Review
Multidisciplinary Sciences
Ashifa Nizam, Suraj Prasannakumari Meera, Ajay Kumar
Summary: Mangroves are salt-tolerant plants adapted to intertidal zones, with unique morphological and physiological adaptations. The nature of the genetic and molecular changes underlying these adaptations is still poorly understood. This review provides updated information on the genetic, epigenetic, and molecular regulation of mangrove adaptive traits.
Article
Biochemistry & Molecular Biology
Connor D. Harris, Ellis L. Torrance, Kasie Raymann, Louis-Marie Bobay
Summary: The core genome represents the set of genes shared by all, or nearly all, strains of a given population or species of prokaryotes. CoreCruncher is a robust and fast program that can construct core genomes across hundreds or thousands of genomes. Compared to other tools, CoreCruncher is more conservative and less sensitive to the presence of paralogs and xenologs.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biotechnology & Applied Microbiology
Wen-Tao Tang, Tian-Wei Hao, Guang-Hao Chen
Summary: Sulfate-reducing prokaryotes (SRPs) play a crucial role in sulfur, carbon, and metal cycling in the environment. This study developed multiple metabolic models for SRPs based on genomic information, revealing different energy generation mechanisms through electron transfer pathways. The constructed models provide insights into the metabolic behaviors of SRPs and can be applied to other environmental and industrial microbes for predictive purposes.
BIOTECHNOLOGY AND BIOENGINEERING
(2021)
Article
Biology
Jonathan M. Monk
Summary: This article analyzes the metabolic diversity and speciation of Escherichia through the construction of genome-scale models. The results indicate that strain-specific metabolic capabilities correspond to different species and nutrient niches. This work marks a first step towards a curated reconstruction of pan-Escherichia metabolism.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Microbiology
Shivendra G. Tewari, Krithika Rajaram, Russell P. Swift, Jaques Reifman, Sean T. Prigge, Anders Wallqvist
Summary: The malaria parasite Plasmodium falciparum adapts to fosmidomycin treatment by increasing purine-based nucleotide synthesis and decreasing phosphatidylcholine synthesis. This metabolic adaptation allows the parasite to compensate for the loss of prenylation modifications and control RNA translation rate during the intraerythrocytic developmental cycle. Combination therapies targeting nucleotide synthesis or ribosomal biogenesis may be more effective than treating the parasite with fosmidomycin alone.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2021)
Article
Biochemistry & Molecular Biology
Sin Man Lam, Jie Li, Huan Sun, Weining Mao, Zongmin Lu, Qingshuo Zhao, Chao Han, Xia Gong, Binhua Jiang, Gek Huey Chua, Zhenwen Zhao, Fanwei Meng, Guanghou Shui
Summary: The neural compartmentalization of lipid distribution and metabolism is associated with troglomorphic traits in Sinocyclocheilus cavefish. This includes reductions in DHA-phospholipids and accumulation of arachidonic acid-phospholipids in the brain, demyelination in serotonergic neurons, and systemic reductions in esterified DHAs in the liver. These adaptations serve to reduce energy expenditure and are crucial for the survival of cavefish in cave environments.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Lina Kloub, Sean Gosselin, Matthew Fullmer, Joerg Graf, Johann Peter Gogarten, Mukul S. Bansal
Summary: Horizontal gene transfer (HGT) is crucial for prokaryotic evolution, yet little is known about the scale of individual HGT events. A computational framework called HoMer is introduced to infer single-gene HGT events and potential multiple-gene transfers, aiding a better understanding of HGT and microbial evolution on a larger scale through systematic inference of HMGTs.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biology
J. H. Arbour, A. A. Curtis, S. E. Santana
Summary: The study found that bats underwent profound adaptive divergences in skull shape during evolution, leading to significant changes in allometric relationships and modularity.
Review
Agriculture, Dairy & Animal Science
Vivien J. Chebii, Emmanuel A. Mpolya, Farai C. Muchadeyi, Jean-Baka Domelevo Entfellner
Summary: Ungulates are essential sources of food, labor, clothing, and transportation for humans, and they possess unique adaptive traits in various habitats. Genomics resources have helped identify genes associated with the adaptability of ungulates to their environments.
