Article
Chemistry, Analytical
Musashi Takenaka, Takanobu Yoshida, Yoshimi Hori, Takahiro Bamba, Masao Mochizuki, Christopher J. Vavricka, Takanari Hattori, Yoshihiro Hayakawa, Tomohisa Hasunuma, Akihiko Kondo
Summary: Data-driven engineering of microbes for sustainable production of high-performance chemicals requires metabolic profiling analysis. A liquid chromatography-tandem mass spectrometry (LC-MS/MS) based methodology was developed to cover a wide range of target compounds with high precision. The method enabled high reproducibility, sensitivity, and accuracy in metabolomic analysis of various microorganisms, establishing it as a comprehensive tool for bioengineering applications.
Article
Chemistry, Analytical
Naoki Saito
Summary: A fresh dual pre-SAT method was developed to accurately quantify analytes near the suppressed water signal in 1H NMR spectra from H2O-rich samples. The method includes an extra dummy pre-SAT with a suitable offset for each analyte signal, in addition to the water pre-SAT. The proposed method achieved accurate quantification of glycine and maleic acid in D2O/H2O solutions.
ANALYTICAL CHEMISTRY
(2023)
Article
Microbiology
Junhyeong Kim, Allen H. Goldstein, Romy Chakraborty, Kolby Jardine, Robert Weber, Patrick O. Sorensen, Shi Wang, Boris Faybishenko, Pawel K. Misztal, Eoin L. Brodie
Summary: Snowmelt dynamics play a significant role in regulating microbial metabolism in soil and affecting global biogeochemical cycles. This study utilized PTR-TOF-MS technology to investigate microbial metabolic trajectories and responses in a subalpine forest soil, revealing robust interactions between microbial volatile compounds and key metabolites such as trimethylamine (TMA). The findings suggest the importance of understanding microbial responses to environmental perturbations for soil ecosystem dynamics.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Gastroenterology & Hepatology
Henrik M. Roager, Catherine Stanton, Lindsay J. Hall
Summary: The development of the infant gut microbiome is crucial for the microbiome ecology, function, and host health. Technological advancements now allow for better profiling of metabolites in the infant gut, providing insights into the roles of microbial-derived metabolites in shaping the microbiome community and influencing host-microbial interactions during early life. This review summarizes the current knowledge on the development of the infant gut microbiota and metabolism within the first year of life, emphasizing the importance of microbial metabolites in enhancing our understanding of early life interactions.
Article
Biochemical Research Methods
Hendri Wasito, Gerrit Hermann, Veronika Fitz, Christina Troyer, Stephan Hann, Gunda Koellensperger
Summary: The study introduced a new concept of yeast-derived biological matrix reference material for metabolomics research, demonstrating its feasibility and effectiveness through standardized extraction and absolute quantification. The method proved to be fit for purpose, with control ranges showing superior or comparable results to established reference materials in the field.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Mir Henglin, Brian L. Claggett, Joseph Antonelli, Mona Alotaibi, Gino Alberto Magalang, Jeramie D. Watrous, Kim A. Lagerborg, Gavin Ovsak, Gabriel Musso, Olga V. Demler, Ramachandran S. Vasan, Martin G. Larson, Mohit Jain, Susan Cheng
Summary: This study compares the performance of traditional and newer statistical learning methods in different types of metabolomics data and finds that, in the analysis of human metabolomics data, multivariate methods perform better than univariate methods as the number of study subjects increases.
Article
Environmental Sciences
Jing Ding, Hongwei Sun, Aiping Liang, Jin Liu, Lehui Song, Min Lv, Dong Zhu
Summary: The exposure to testosterone significantly altered the bacterial community structure and metabolic profiles in soils in Ningbo and Kunming, China. This resulted in a decrease in the abundance of bacterial taxa associated with nutrient cycling and downregulation of metabolites related to amino acid metabolism. The close connection between bacterial taxa and specific metabolites was confirmed by Procrustes tests and a co-occurrence network analysis.
ENVIRONMENTAL POLLUTION
(2021)
Review
Engineering, Environmental
Elizabeth A. McDaniel, Sebastian Aljoscha Wahl, Shun' ichi Ishii, Ameet Pinto, Ryan Ziels, Per Halkjaer Nielsen, Katherine D. McMahon, Rohan B. H. Williams
Summary: Advances in high-throughput sequencing technologies and bioinformatics approaches over the last three decades have greatly enhanced our ability to explore microorganisms and their functions. Genome-resolved metagenomic approaches have enabled more accurate linking of functional predictions with specific taxonomical groups. These developments have shifted microbiome science towards mechanistic and predictive frameworks, allowing for the design and utilization of microbial communities for desired beneficial outcomes.
