Article
Physics, Multidisciplinary
Jacob Moran, Mikhail Tikhonov
Summary: Microbial ecosystems, despite their complexity, can be partially described by effective models with lower dimensions. Recent studies show that functionally relevant diversity exists at all resolution levels. Building a theoretical framework to predict which ecosystem properties can be predictable by coarse-grained models in different environmental conditions is important.
Article
Environmental Sciences
Michael Doering, Remo Freimann, Nadine Antenen, Alexia Roschi, Christopher T. Robinson, Fabio Rezzonico, Theo H. M. Smits, Diego Tonolla
Summary: The study investigated the seasonal and spatial dynamics of microbial communities in floodplain systems, revealing that microbial communities differed more among floodplain habitats than between riverine floodplains. An experimental flood caused a temporary shift in microbial communities, but pelagic bacteria did not persist within floodplain habitats over time after the flood.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Environmental Sciences
Okugbe Ebiotubo Ohore, Yunjie Wei, Jinhui Wang, Yuwen Wang, Binessi Edouard Ifon, Wenhua Liu, Zhen Wang
Summary: Changes in aquatic environmental conditions can affect microbial community assemblages and genome repertoire. Increasing water depth leads to higher bacterial and eukaryotic diversity and composition. Different microbes show differential nestedness at different water depths. The bottom depth is the most ecologically stable area with more profound ecosystem services.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Environmental Sciences
Okugbe Ebiotubo Ohore, Binessi Edouard Ifon, Yuwen Wang, Syed Shabi Ul Hassan Kazmi, Jingli Zhang, Edmond Sanganyado, Xiaoyang Jiao, Wenhua Liu, Zhen Wang
Summary: The influence of vertical changes in water depth on the distribution of emerging pollutants and microbial food webs is not well understood. This study investigated the effects of vertical transition in water depth on environmental variables, antibiotics and antibiotic resistomes, and microbial community structures in estuary and marine ecosystems (0-50 m). The results showed that changes in water salinity were the most influential factor for fluoroquinolone and macrolide concentrations, while dissolved oxygen and turbidity were key influencers for sulfonamide and beta-lactam concentrations. Bacterial and eukaryotic diversity and niche breadth increased significantly with increasing water depth, and the ecosystem food web structure was more stable at the bottom depths. The abundance of antibiotic resistance genes (ARGs) was significantly higher at the surface depth compared to the middle and bottom depths.
ENVIRONMENT INTERNATIONAL
(2023)
Article
Environmental Sciences
Sunghyun Kim, Hojeong Kang, J. Patrick Megonigal, Melissa McCormick
Summary: This study investigates the relationship between plant species and their enzyme activities with microbial diversity in wetland ecosystems. The research found that plant species with high biomass increased activities of certain hydrolase enzymes, leading to higher microbial diversity in the rhizosphere.
ESTUARIES AND COASTS
(2022)
Article
Biochemical Research Methods
Ilija Dukovski, Djordje Bajic, Jeremy M. Chacon, Michael Quintin, Jean C. C. Vila, Snorre Sulheim, Alan R. Pacheco, David B. Bernstein, William J. Riehl, Kirill S. Korolev, Alvaro Sanchez, William R. Harcombe, Daniel Segre
Summary: The genome-scale stoichiometric modeling of metabolism is a standard systems biology tool, with extensions like COMETS providing simulations of multiple microbial species in complex environments. The new version of COMETS incorporates a more accurate biophysical model and user-friendly interfaces for compatibility with COBRA models, making it a valuable tool for studying microbial communities.
Article
Ecology
Robyn A. Zerebecki, Kenneth L. Jr Jr Heck, John F. Valentine
Summary: This study used a meta-analytic approach to synthesize the results of 5 mesocosm studies and found that biodiversity can influence the effects of oiling on coastal ecosystems, but the direction and magnitude of this diversity effect varied. Diversity reduced the negative impact of oiling for within-trophic-level responses, especially for taxonomic diversity. Additionally, diversity effects were primarily driven by the presence of highly resistant or quick to recover taxa and genotypes, but had no effect on the response to the combination of oil and dispersant exposure.
ECOLOGY AND EVOLUTION
(2022)
Article
Environmental Sciences
Shun Wang, Youbiao Hu, Tingyu Fan, Wangkai Fang, Xiaopeng Liu, Liangji Xu, Bing Li, Xiangping Wei
Summary: Different types of subsidence lakes formed by underground coal mining are heavily polluted, and it is important to investigate the microbial community diversity in order to utilize the water resources effectively. This study explored the bacterial communities in open and closed subsidence lakes using high-throughput sequencing. Results showed significant differences in bacterial diversity and community composition between open and closed lakes. Factors such as pH, NH4+, and COD were found to play important roles in shaping the bacterial communities. Stochastic processes were identified as the main factor influencing bacterial community assembly in both closed and open lakes.
