Article
Environmental Sciences
Bharti Thakur, Rajiv Yadav, Arkadeep Mukherjee, Delphine Melayah, Roland Marmeisse, Laurence Fraissinet-Tachet, Mondem Sudhakara Reddy
Summary: Using a functional metagenomics approach, a potentially toxic metal tolerance gene was identified from contaminated soil community, with the specific gene PLCc43 showing tolerance to various metals and oxidative stress. This gene may serve as a biomarker for detoxification of toxic metals in contaminated sites.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2021)
Article
Biology
Akil Akhtar, Madhu Lata, Sonali Sunsunwal, Amit Yadav, Kajal Lnu, Srikrishna Subramanian, T. N. C. Ramya
Summary: Uncultured microbes are a valuable source of novel genes and gene products. Functional metagenomics can be used to identify and annotate these novel gene products. In this study, a metagenomic phage display library was constructed and screened to identify previously unannotated carbohydrate binding domains. Several new carbohydrate binding domains were discovered, including a levan binding domain and four complex N-glycan binding domains.
COMMUNICATIONS BIOLOGY
(2023)
Article
Cell Biology
Frank J. Piscotta, Shawn T. Whitfield, Toshiki G. Nakashige, Andreia B. Estrela, Thahmina Ali, Sean F. Brady
Summary: The human microbiota is crucial for host health, with proper development of the infant microbiome being particularly important. Dysbiosis of the microbiome can lead to short-term health issues and long-term disorders. Through the analysis of a metagenomic library constructed from infant stool samples, this study identified bioactive metabolites and previously uncharacterized operons that influence host pathways. This work expands our understanding of microbial effector molecules and their impact on host processes.
Article
Biochemistry & Molecular Biology
Stefanie Neun, Paul Brear, Eleanor Campbell, Theodora Tryfona, Kamel El Omari, Armin Wagner, Paul Dupree, Marko Hyvonen, Florian Hollfelder
Summary: The abundance of protein sequence data is not matched by the number of experimentally verified functional annotations. In this study, we used high-throughput microfluidic droplet screening to identify a new beta-glucuronidase enzyme with little homology to previously studied enzymes. This finding demonstrates the potential of functional metagenomics in uncovering the function of enzymes that cannot be predicted by bioinformatics.
NATURE CHEMICAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Mami Oikawa, Hisato Kobayashi, Makoto Sanbo, Naoaki Mizuno, Kenyu Iwatsuki, Tomoya Takashima, Keiko Yamauchi, Fumika Yoshida, Takuya Yamamoto, Takashi Shinohara, Hiromitsu Nakauchi, Kazuki Kurimoto, Masumi Hirabayashi, Toshihiro Kobayashi
Summary: The in vitro generation of germ cells from pluripotent stem cells has significant implications for reproductive medicine and animal breeding. In this study, researchers successfully induced functional primordial germ cell-like cells from rat pluripotent stem cells and generated functional spermatids through transplantation. This research provides insights into the mechanisms of in vitro gametogenesis and has implications for broader applications.
Article
Chemistry, Multidisciplinary
Emily R. Ruskowitz, Brizzia G. Munoz-Robles, Alder C. Strange, Carson H. Butcher, Sebastian Kurniawan, Jeremy R. Filteau, Cole A. DeForest
Summary: Proteins play a crucial role in regulating various biological processes, and new techniques are needed to effectively control protein activity in living systems and biomaterials to study cell signaling and guide biological fate. This study presents a generalizable strategy for activating protein function with precise spatiotemporal control. By using a genetically encoded and light-activated SpyLigation (LASL), bioactive proteins can be reassembled from non-functional fragments with the help of cytocompatible light. The researchers demonstrate protein activation and subcellular localization control in solution, biomaterials, and living mammalian cells. These photoclick-based optogenetic approaches are expected to greatly contribute to understanding and directing complex cellular fates in both time and three-dimensional space.
