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Fukuyama Y, Shimamura S, Sakai S, Michimori Y, Sumida T, Chikaraishi Y, Atomi H, Nunoura T. Development of a rapid and highly accurate method for 13C tracer-based metabolomics and its application on a hydrogenotrophic methanogen. ISME COMMUNICATIONS 2024; 4:ycad006. [PMID: 38282645 PMCID: PMC10809761 DOI: 10.1093/ismeco/ycad006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 11/24/2023] [Accepted: 12/01/2023] [Indexed: 01/30/2024]
Abstract
Microfluidic capillary electrophoresis-mass spectrometry (CE-MS) is a rapid and highly accurate method to determine isotopomer patterns in isotopically labeled compounds. Here, we developed a novel method for tracer-based metabolomics using CE-MS for underivatized proteinogenic amino acids. The method consisting of a ZipChip CE system and a high-resolution Orbitrap Fusion Tribrid mass spectrometer allows us to obtain highly accurate data from 1 μl of 100 nmol/l amino acids comparable to a mere 1 [Formula: see text] 104-105 prokaryotic cells. To validate the capability of the CE-MS method, we analyzed 16 protein-derived amino acids from a methanogenic archaeon Methanothermobacter thermautotrophicus as a model organism, and the mass spectra showed sharp peaks with low mass errors and background noise. Tracer-based metabolome analysis was then performed to identify the central carbon metabolism in M. thermautotrophicus using 13C-labeled substrates. The mass isotopomer distributions of serine, aspartate, and glutamate revealed the occurrence of both the Wood-Ljungdahl pathway and an incomplete reductive tricarboxylic acid cycle for carbon fixation. In addition, biosynthesis pathways of 15 amino acids were constructed based on the mass isotopomer distributions of the detected protein-derived amino acids, genomic information, and public databases. Among them, the presence of alternative enzymes of alanine dehydrogenase, ornithine cyclodeaminase, and homoserine kinase was suggested in the biosynthesis pathways of alanine, proline, and threonine, respectively. To our knowledge, the novel 13C tracer-based metabolomics using CE-MS can be considered the most efficient method to identify central carbon metabolism and amino acid biosynthesis pathways and is applicable to any kind of isolated microbe.
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Affiliation(s)
- Yuto Fukuyama
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima-cho, Yokosuka, Kanagawa 237–0061, Japan
| | - Shigeru Shimamura
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima-cho, Yokosuka, Kanagawa 237–0061, Japan
| | - Sanae Sakai
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima-cho, Yokosuka, Kanagawa 237–0061, Japan
| | - Yuta Michimori
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Tomomi Sumida
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima-cho, Yokosuka, Kanagawa 237–0061, Japan
| | - Yoshito Chikaraishi
- Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo 060-0819, Japan
| | - Haruyuki Atomi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima-cho, Yokosuka, Kanagawa 237–0061, Japan
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Hu H, Hao M, Wang H, Hao H, Lu Z, Shi B. Occurrence of metals, phthalate esters, and perfluoroalkyl substances in cellar water and their relationship with bacterial community in rural areas of China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 900:165876. [PMID: 37517737 DOI: 10.1016/j.scitotenv.2023.165876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/20/2023] [Accepted: 07/27/2023] [Indexed: 08/01/2023]
Abstract
Water cellars are traditional rainwater harvesting facilities that have been widely used in rural areas of northwest China. However, there are few reports about the water quality and health risk caused by the cellar water, especially phthalate esters (PAEs) and perfluoroalkyl substances (PFASs). This study investigated and assessed the health risks caused by the metals, PAEs, PFASs and bacterial communities in cellar water. The results showed that the turbidity and total number of bacterial colonies ranged from 4.7 to 58.5 NTU and 5-557 CFU/mL, respectively. The turbidity and total number of bacterial colonies were the main water quality problems. Due to high concentration of Tl (0.005-0.171 μg/L), the samples reached a high level of metal pollution. PAEs showed no non-carcinogenic and carcinogenic risk. The perfluorobutanoic acid (PFBA), perfluorobutanesulfonic acid (PFBS), perfluorooctanoic acid (PFOA), and perfluorooctane sulfonate (PFOS) were the main components of PFASs. PFOA and PFOS reached a moderate risk level in many cellar water samples. Moreover, Tl, Pb, As, PFBA and PFBS could change the bacterial community composition and induce the enrichment of bacterial functions related to human diseases. Besides these parameters, dissolved oxygen (DO) also affected the bacterial functions related to human diseases. Therefore, more attention should be paid to turbidity, DO, Tl, Pb, As, PFOA, PFOS, PFBA and PFBS in the cellar water. These results are meaningful for the water quality guarantee and health protection in rural areas of China.