Article
Microbiology
Anais Cario, Marina Larzilliere, Olivier Nguyen, Karine Alain, Samuel Marre
Summary: In this study, a novel methodology based on high-pressure microfluidics was developed for rapid temperature-based phenotyping of microbial strains from deep-sea environments. The main advantage lies in the ability to achieve multiple on-chip temperature conditions at pressures representative of the deep-sea in a single experiment, overcoming the limitations of conventional large-scale batch metal reactors. Results showed that the growth of the model strain Thermococcus barophilus could be monitored over 40 temperature and pressure conditions in just 1 week without any decompression, which is significantly faster compared to conventional approaches. The robustness of this methodology was further demonstrated with an additional example using a hydrogenotrophic methanogen strain.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Eun Ju Yun, Seung-Oh Seo, Suryang Kwak, Eun Joong Oh, Sun-Hee Lee, Yong-Su Jin, Kyoung Heon Kim
Summary: The study showed that the cold methanol quenching method resulted in severe losses of intracellular metabolites, while the fast filtration method better preserved most metabolites with less extracellular contamination. This suggests that the fast filtration method with a vacuum manifold system can be widely applied to yeast metabolome analysis due to its simplicity, robustness, and lack of significant intracellular metabolite loss.
PROCESS BIOCHEMISTRY
(2021)
Article
Computer Science, Software Engineering
Daqi Lin, Chris Wyman, Cem Yuksel
Summary: In this study, a new direct illumination sampling technique is extended to multi-dimensional path space for volumetric media, resulting in efficient convergence of the volumetric path tracer. Through proper estimation of the sample's probability, the method achieves low-noise, interactive volumetric rendering.
ACM TRANSACTIONS ON GRAPHICS
(2021)
Article
Engineering, Environmental
Robert W. Brown, David R. Chadwick, Huadong Zang, Martine Graf, Xuejun Liu, Kai Wang, Lucy M. Greenfield, Davey L. Jones
Summary: Microplastic contamination is a significant threat to agroecosystem functioning. Biodegradable alternatives have been explored, however, their impact on plant and soil health has been relatively ignored. This study investigated the effects of biobased microplastic PHBV on soil and plant health and function. The results showed that PHBV caused a dose-dependent reduction in plant growth and foliar nitrogen content, and also led to shifts in foliar metabolic function, reduced availability of ammonium and nitrate in soil, and suppressed microbial activity and diversity.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Article
Environmental Sciences
Maya E. Natnan, Chen-Fei Low, Chou-Min Chong, Hamidun Bunawan, Syarul N. Baharum
Summary: The increasing demand for fish protein has led to a rise in fish production through aquaculture and wild capture. Pathogen infections in hatcheries and grow-out ponds have resulted in reduced productivity and economic losses for farmers. Utilizing omics datasets and systems biology approaches can help scientists understand complex host-pathogen interactions and identify new targets for combating diseases in aquaculture. Various omics approaches such as genomics, transcriptomics, proteomics, and metabolomics are valuable tools in developing treatment and prevention strategies to address aquaculture diseases caused by microbial infections.
FRONTIERS IN MARINE SCIENCE
(2021)
Review
Plant Sciences
Mohamed A. Salem, Jian You Wang, Salim Al-Babili
Summary: Plants release chemical compounds into the rhizosphere, which plays important roles in inhibiting harmful microorganisms and promoting beneficial microbes, with applications in crop yield and phytoremediation.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Chemistry, Analytical
Wangjie Lv, Zhongda Zeng, Yuqing Zhang, Qingqing Wang, Lichao Wang, Zhaoxuan Zhang, Xianzhe Shi, Xinjie Zhao, Guowang Xu
Summary: In this study, an alternate RPLC-MS method was developed to quantitatively determine metabolites and lipids. A wide set of reference standards and real samples were used to define multiple reaction monitoring (MRM) transitions for metabolomic and lipidomic analyses, resulting in the quantification of over 1000 metabolites and lipids. The developed method showed good analytical characteristics and was successfully validated using standard reference material.
ANALYTICA CHIMICA ACTA
(2022)
Review
Biochemical Research Methods
Pei-Ru Chen, Peng-Fei Xia
Summary: Carbon dioxide plays a crucial role in mitigating global climate change and supporting life on Earth. Synthetic biology and metabolic engineering offer a promising approach to enhance CO2 fixation by combining the advantages of autotrophic and heterotrophic organisms. This article reviews the current progress in constructing synthetic CO2 fixation pathways, discusses the underlying design principles and challenges, and provides insights into the future of carbon recycling through engineered synthetic carbon fixation pathways.
CURRENT OPINION IN BIOTECHNOLOGY
(2024)