Article
Biochemistry & Molecular Biology
Liyan Kong, Xiaonan Li, Zongxiang Zhan, Zhongyun Piao
Summary: Plasmodiophora brassicae, an intracellular pathogen, has unique sugar transporters that enable it to utilize the host's carbohydrates for survival. These transporters are upregulated during late infection stages when a significant amount of energy is required.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Toshihiro Kobayashi, Teppei Goto, Mami Oikawa, Makoto Sanbo, Fumika Yoshida, Reiko Terada, Naoko Niizeki, Naoyo Kajitani, Kanako Kazuki, Yasuhiro Kazuki, Shinichi Hochi, Hiromitsu Nakauchi, M. Azim Surani, Masumi Hirabayashi
Summary: The study demonstrates efficient germline transmission of difficult PSCs by complementing blastocysts from germline-deficient Prdm14 knockout rats, showing the potential for creating genetically modified animals and cross-species germline transmission.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Oluwapelumi O. Adeyemi, Joseph C. Ward, Joseph S. Snowden, Morgan R. Herod, David J. Rowlands, Nicola J. Stonehouse
Summary: This study investigated the relationship between gene duplication and advantages in maintaining gene replication in small genomes of RNA viruses. The expansion of 3B copy numbers within the FMDV genome allows for the evolution of separate cis and trans acting functions, providing selective pressure to maintain multiple copies of 3B.
Article
Biotechnology & Applied Microbiology
Chuan Hao Tan, Yee Phan Yeo, Muhammad Hafiz, Noele Kai Jing Ng, Sujatha Subramoni, Shireen Taj, Martin Tay, Xie Chao, Staffan Kjelleberg, Scott A. Rice
Summary: By conducting metagenomic screening and functional validation of AHL genes in the activated sludge microbial community from the Ulu Pandan wastewater treatment plant in Singapore, functional QS genes LuxI and LuxR were identified, indicating that Nitrospira spp. may be active in the activated sludge community.
NPJ BIOFILMS AND MICROBIOMES
(2021)
Article
Microbiology
Carlos Sabater, Natalia Molinero, Manuel Ferrer, Carmen Maria Garcia Bernardo, Susana Delgado, Abelardo Margolles
Summary: This study characterized three gallbladder metagenomes and a fosmid library, focusing on the metagenomic dark matter fraction. Several protein functional domains were annotated in the dark matter fraction, along with the discovery of a novel deacetylase enzyme. Computational pipelines used in this study can help in discovering novel microbial enzymes with previously uncharacterized functions.
Article
Engineering, Environmental
Xiaodong Zhao, Xiaojing Li, Yue Li, Xiaolin Zhang, Feihong Zhai, Tianzhi Ren, Yongtao Li
Summary: Microbial fuel cells (MFCs) have been shown to effectively remove tetracycline in soil by enhancing degradation efficiency and reducing antibiotic resistance genes through the addition of phosphate. Specific bacteria like Geobacter, Desulfurispora, and Anaeroomyxobacter play key roles in bioelectricity generation in the anode, while Gemmatimonadetes bacterium SCN 70-22 and other potential electrotrophic microbes are identified in the cathode. The expression of flavoproteins and enzymes like quinol oxidase in the cathode can improve electron transfer efficiency and accelerate the biodegradation rate of tetracycline.
JOURNAL OF HAZARDOUS MATERIALS
(2021)
Article
Microbiology
Madangchanok Imchen, V. T. Anju, Siddhardha Busi, Mahima S. Mohan, Pattnaik Subhaswaraj, Madhu Dyavaiah, Ranjith Kumavath
Summary: Biofilms formed by microbial cells on surfaces serve as a breeding ground for drug-resistant pathogens and ARG enrichment, but they also play beneficial roles in promoting plant growth and wastewater treatment. Inhibiting biofilm formation through quorum quenching is a feasible approach. Surveillance of biofilm microbiome is crucial for assessing risks and harnessing bioactive potential. Metagenomics is a preferred method for studying biofilm microbiome and discovering new species.
MICROBIOLOGICAL RESEARCH
(2022)
Article
Immunology
Huai Xu, Andrea L. Krieter, Nagendraprabhu Ponnuraj, Yvette (Yung-Tien) Tien, Taejoong Kim, Keith W. Jarosinski
Summary: Functional complementation between vaccines and virulent viruses has been observed, suggesting it as a potential mechanism for vaccine-mediated viral evolution. This phenomenon should be considered during the development of novel vaccines.
Article
Microbiology
Yulan Cai, Yanhong Luo, Ninan Dai, Yan Yang, Ying He, Huajun Chen, Manlu Zhao, Xiaoyun Fu, Tao Chen, Zhouxiong Xing
Summary: Hyperoxia induces dysbiosis in the gut microbiome and disrupts carbohydrate and lipid metabolism. Moreover, it impairs unsaturated fatty acid metabolism in the gut and inhibits HIF-1 and glucagon signaling pathways in the serum.
