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Ganbat D, Ganbat S, Sung JY, Kim SB, Lee DW, Lee SJ. Complete genome sequence of a polyhydroxyalkaonate-accumulating bacterium, Schlegelella aquatica HS-12-14, isolated from a Korean hot spring. Microbiol Resour Announc 2025; 14:e0122624. [PMID: 39868777 PMCID: PMC11895455 DOI: 10.1128/mra.01226-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2024] [Accepted: 12/11/2024] [Indexed: 01/28/2025] Open
Abstract
We present the complete genome sequence of polyhydroxyalkaonate-accumulating moderately thermophilic Schlegelella aquatica HS-12-14 strain, isolated from a Korean hot spring. These findings contribute to valuable insights into the biosynthesis of polyhydroxyalkaonates in thermophiles and enhance understanding of Schlegelella strains.
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Affiliation(s)
- Dariimaa Ganbat
- Department of Bioscience and Research Center for Extremophiles and Marine Microbiology, Silla University, Busan, South Korea
| | - Sondor Ganbat
- Department of Bioscience and Research Center for Extremophiles and Marine Microbiology, Silla University, Busan, South Korea
| | - Jae-Yoon Sung
- Department of Biotechnology, Yonsei University, Seoul, South Korea
| | - Seong-Bo Kim
- Bio-Living Engineering Major, Global Leaders College, Yonsei University, Seoul, South Korea
| | - Dong-Woo Lee
- Department of Biotechnology, Yonsei University, Seoul, South Korea
| | - Sang-Jae Lee
- Department of Bioscience and Research Center for Extremophiles and Marine Microbiology, Silla University, Busan, South Korea
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Grybchuk‐Ieremenko A, Lipovská K, Kouřilová X, Obruča S, Dvořák P. An Initial Genome Editing Toolset for Caldimonas thermodepolymerans, the First Model of Thermophilic Polyhydroxyalkanoates Producer. Microb Biotechnol 2025; 18:e70103. [PMID: 39980168 PMCID: PMC11842462 DOI: 10.1111/1751-7915.70103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2024] [Revised: 01/22/2025] [Accepted: 01/24/2025] [Indexed: 02/22/2025] Open
Abstract
The limited number of well-characterised model bacteria cannot address all the challenges in a circular bioeconomy. Therefore, there is a growing demand for new production strains with enhanced resistance to extreme conditions, versatile metabolic capabilities and the ability to utilise cost-effective renewable resources while efficiently generating attractive biobased products. Particular thermophilic microorganisms fulfil these requirements. Non-virulent Gram-negative Caldimonas thermodepolymerans DSM15344 is one such attractive thermophile that efficiently converts a spectrum of plant biomass sugars into high quantities of polyhydroxyalkanoates (PHA)-a fully biodegradable substitutes for synthetic plastics. However, to enhance its biotechnological potential, the bacterium needs to be 'domesticated'. In this study, we established effective homologous recombination and transposon-based genome editing systems for C. thermodepolymerans. By optimising the electroporation protocol and refining counterselection methods, we achieved significant improvements in genetic manipulation and constructed the AI01 chassis strain with improved transformation efficiency and a ΔphaC mutant that will be used to study the importance of PHA synthesis in Caldimonas. The advances described herein highlight the need for tailored approaches when working with thermophilic bacteria and provide a springboard for further genetic and metabolic engineering of C. thermodepolymerans, which can be considered the first model of thermophilic PHA producer.