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Affiliation(s)
- Haotian Hu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Mingming Hao
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Haibo Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Haotian Hao
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Zhili Lu
- Institute of Environmental and Municipal Engineering, North China University of Water Resources and Electric Power, Zhengzhou 450045, China
| | - Baoyou Shi
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
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Ding S, Tian M, Yang L, Pan Y, Suo L, Zhu X, Ren D, Yu H. Diversity and dynamics of microbial population during fermentation of gray sufu and their correlation with quality characteristics. Lebensm Wiss Technol 2023. [DOI: 10.1016/j.lwt.2023.114711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
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Gupta RK, Singh AK, Bajaj A, Khardenavis AA, Purohit HJ. Phylogenomic analysis of Citrobacter sp. strain AAK_AS5 and its metabolic capabilities to support nitrogen removal behavior. J Basic Microbiol 2023; 63:359-376. [PMID: 36453555 DOI: 10.1002/jobm.202200323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 09/02/2022] [Accepted: 10/22/2022] [Indexed: 12/03/2022]
Abstract
Despite the ubiquity of the genus Citrobacter in clinical, industrial, and environmental scenarios, a large number of Citrobacter strains have not been explored at the genome-scale level. In this study, accurate taxonomic assignment of strain AAK_AS5 isolated from activated sludge was achieved by in-silico genomic comparison using Overall Genome-based Relatedness Indices (ANI(OAT): 97.55%, ANIb:97.28%, and ANIm: 97.83%) that indicated its closest identity to the related strain Citrobacter portucalensis A60T . Results were consistent with a digital DNA-DNA hybridization value of 80% with C. portucalensis A60T which was greater than the species boundary value >70% for delineating closely related bacterial species. Gene mining through Kyoto Encyclopedia of Genes and Genomes (KEGG), and annotation using rapid annotation subsystem technology (RAST) revealed the notable gene contents for nitrogen metabolism and other pathways associated with nitrate/nitrite ammonification (28 genes), ammonia assimilation (22 genes), and denitrification pathways (14 genes). Furthermore, the strain AAK_AS5 also exhibited a high soluble chemical oxygen demand (sCOD), NH4 + -N, and NO3 - -N removal efficiency of 91.4%, 90%, and 93.6%, respectively thus validating its genetic capability for utilizing both (NH4 )2 SO4 and KNO3 as the nitrogen source. The study provided deeper insights into the phylogenomics and the genetic potential of Citrobacter, sp. strain AAK AS5 associated with nitrogen metabolism thus signifying the potential application of the isolate for treating nitrogen-rich wastewaters.
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Affiliation(s)
- Rakesh K Gupta
- Environmental Biotechnology and Genomics Division (EBGD), CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Ashish K Singh
- Environmental Biotechnology and Genomics Division (EBGD), CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Abhay Bajaj
- Environmental Biotechnology and Genomics Division (EBGD), CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Anshuman A Khardenavis
- Environmental Biotechnology and Genomics Division (EBGD), CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Hemant J Purohit
- Environmental Biotechnology and Genomics Division (EBGD), CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, India
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Shrestha P, Karmacharya J, Han SR, Park H, Oh TJ. In silico analysis and a comparative genomics approach to predict pathogenic trehalase genes in the complete genome of Antarctica Shigella sp. PAMC28760. Virulence 2022; 13:1502-1514. [PMID: 36040103 PMCID: PMC9450901 DOI: 10.1080/21505594.2022.2117679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Although four Shigella species (S. flexneri, S. sonnei, S. dysenteriae, and S. boydii) have been reported, S. sp. PAMC 28760, an Antarctica isolate, is the only one with a complete genome deposited in NCBI database as an uncharacterized isolate. Because it is the world’s driest, windiest, and coldest continent, Antarctica provides an unfavourable environment for microorganisms. Computational analysis of genomic sequences of four Shigella species and our uncategorized Antarctica isolates Shigella sp. PAMC28760 was performed using MP3 (offline version) program to predict trehalase encoding genes as a pathogenic or non-pathogenic form. Additionally, we employed RAST and Prokka (offline version) annotation programs to determine locations of periplasmic (treA) and cytoplasmic (treF) trehalase genes in studied genomes. Our results showed that only 56 out of 134 Shigella strains had two different trehalase genes (treF and treA). It was revealed that the treF gene tends to be prevalent in Shigella species. In addition, both treA and treF genes were present in our strain S. sp. PAMC28760. The main objective of this study was to predict the prevalence of two different trehalase genes (treF and treA) in the complete genome of Shigella sp. PAMC28760 and other complete genomes of Shigella species. Till date, it is the first study to show that two types of trehalase genes are involved in Shigella species, which could offer insight on how the bacteria use accessible carbohydrate like glucose produced from the trehalose degradation pathway, and importance of periplasmic trehalase involvement in bacterial virulence.
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Affiliation(s)
- Prasansah Shrestha
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, Korea
| | - Jayram Karmacharya
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, Korea
| | - So-Ra Han
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, Korea
| | - Hyun Park
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Korea
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, Korea.,Department of Life Science and Biochemical Engineering, SunMoon Univesity, Genome-based BioIT Convergence Institute, Asan, Korea.,Department of Pharmaceutical Engineering and Biotechnology, SunMoon University, Asan, Korea
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Bao W, He Y, Yu J, Yang X, Liu M, Ji R. Diversity analysis and gene function prediction of bacteria and fungi of Bactrian camel milk and naturally fermented camel milk from Alxa in Inner Mongolia. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.114001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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