Article
Multidisciplinary Sciences
N. Chemidlin Prevost-Boure, B. Karimi, S. Sadet-Bourgeteau, C. Djemiel, M. Brie, J. Dumont, M. Campedelli, V. Nowak, P. Guyot, C. Letourneur, V. Manneville, F. Gillet, Y. Bouton
Summary: The specificity of dairy Protected Designation of Origin (PDO) products is closely related to the terroir of production and influenced by agroecosystems. The microbial diversity plays a key role in linking a PDO product to its terroir, with farming practices being a determining factor.
SCIENTIFIC REPORTS
(2021)
Review
Biochemistry & Molecular Biology
Larissa Balabanova, Liudmila Averianova, Maksim Marchenok, Oksana Son, Liudmila Tekutyeva
Summary: The biosynthesis of vitamin B12 has been successfully studied and applied in natural ecosystems and industrial production, utilizing microbial and genetic resources. Metabolic engineering techniques and renewable resources have improved the bioprocess of vitamins, benefiting both economics and environment. Commercial production mainly relies on two industrial strains, but there are still unresolved issues in biosynthesis that need clarification for future improvements.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Environmental Sciences
Shuai Ma, Huanhuan Geng, Changchun Yan, Xiaomin Han, Dan Xu, Furong Zhao, Ruth E. Blake, Beihai Zhou, Huilun Chen, Rongfang Yuan, Baoshi Jin, Haijun Liu, Fei Wang
Summary: The bacterial community in sediments of lakes dominated by macrophytes and lakes without macrophytes show different sensitivities to excessive nutrients. Bacterial communities in macrophyte-dominated areas are more susceptible to changes in nutrient levels and have lower stability compared to macrophyte-free areas.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2023)
Article
Physics, Multidisciplinary
Ada Altieri, Giulio Biroli
Summary: We analyze the role of the Allee effect in ecological communities formed by a large number of species using the generalized Lotka-Volterra model. Our findings highlight the significant role played by the functional response in determining aggregate behaviors of large ecosystems.
Article
Ecology
Xuetao Qiao, Thomas Lamy, Shaopeng Wang, Yann Hautier, Yan Geng, Zhuoxiu Han, Naili Zhang, Huaijiang He, Zhonghui Zhang, Chunyu Zhang, Xiuhai Zhao, Klaus von Gadow
Summary: Selective logging is a common land use practice in forests worldwide, but it has negative effects on biodiversity and ecosystem functioning. This study found that selective logging destabilizes both the aggregate functioning and species composition of forest ecosystems at multiple spatial scales. It highlights the importance of avoiding excessive selective logging and protecting forest diversity for the sustainability of forest ecosystems.
Article
Ecology
Qiang Fu, Yizhen Shao, Senlin Wang, Fengqin Liu, Guohang Tian, Yun Chen, Zhiliang Yuan, Yongzhong Ye
Summary: This study investigated the influence of different vegetation types on soil microbes in a temperate urban forest in China using high-throughput sequencing techniques. The results showed that different vegetation types have varying impacts on the abundance and spatial distribution of soil microbes, highlighting the importance of vegetation types for microbial biodiversity conservation in urban forests.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Article
Microbiology
Eva Garcia-Lopez, Fatima Ruiz-Blas, Silvia Sanchez-Casanova, Sonia Pena Perez, Maria Luisa Martin-Cerezo, Cristina Cid
Summary: This study examines the microbial diversity and characteristics of bacterial communities in volcanic glaciers in Deception Island, Antarctica, and the Kamchatka peninsula. Various glacier environmental factors were considered, and a comparative analysis of the biogeochemical cycles involving these microbiomes was attempted.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Alexei Tkachenko, Sergei Maslov, Ahmed Elbanna, George N. Wong, Zachary J. Weiner, Nigel Goldenfeld
Summary: Research shows that during the early stages of an epidemic, a transient collective immunity state may emerge as herd immunity forms, but this state is fragile and fades over time, meaning that the infection peak does not necessarily indicate long-lasting herd immunity; factors such as seasonal changes can lead to subsequent waves.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Biochemical Research Methods
Fangfang Xia, Jonathan Allen, Prasanna Balaprakash, Thomas Brettin, Cristina Garcia-Cardona, Austin Clyde, Judith Cohn, James Doroshow, Xiaotian Duan, Veronika Dubinkina, Yvonne Evrard, Ya Ju Fan, Jason Gans, Stewart He, Pinyi Lu, Sergei Maslov, Alexander Partin, Maulik Shukla, Eric Stahlberg, Justin M. Wozniak, Hyunseung Yoo, George Zaki, Yitan Zhu, Rick Stevens
Summary: To enable personalized cancer treatment, machine learning models have been developed to predict drug response based on tumor and drug features. This study used machine learning to analyze five publicly available cell line-based data sets and rigorously evaluated the model generalizability between different studies. The results showed that a multitasking deep neural network achieved the best cross-study generalizability, with models trained on the CTRP data set providing the most accurate predictions on testing data, and the gCSI data set being the most predictable among the cell line data sets.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Multidisciplinary Sciences
Zihan Wang, Akshit Goyal, Veronika Dubinkina, Ashish B. George, Tong Wang, Yulia Fridman, Sergei Maslov
Summary: Many microbes grow diauxically, utilizing resources one at a time rather than simultaneously. This study developed a minimal model of diauxic microbial communities assembling in a serially diluted culture, providing testable predictions for the assembly of natural as well as synthetic communities of diauxically shifting microorganisms.