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Affiliation(s)
- Anastasiia Grybchuk‐Ieremenko
- Department of Experimental Biology (Section of Microbiology), Faculty of ScienceMasaryk UniversityBrnoCzech Republic
| | - Kristýna Lipovská
- Department of Experimental Biology (Section of Microbiology), Faculty of ScienceMasaryk UniversityBrnoCzech Republic
| | - Xenie Kouřilová
- Faculty of Chemistry, Institute of Food Science and BiotechnologyBrno University of TechnologyBrnoCzech Republic
| | - Stanislav Obruča
- Faculty of Chemistry, Institute of Food Science and BiotechnologyBrno University of TechnologyBrnoCzech Republic
| | - Pavel Dvořák
- Department of Experimental Biology (Section of Microbiology), Faculty of ScienceMasaryk UniversityBrnoCzech Republic
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Vajente M, Clerici R, Ballerstedt H, Blank LM, Schmidt S. Using Cupriavidus necator H16 to Provide a Roadmap for Increasing Electroporation Efficiency in Nonmodel Bacteria. ACS Synth Biol 2024. [PMID: 39482869 DOI: 10.1021/acssynbio.4c00380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2024]
Abstract
Bacteria are a treasure trove of metabolic reactions, but most industrial biotechnology applications rely on a limited set of established host organisms. In contrast, adopting nonmodel bacteria for the production of various chemicals of interest is often hampered by their limited genetic amenability coupled with their low transformation efficiency. In this study, we propose a series of steps that can be taken to increase electroporation efficiency in nonmodel bacteria. As a test strain, we use Cupriavidus necator H16, a lithoautotrophic bacterium that has been engineered to produce a wide range of products from CO2 and hydrogen. However, its low electroporation efficiency hampers the high-throughput genetic engineering required to develop C. necator into an industrially relevant host organism. Thus, conjugation has often been the method of choice for introducing exogenous DNA, especially when introducing large plasmids or suicide plasmids. We first propose a species-independent technique based on natively methylated DNA and Golden Gate assembly to increase one-pot cloning and electroporation efficiency by 70-fold. Second, bioinformatic tools were used to predict defense systems and develop a restriction avoidance strategy that was used to introduce suicide plasmids by electroporation to obtain a domesticated strain. The results are discussed in the context of metabolic engineering of nonmodel bacteria.
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Affiliation(s)
- Matteo Vajente
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen 9713AV, The Netherlands
| | - Riccardo Clerici
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Hendrik Ballerstedt
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Lars M Blank
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Sandy Schmidt
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen 9713AV, The Netherlands
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Chen W, Liu Z, Sun W, Li S, Liu J, Huo W, Jia J, Shen W, Wang Y, Chen G. Electrotransformation of Foodborne Pathogen Cronobacter sakazakii by a Simple Method. Foodborne Pathog Dis 2024; 21:61-67. [PMID: 37856143 DOI: 10.1089/fpd.2023.0048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023] Open
Abstract
Cronobacter sakazakii is an opportunistic foodborne pathogen that mainly infects infants and immunocompromised people, with a high mortality rate. However, the efficient transformation method of this bacterium has not been systematically reported. In this study, we developed a fast and efficient transformation method for C. sakazakii by cold sucrose treatment. Compared with CaCl2 or glycerol treatment, the transformation efficiency of this method is significantly high when bacteria were cultured overnight at 42°C before cold sucrose treatment. Furthermore, applying this method, we successfully knocked out the pppA gene by direct electroporation. Collectively, our study provides a simple, time-saving, and efficient method for competent cell preparation of C. sakazakii, which is conducive to the further research of C. sakazakii.