FRONTIERS IN MICROBIOLOGY
(2023)
Editorial Material
Biochemistry & Molecular Biology
M. J. Ryan, M. Schloter, G. Berg, T. Kostic, L. L. Kinkel, K. Eversole, J. A. Macklin, B. Schelkle, M. Kazou, I. Sarand, B. K. Singh, D. Fischer, E. Maguin, I. Ferrocino, N. Lima, R. S. McClure, T. C. Charles, R. S. C. de Souza, G. S. Kiran, H. L. Krug, J. Taffner, H. Roume, J. Selvin, D. Smith, D. Rybakova, A. Sessitsch
Summary: The microbiome research field is rapidly advancing and requires a well-established biobanking infrastructure for preserving microbiome samples and their functional potential. There is an urgent need for assessing how biobanks can support research in this rapidly evolving field.
TRENDS IN MICROBIOLOGY
(2021)
Correction
Biochemistry & Molecular Biology
M. J. Ryan, M. Schloter, G. Berg, T. Kostic, L. L. Kinkel, K. Eversole, J. A. Macklin, B. Schelkle, M. Kazou, I. Sarand, B. K. Singh, D. Fischer, E. Maguin, I. Ferrocino, N. Lima, R. S. McClure, T. C. Charles, R. S. C. de Souza, G. S. Kiran, H. L. Krug, J. Taffner, H. Roume, J. Selvin, D. Smith, D. Rybakova, A. Sessitsch
TRENDS IN MICROBIOLOGY
(2021)
Article
Environmental Sciences
Gem Thomas-Barry, Chaney C. G. St Martin, Michael D. J. Lynch, Adesh Ramsubhag, Judy Rouse-Miller, Trevor C. Charles
Summary: This study investigated the changes in rhizobacteriome community structure in hyper-seasonal edaphic savannas, showing that soil and season were key determinants influencing the community structure. Plant biomass, root traits, and rhizobacterial community compositions were found to be influenced by seasonal changes and savanna-specific drivers.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Biochemistry & Molecular Biology
Karla N. Valenzuela-Valderas, Gabriel Moreno-Hagelsieb, John R. Rohde, Rafael A. Garduno
Summary: Research has shown that the bacterial pathogen Legionella pneumophila's chaperonin protein HtpB has a unique function in interaction with the eukaryotic protein ECM29, which can be mapped to specific amino acid positions.
Article
Genetics & Heredity
Victor H. Tierrafria, Claire Rioualen, Heladia Salgado, Paloma Lara, Socorro Gama-Castro, Patrick Lally, Laura Gomez-Romero, Pablo Pena-Loredo, Andres G. Lopez-Almazo, Gabriel Alarcon-Carranza, Felipe Betancourt-Figueroa, Shirley Alquicira-Hernandez, J. Enrique Polanco-Morelos, Jair Garcia-Sotelo, Estefani Gaytan-Nunez, Carlos-Francisco Mendez-Cruz, Luis J. Muniz, Cesar Bonavides-Martinez, Gabriel Moreno-Hagelsieb, James E. Galagan, Joseph T. Wade, Julio Collado-Vides
Summary: This paper presents a radical upgrade of RegulonDB, offering more than 2000 high-throughput datasets on transcriptional regulation. The datasets have been processed for comparison and include information on transcription termination sites, transcription units, transcription factor binding interactions, and expression profiles. The browsing and visualization tools have also been expanded, allowing comparisons against previous knowledge, genome viewing, and metadata querying.
MICROBIAL GENOMICS
(2022)
Editorial Material
Microbiology
Vanessa A. Varaljay, Trevor C. Charles, Rolf Daniel
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Xueya Zhang, Shuang Liang, Qingnan Wu, Trevor C. Charles, Rui He, Jiakai Wu, Yuhui Zhao, Zhiyi Zhao, Hezhong Wang
Summary: This study investigated the mode of action of nanochitin whisker (NC) against Fusarium pseudograminearum (Fpg), an important pathogenic fungus causing wheat crown rot disease. The results showed that NC significantly reduced hyphal growth and spore germination rate of Fpg. It exerted its effects by disrupting cell wall structure, altering membrane integrity, decreasing enzyme activity related to energy-supply, and reducing mycotoxin production.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Multidisciplinary Sciences
Juan M. Escorcia-Rodriguez, Mario Esposito, Julio A. Freyre-Gonzalez, Gabriel Moreno-Hagelsieb
Summary: Orthologs and paralogs exhibit differences in functional stability and divergence based on gene mutation rates and protein similarity. Choosing orthologs as functionally coherent genes remains the right approach in comparative genomics.
