEMs for describing the metabolic interactions of microbial communities and applying them to pollutant biodegradation.
CRITICAL REVIEWS IN ENVIRONMENTAL SCIENCE AND TECHNOLOGY
(2023)
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)
Review
Agronomy
Gustavo Santoyo, Paulina Guzman-Guzman, Fannie Isela Parra-Cota, Sergio de los Santos-Villalobos, Ma. del Carmen Orozco-Mosqueda, Bernard R. Glick
Summary: Plant-associated microorganisms play a crucial role in promoting plant growth, especially when microbial consortia are involved, leading to additive or synergistic effects. Research focuses on understanding the mechanisms by which different microorganisms interact to enhance plant growth.
Review
Microbiology
Christian Diener, Sean M. Gibbons
Summary: Microbial consortia play a crucial role in various essential processes, but it is challenging to understand their functional capacities based on their composition alone. Community-scale metabolic models have the potential to simulate complex microbial communities, but there is no consensus on the fitness function and community-wide growth. Transitioning from single-taxon models to multitaxon models poses challenges as well. Dynamic approaches are a solution but are computationally expensive, while two steady-state approaches provide ecologically relevant solutions with improved scalability.
Article
Engineering, Marine
Taoshu Wei, Yanwen Liao, Yong Wang, Junyuan Li, Lisheng He
Summary: This study comparatively investigated the gut microbiota of amphipods inhabiting different marine zones and found that amphipods in the hadal zone had the lowest richness and diversity of gut microbiome, and shared fewer microorganisms with the surrounding seawater. Amphipods in different habitats had discriminant taxa for their gut microbial communities.
JOURNAL OF MARINE SCIENCE AND ENGINEERING
(2023)
Article
Mathematical & Computational Biology
Poonam Phalak, Jin Chen, Ross P. Carlson, Michael A. Henson
BMC SYSTEMS BIOLOGY
(2016)
Article
Mathematical & Computational Biology
Jin Chen, Jose A. Gomez, Kai Hoeffner, Poonam Phalak, Paul I. Barton, Michael A. Henson
BMC SYSTEMS BIOLOGY
(2016)
Review
Biochemistry & Molecular Biology
Ross P. Carlson, Ashley E. Beck, Poonam Phalak, Matthew W. Fields, Tomas Gedeon, Luke Hanley, William R. Harcombe, Michael A. Henson, Jeffrey J. Heys
BIOCHEMICAL SOCIETY TRANSACTIONS
(2018)
Article
Biochemical Research Methods
Michael A. Henson, Poonam Phalak
PLOS COMPUTATIONAL BIOLOGY
(2018)
Article
Engineering, Chemical
Poonam Phalak, Michael A. Henson
Article
Microbiology
Michael A. Henson, Giulia Orazi, Poonam Phalak, George A. O'Toole
Article
Biotechnology & Applied Microbiology
P. Phalak, M. A. Henson
JOURNAL OF APPLIED MICROBIOLOGY
(2019)
Article
Mathematical & Computational Biology
Michael A. Henson, Poonam Phalak
BMC SYSTEMS BIOLOGY
(2017)
Proceedings Paper
Automation & Control Systems
Poonam Phalak, Jin Chen, Ross P. Carlson, Michael A. Henson
Proceedings Paper
Automation & Control Systems
Michael A. Henson, Poonam Phalak