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Affiliation(s)
- Wei Chen
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
- School of Medicine, Northwest University, Xi'an, China
| | - Zhimeng Liu
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
- School of Medicine, Northwest University, Xi'an, China
| | - Wenjie Sun
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
- School of Medicine, Northwest University, Xi'an, China
| | - Siqi Li
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
- School of Medicine, Northwest University, Xi'an, China
| | - Jiajia Liu
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
- School of Medicine, Northwest University, Xi'an, China
| | - Weiping Huo
- School of Medicine, Northwest University, Xi'an, China
| | - Jia Jia
- School of Medicine, Northwest University, Xi'an, China
| | - Wenyan Shen
- College of Medical Technology, Shaanxi University of Chinese Medicine, Xi Xian New Area, China
| | - Yuanyuan Wang
- College of Medical Technology, Shaanxi University of Chinese Medicine, Xi Xian New Area, China
| | - Gukui Chen
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
- School of Medicine, Northwest University, Xi'an, China
- ShaanXi Provincial Key Laboratory of Biotechnology, Xi'an, China
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Ochoa-Hernández ME, Reynoso-Varela A, Martínez-Córdova LR, Rodelas B, Durán U, Alcántara-Hernández RJ, Serrano-Palacios D, Calderón K. Linking the shifts in the metabolically active microbiota in a UASB and hybrid anaerobic-aerobic bioreactor for swine wastewater treatment. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 344:118435. [PMID: 37379625 DOI: 10.1016/j.jenvman.2023.118435] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 06/05/2023] [Accepted: 06/14/2023] [Indexed: 06/30/2023]
Abstract
Due to the high concentration of pollutants, swine wastewater needs to be treated prior to disposal. The combination of anaerobic and aerobic technologies in one hybrid system allows to obtain higher removal efficiencies compared to those achieved via conventional biological treatment, and the performance of a hybrid system depends on the microbial community in the bioreactor. Here, we evaluated the community assembly of an anaerobic-aerobic hybrid reactor for swine wastewater treatment. Sequencing of partial 16S rRNA coding genes was performed using Illumina from DNA and retrotranscribed RNA templates (cDNA) extracted from samples from both sections of the hybrid system and from a UASB bioreactor fed with the same swine wastewater influent. Proteobacteria and Firmicutes were the dominant phyla and play a key role in anaerobic fermentation, followed by Methanosaeta and Methanobacterium. Several differences were found in the relative abundances of some genera between the DNA and cDNA samples, indicating an increase in the diversity of the metabolically active community, highlighting Chlorobaculum, Cladimonas, Turicibacter and Clostridium senso stricto. Nitrifying bacteria were more abundant in the hybrid bioreactor. Beta diversity analysis revealed that the microbial community structure significantly differed among the samples (p < 0.05) and between both anaerobic treatments. The main predicted metabolic pathways were the biosynthesis of amino acids and the formation of antibiotics. Also, the metabolism of C5-branched dibasic acid, Vit B5 and CoA, exhibited an important relationship with the main nitrogen-removing microorganisms. The anaerobic-aerobic hybrid bioreactor showed a higher ammonia removal rate compared to the conventional UASB system. However, further research and adjustments are needed to completely remove nitrogen from wastewater.
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Affiliation(s)
- María E Ochoa-Hernández
- Departamento de Investigaciones Científicas y Tecnológicas, Universidad de Sonora, Blvd. Luis Donaldo Colosio S/N. CP., 83000, Hermosillo, Sonora, Mexico
| | - Andrea Reynoso-Varela
- Departamento de Ciencias del Agua y Medio Ambiente, Instituto Tecnológico de Sonora, 5 de febrero 818 Sur., Ciudad Obregón, Sonora, CP.85000, Mexico
| | - Luis R Martínez-Córdova
- Departamento de Investigaciones Científicas y Tecnológicas, Universidad de Sonora, Blvd. Luis Donaldo Colosio S/N. CP., 83000, Hermosillo, Sonora, Mexico
| | - Belén Rodelas
- Department of Microbiology and Institute of Water Research, University of Granada, Spain
| | - Ulises Durán
- Universidad Autónoma Metropolitana, Biotechnology Dept., P.A. 55-535, 09340, Iztapalapa, Mexico City, Mexico
| | - Rocío J Alcántara-Hernández
- Instituto de Geología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Av. Universidad 3000, Del. Coyoacán, 04510, Ciudad de México, Mexico
| | - Denisse Serrano-Palacios
- Departamento de Ciencias del Agua y Medio Ambiente, Instituto Tecnológico de Sonora, 5 de febrero 818 Sur., Ciudad Obregón, Sonora, CP.85000, Mexico.
| | - Kadiya Calderón
- Departamento de Investigaciones Científicas y Tecnológicas, Universidad de Sonora, Blvd. Luis Donaldo Colosio S/N. CP., 83000, Hermosillo, Sonora, Mexico.