Article
Microbiology
Nicole Pearcy, Yue Hu, Michelle Baker, Alexandre Maciel-Guerra, Ning Xue, Wei Wang, Jasmeet Kaler, Zixin Peng, Fengqin Li, Tania Dottorini
Summary: The study focuses on the identification of genetic determinants associated with antimicrobial resistance in E. coli using a computational approach that integrates machine learning with metabolic modeling. The findings reveal key genetic determinants linked to growth and metabolic adaptations, providing insights into the complex interplay between antibiotic resistance and metabolic rewiring in bacteria. This computational solution has the potential to be applied to other human and animal pathogens for further studies on antimicrobial resistance.
Article
Biology
Xiangyu Pan, Yudong Cai, Zongjun Li, Xianqing Chen, Rasmus Heller, Nini Wang, Yu Wang, Chen Zhao, Yong Wang, Han Xu, Songhai Li, Ming Li, Cunyuan Li, Shengwei Hu, Hui Li, Kun Wang, Lei Chen, Bin Wei, Zhuqing Zheng, Weiwei Fu, Yue Yang, Tingting Zhang, Zhuoting Hou, Yueyang Yan, Xiaoyang Lv, Wei Sun, Xinyu Li, Shisheng Huang, Lixiang Liu, Shengyong Mao, Wenqing Liu, Jinlian Hua, Zhipeng Li, Guojie Zhang, Yulin Chen, Xihong Wang, Qiang Qiu, Brian P. Dalrymple, Wen Wang, Yu Jiang
Summary: The study identified genetic changes underlying rumen functional innovations, including coding mutations, newly evolved genes, and changes of regulatory elements. It was validated that the key ketogenesis gene HMGCS2 is under positive selection and exhibits higher synthesis activity in ruminants. Two newly evolved genes, LYZ1 and DEFB1, may regulate microbial community equilibrium by resisting Gram-positive bacteria.
SCIENCE CHINA-LIFE SCIENCES
(2021)
Article
Plant Sciences
Yariv Brotman, Cindy Llorente-Wiegand, Glenn Oyong, Saurabh Badoni, Gopal Misra, Roslen Anacleto, Sabiha Parween, Erstelle Pasion, Rhowell N. Tiozon, Joanne J. Anonuevo, Maria K. deGuzman, Saleh Alseekh, Edwige G. N. Mbanjo, Lesley A. Boyd, Alisdair R. Fernie, Nese Sreenivasulu
Summary: The study explores the genetic basis of metabolic diversity in brown rice through metabolite profiling of 320 rice cultivars, identifying genetic variants impacting diverse metabolic targets. This multi-disciplinary nutrigenomics approach links genetic variants to complex nutritional targets, revealing the genetic basis of human health benefits in the metabolome of brown rice.
Article
Microbiology
Lucio Aliperti, Ariel A. Aptekmann, Gonzalo Farfanuk, Luciana L. Couso, Alfonso Soler-Bistue, Ignacio E. Sanchez
Summary: The GC content of prokaryotic genomes is species-specific, with high GC content being associated with r-strategists that have broad adaptability and low proteome costs, while low GC content is associated with K-strategists specialized for stable environments.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Jingjing Liu, Gaosheng Zhou, Xiaoting Wang, Dawei Liu
Summary: The importance of cell metabolism alterations during sepsis is overlooked. Metabolic reprogramming plays a crucial role in immune imbalance and organ failure associated with sepsis. It is both necessary for immune cell activation and a cause of immunosuppression. The metabolites produced by metabolic reprogramming can control the immune response. Energy shortage in sepsis leads to cell and organ dysfunction. Metabolic reprogramming can alleviate the energy crisis and enhance cell adaptation, but switching from glycolysis to OXPHOS is essential for restoring cell function.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Review
Microbiology
Ruben D. Arroyo-Olarte, Ricardo Bravo Rodriguez, Edgar Morales-Rios
Summary: CRISPR-Cas technology has revolutionized genome editing in eukaryotic organisms with its simplicity and programmability, but faces challenges in bacterial genome editing. Alternative approaches are being explored to overcome these issues and expand the application of genome editing in bacteria.
Article
Microbiology
Vaibhhav Sinha, Akshit Goyal, Sine L. Svenningsen, Szabolcs Semsey, Sandeep Krishna
FRONTIERS IN MICROBIOLOGY
(2017)
Article
Ecology
Akshit Goyal, Veronika Dubinkina, Sergei Maslov
Article
Physics, Multidisciplinary
Akshit Goyal, Sergei Maslov
PHYSICAL REVIEW LETTERS
(2018)
Article
Biochemical Research Methods
Tong Wang, Akshit Goyal, Veronika Dubinkina, Sergei Maslov
PLOS COMPUTATIONAL BIOLOGY
(2019)
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
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)