NATURE COMMUNICATIONS
(2021)
Article
Biology
Alexei Tkachenko, Sergei Maslov, Tong Wang, Ahmed Elbana, George N. Wong, Nigel Goldenfeld
Summary: This article discusses the importance of dynamic heterogeneity in the spread of epidemics, and demonstrates the emergence of a new long timescale by integrating the stochastic dynamics of social activity into traditional epidemiological models.
Article
Biology
Akshit Goyal, Leonora S. Bittleston, Gabriel E. Leventhal, Lu Lu, Otto X. Cordero
Summary: Genomic data reveals the abundance of genotypic variants within natural microbial communities. This study tracks diverse microbial communities for over 300 generations to understand the ecological equivalence of the strains and the genetic distance at which distinct interactions and dynamics occur. The findings show that most strains are not ecologically equivalent and exhibit different dynamics, often being more correlated with strains from other species. Mathematical models and genomic analysis suggest that these patterns emerge from ecological interactions between strains.
Article
Biology
Ali Ebrahimi, Akshit Goyal, Otto X. Cordero
Summary: Microbial foraging in patchy environments, particularly in the oceans, is influenced by the interaction between detachment rates from particles and net growth and mortality rates. Our mathematical model explains how different detachment rates can lead to stable coexistence of marine populations. Fluctuating environments increase the likelihood of coexistence by favoring both growth and mortality.
Editorial Material
Ecology
Akshit Goyal
Summary: A computational method supports the classic theory that higher diversity in microbial communities remains stable as long as they have low complexity and weaker interactions.
NATURE ECOLOGY & EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Diana Rose E. Ranoa, Robin L. Holland, Fadi G. Alnaji, Kelsie J. Green, Leyi Wang, Richard L. Fredrickson, Tong Wang, George N. Wong, Johnny Uelmen, Sergei Maslov, Zachary J. Weiner, Alexei Tkachenko, Hantao Zhang, Zhiru Liu, Ahmed Ibrahim, Sanjay J. Patel, John M. Paul, Nickolas P. Vance, Joseph G. Gulick, Sandeep Puthanveetil Satheesan, Isaac J. Galvan, Andrew Miller, Joseph Grohens, Todd J. Nelson, Mary P. Stevens, P. Mark Hennessy, Robert C. Parker, Edward Santos, Charles Brackett, Julie D. Steinman, Melvin R. Fenner, Kirstin Dohrer, Michael DeLorenzo, Laura Wilhelm-Barr, Brian R. Brauer, Catherine Best-Popescu, Gary Durack, Nathan Wetter, David M. Kranz, Jessica Breitbarth, Charlie Simpson, Julie A. Pryde, Robin N. Kaler, Chris Harris, Allison C. Vance, Jodi L. Silotto, Mark Johnson, Enrique Andres Valera, Patricia K. Anton, Lowa Mwilambwe, Stephen P. Bryan, Deborah S. Stone, Danita B. Young, Wanda E. Ward, John Lantz, John A. Vozenilek, Rashid Bashir, Jeffrey S. Moore, Mayank Garg, Julian C. Cooper, Gillian Snyder, Michelle H. Lore, Dustin L. Yocum, Neal J. Cohen, Jan E. Novakofski, Melanie J. Loots, Randy L. Ballard, Mark Band, Kayla M. Banks, Joseph D. Barnes, Iuliana Bentea, Jessica Black, Jeremy Busch, Abigail Conte, Madison Conte, Michael Curry, Jennifer Eardley, April Edwards, Therese Eggett, Judes Fleurimont, Delaney Foster, Bruce W. Fouke, Nicholas Gallagher, Nicole Gastala, Scott A. Genung, Declan Glueck, Brittani Gray, Andrew Greta, Robert M. Healy, Ashley Hetrick, Arianna A. Holterman, Nahed Ismail, Ian Jasenof, Patrick Kelly, Aaron Kielbasa, Teresa Kiesel, Lorenzo M. Kindle, Rhonda L. Lipking, Yukari C. Manabe, Reubin McGuffin, Kenton G. McHenry, Agha Mirza, Jada Moseley, Heba H. Mostafa, Melody Mumford, Kathleen Munoz, Arika D. Murray, Moira Nolan, Nil A. Parikh, Andrew Pekosz, Janna Pflugmacher, Janise M. Phillips, Collin Pitts, Mark