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Expansion of the Plaquing Host Range and Improvement of the Absorption Rate of a T5-like Salmonella Phage by Altering the Long Tail Fibers. Appl Environ Microbiol 2022; 88:e0089522. [PMID: 35969059 PMCID: PMC9469705 DOI: 10.1128/aem.00895-22] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The high host specificity of phages is a real challenge in the therapy applications of the individual phages. This study aimed to edit the long tail fiber proteins (pb1) of a T5-like phage to obtain the engineered phages with expanded plaquing host range. Two T5-like Salmonella phages with high genome sequence homology but different plaquing host ranges, narrow-host range phage vB STyj5-1 (STyj5-1) and wide-host range phage vB BD13 (BD13), were isolated and characterized. The pb1 parts of STyj5-1 were replaced by the corresponding part of BD13 using homologous recombination method to obtain the engineered phages. The alterations of the whole pb1 part or the N-terminal amino acids 1-400 of pb1 of STyj5-1 could expand their plaquing host ranges (from 20 strains to 30 strains) and improve their absorption rates (from 0.28-28.84% to 28.10-99.49%). Besides, the one-step growth curves of these engineered phages with modified pb1 parts were more similar to that of STyj5-1. The burst sizes of phages BD13, STyj5-1 and the engineered phages were 250, 236, 166, and 223 PFU per cell, respectively. The expanded plaquing host range and improved absorption rates of these engineered phages revealed that the pb1 part might be the primary determinant of the host specificities of some T5-like phages. IMPORTANCE Genetic editing can be used to change or expand the host range of phages and have been successfully applied in T2, T4 and other phages to obtain engineered phages. However, there are hardly any similar reports on T5-like phages due to that the determinant regions related to their host ranges have not been completely clarified and the editing of T5-like phages is more difficult compared to other phages. This study attempted and successfully expanded the host range of a narrow-host range T5-like phage (STyj5-1) by exchanging its whole pb1 part or the N-terminal 1-400aa of that part by a broad-host range phage (BD13). These demonstrated the pb1 part might be the primary determinant of the host specificities for some T5-like phages and provided an effective method of extension plaquing host range of these phages.
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Zhang N, He J, Muhammad A, Shao Y. CRISPR/Cas9–Mediated Genome Editing for Pseudomonas fulva, a Novel Pseudomonas Species with Clinical, Animal, and Plant–Associated Isolates. Int J Mol Sci 2022; 23:ijms23105443. [PMID: 35628253 PMCID: PMC9145825 DOI: 10.3390/ijms23105443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/08/2022] [Accepted: 05/09/2022] [Indexed: 12/23/2022] Open
Abstract
As one of the most widespread groups of Gram–negative bacteria, Pseudomonas bacteria are prevalent in almost all natural environments, where they have developed intimate associations with plants and animals. Pseudomonas fulva is a novel species of Pseudomonas with clinical, animal, and plant–associated isolates, closely related to human and animal health, plant growth, and bioremediation. Although genetic manipulations have been proven as powerful tools for understanding bacterial biological and biochemical characteristics and the evolutionary origins, native isolates are often difficult to genetically manipulate, thereby making it a time–consuming and laborious endeavor. Here, by using the CRISPR–Cas system, a versatile gene–editing tool with a two–plasmid strategy was developed for a native P. fulva strain isolated from the model organism silkworm (Bombyx mori) gut. We harmonized and detailed the experimental setup and clarified the optimal conditions for bacteria transformation, competent cell preparation, and higher editing efficiency. Furthermore, we provided some case studies, testing and validating this approach. An antibiotic–related gene, oqxB, was knocked out, resulting in the slow growth of the P. fulva deletion mutant in LB containing chloramphenicol. Fusion constructs with knocked–in gfp exhibited intense fluorescence. Altogether, the successful construction and application of new genetic editing approaches gave us more powerful tools to investigate the functionalities of the novel Pseudomonas species.
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Affiliation(s)
- Nan Zhang
- Max Planck Partner Group, Faculty of Agriculture, Life and Environmental Sciences, Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China (A.M.)
| | - Jintao He
- Max Planck Partner Group, Faculty of Agriculture, Life and Environmental Sciences, Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China (A.M.)
| | - Abrar Muhammad
- Max Planck Partner Group, Faculty of Agriculture, Life and Environmental Sciences, Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China (A.M.)
| | - Yongqi Shao
- Max Planck Partner Group, Faculty of Agriculture, Life and Environmental Sciences, Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China (A.M.)
- Key Laboratory for Molecular Animal Nutrition, Ministry of Education, Hangzhou 310058, China
- Correspondence: ; Fax: +86-571-88982757
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