Review
Environmental Sciences
Aleksander Cholewinski, Eugenia Dadzie, Cassandra Sherlock, William A. Anderson, Trevor C. Charles, Komal Habib, Steven B. Young, Boxin Zhao
Summary: The resilience and low cost of plastics have led to their widespread use, but also contribute to their abundance and persistence as waste. Plastic pollution is a major concern for global ecosystems and their health. Material flow analysis, previously used in other industries, has been applied to plastics to understand how waste enters the environment. However, research on degradation strategies for microplastics has been limited and material flow analysis lacks data. The variety of plastics, their additives, and contaminants present significant challenges in degrading microplastic particles.
ENVIRONMENTAL POLLUTION
(2022)
Article
Environmental Sciences
Rashmi Chandra, Aranksha Thakor, Tizazu H. Mekonnen, Trevor C. Charles, Hyung-Sool Lee
Summary: The production of polyhydroxyalkanoates (PHAs) with high carboxylate concentration accumulated from solid-state fermentation (SSF) of food waste (FW) was tested using Pseudomonas putida strain KT2440. The mixed-culture SSF of FW supplied in a high carboxylate concentration led to a high PHA production of 0.56 g PHA/g CDM under nutrients control. The dominant PHA building block produced was 3-hydroxybutyrate, followed by 3-hydroxy-2-methylvalerate and 3-hydroxyhexanoate, indicating that acetate, butyrate, and propionate were the main precursors to PHA.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2023)
Article
Microbiology
Meghan Donovan, Calvin S. Mackey, Michael D. J. Lynch, Grayson N. Platt, Amber N. Brown, Brian K. Washburn, Darryl J. Trickey, J. Thomas Curtis, Yan Liu, Trevor C. Charles, Zuoxin Wang, Kathryn M. Jones
Summary: Research on the role of gut microbiota in behavior has advanced significantly. The probiotic L. reuteri can affect social and stress-related behaviors, but the mechanisms behind this are still unclear. Using prairie voles, a socially-monogamous species, the study found that treatment with live L. reuteri led to decreased social affiliation compared to heat-killed L. reuteri in females but not males. There were also differences in neurochemical markers, gut microbiome composition, and behaviors between the sexes and treatments.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Xin Wei, Gabriel Moreno-Hagelsieb, Bernard R. Glick, Andrew C. Doxey
Summary: Cytokinin, the plant hormone used in agriculture, is synthesized by the enzyme Isopentenyl transferase (IPT). Comparisons of IPT genes between plant pathogens and plant growth-promoting bacteria (PGPB) show differences in gene structure, regulation, and activity levels, which may determine their effects on host plants.
Review
Microbiology
Angela Sessitsch, Steve Wakelin, Michael Schloter, Emmanuelle Maguin, Tomislav Cernava, Marie-Christine Champomier-Verges, Trevor C. Charles, Paul D. Cotter, Ilario Ferrocino, Aicha Kriaa, Pedro Lebre, Don Cowan, Lene Lange, Seghal Kiran, Lidia Markiewicz, Annelein Meisner, Marta Olivares, Inga Sarand, Bettina Schelkle, Joseph Selvin, Hauke Smidt, Leo van Overbeek, Gabriele Berg, Luca Cocolin, Yolanda Sanz, Wilson Lemos Fernandes, S. J. Liu, Matthew Ryan, Brajesh Singh, Tanja Kostic
Summary: Microbiomes play crucial roles in ecosystem functioning, supporting planetary health through nutrient cycling, climate regulation, and water filtration. They are closely associated with complex multicellular organisms and contribute to the health of their hosts. However, there is still limited understanding of microbiome transfer and connectivity.
MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS
(2023)
Article
Multidisciplinary Sciences
Julie E. Hernandez-Salmeron, Tanya Irani, Gabriel Moreno-Hagelsieb
Summary: Average Nucleotide Identity (ANI) is a standard measure for bacterial species delimitation, but its calculation time is often longer than similarity estimates based on short nucleotide sampling. In this study, two sketching programs, mash and dashing, were compared to ANI in delimiting species among Esterobacterales genomes. The results showed that fast estimates of genome similarity were as accurate as ANI for species delimitation, indicating their potential use in efficient bacterial identification and clustering.
Review
Biotechnology & Applied Microbiology
Nicole LeBlanc, Trevor C. Charles
Summary: Bacterial cells are commonly used for the production of value-added products. However, their own metabolism, genetic instability, and the toxicity of the product often hinder efficient production. Genome reductions have been performed to create strains that can serve as chassis for downstream applications. Despite improvements in cellular characteristics, the construction of these cells efficiently and rapidly remains a major challenge.
FRONTIERS IN GENOME EDITING
(2022)