C. Potter, James Quisenberry, Janelle Rear, Matthew L. Robinson, Edith Rosillo, Leslie N. Rye, MaryEllen Sherwood, Anna Simon, Jamie M. Singson, Carly Skadden, Tina H. Skelton, Charlie Smith, Mary Stech, Ryan Thomas, Matthew A. Tomaszewski, Erika A. Tyburski, Scott Vanwingerden, Evette Vlach, Ronald S. Watkins, Karriem Watson, Karen C. White, Timothy L. Killeen, Robert J. Jones, Andreas C. Cangellaris, Susan A. Martinis, Awais Vaid, Christopher B. Brooke, Joseph T. Walsh, Ahmed Elbanna, William C. Sullivan, Rebecca L. Smith, Nigel Goldenfeld, Timothy M. Fan, Paul J. Hergenrother, Martin D. Burke
Summary: This study reports on a case study at the University of Illinois at Urbana-Champaign, where a program of public health measures and other non-pharmaceutical interventions were employed to keep classrooms and laboratories open during the COVID-19 pandemic. The results showed that fast/frequent testing and other interventions helped mitigate transmission of SARS-CoV-2 at the university.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Yulia Fridman, Zihan Wang, Sergei Maslov, Akshit Goyal
Summary: Recent observations have shown that closely related strains of the same microbial species can stably coexist in different environments. A consumer-resource model of microbial ecosystems suggests that differentiation of strains based on their growth rates in high and low nutrient conditions enables coexistence. The model also demonstrates that between 1 and 3 strains of a species typically coexist, consistent with experimental observations.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Editorial Material
Biochemistry & Molecular Biology
Avi I. Flamholz, Akshit Goyal
Summary: Recent research supports the idea that microbes allocate their biosynthetic capacity to maximize growth rate. However, many microbes can grow much faster after laboratory evolution. Chure and Cremer propose a resource-allocation model derived from first principles, which helps resolve this paradox.
TRENDS IN MICROBIOLOGY
(2023)
Article
Ecology
Xiaoyu Shan, Akshit Goyal, Rachel Gregor, Otto X. Cordero
Summary: This study develops an unsupervised, annotation-free method that can identify microbial functional groups based on variation in microbiome data and environmental variables. The authors demonstrate its application in various datasets, including the Tara oceans microbiome and animal gut microbiomes. This work advances our understanding of structure-function relationships in complex microbiomes and provides an objective and systematic approach to discover functional groups.
NATURE ECOLOGY & EVOLUTION
(2023)
Article
Computer Science, Artificial Intelligence
Tong Wang, Xu-Wen Wang, Kathleen A. Lee-Sarwar, Augusto A. Litonjua, Scott T. Weiss, Yizhou Sun, Sergei Maslov, Yang-Yu Liu
Summary: The authors introduce a deep learning method called mNODE for predicting metabolic profiles of microbial communities. mNODE outperforms existing methods and can reveal microbe-metabolite interactions, providing valuable insights for precision nutrition research.
NATURE MACHINE INTELLIGENCE
(2023)
Article
Biochemical Research Methods
Ananthan Nambiar, Simon Liu, Maeve Heflin, John Malcolm Forsyth, Sergei Maslov, Mark Hopkins, Anna Ritz
Summary: The scientific community is generating protein sequence information rapidly, but only a small fraction can be experimentally validated. We propose a Transformer neural network that fine-tunes task-agnostic sequence representations for protein prediction tasks, achieving satisfactory results.
JOURNAL OF COMPUTATIONAL BIOLOGY
(2023)
Meeting Abstract
Pharmacology & Pharmacy
F. Rashid, V. Dubinkina, S. Maslov, J. Irudayaraj
INTERNATIONAL JOURNAL OF TOXICOLOGY
(2022)
