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Guo X, Ren J, Zhou X, Zhang M, Lei C, Chai R, Zhang L, Lu D. Strategies to improve the efficiency and quality of mutant breeding using heavy-ion beam irradiation. Crit Rev Biotechnol 2024; 44:735-752. [PMID: 37455421 DOI: 10.1080/07388551.2023.2226339] [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] [Received: 08/09/2022] [Accepted: 04/15/2023] [Indexed: 07/18/2023]
Abstract
Heavy-ion beam irradiation (HIBI) is useful for generating new germplasm in plants and microorganisms due to its ability to induce high mutagenesis rate, broad mutagenesis spectrum, and excellent stability of mutants. However, due to the random mutagenesis and associated mutant breeding modalities, it is imperative to improve HIBI-based mutant breeding efficiency and quality. This review discusses and summarizes the findings of existing theoretical and technical studies and presents a set of tandem strategies to enable efficient and high-quality HIBI-based mutant breeding practices. These strategies: adjust the mutation-inducing techniques, regulate cellular response states, formulate high-throughput screening schemes, and apply the generated superior genetic elements to genetic engineering approaches, thereby, improving the implications and expanding the scope of HIBI-based mutant breeding. These strategies aim to improve the mutagenesis rate, screening efficiency, and utilization of positive mutations. Here, we propose a model based on the integration of these strategies that would leverage the advantages of HIBI while compensating for its present shortcomings. Owing to the unique advantages of HIBI in creating high-quality genetic resources, we believe this review will contribute toward improving HIBI-based breeding.
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Affiliation(s)
- Xiaopeng Guo
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, China
| | - Junle Ren
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiang Zhou
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Miaomiao Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Cairong Lei
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ran Chai
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, China
| | - Lingxi Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Dong Lu
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
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Wu R, Ji P, Hua Y, Li H, Zhang W, Wei Y. Research progress in isolation and identification of rumen probiotics. Front Cell Infect Microbiol 2024; 14:1411482. [PMID: 38836057 PMCID: PMC11148321 DOI: 10.3389/fcimb.2024.1411482] [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] [Received: 04/03/2024] [Accepted: 04/30/2024] [Indexed: 06/06/2024] Open
Abstract
With the increasing research on the exploitation of rumen microbial resources, rumen probiotics have attracted much attention for their positive contributions in promoting nutrient digestion, inhibiting pathogenic bacteria, and improving production performance. In the past two decades, macrogenomics has provided a rich source of new-generation probiotic candidates, but most of these "dark substances" have not been successfully cultured due to the restrictive growth conditions. However, fueled by high-throughput culture and sorting technologies, it is expected that the potential probiotics in the rumen can be exploited on a large scale, and their potential applications in medicine and agriculture can be explored. In this paper, we review and summarize the classical techniques for isolation and identification of rumen probiotics, introduce the development of droplet-based high-throughput cell culture and single-cell sequencing for microbial culture and identification, and finally introduce promising cultureomics techniques. The aim is to provide technical references for the development of related technologies and microbiological research to promote the further development of the field of rumen microbiology research.
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Affiliation(s)
| | - Peng Ji
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
| | | | | | | | - Yanming Wei
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
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Zhang Y, Zhang X, Wang M. Product-driven high-throughput screening of industrial filamentous actinomycetes. Trends Biotechnol 2023; 41:1109-1112. [PMID: 36863908 DOI: 10.1016/j.tibtech.2023.02.004] [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] [Received: 11/11/2022] [Revised: 02/05/2023] [Accepted: 02/14/2023] [Indexed: 03/04/2023]
Abstract
Traditional strain breeding of industrial filamentous actinomycetes has long been hampered by insufficient screening throughput. From microtiter plate based methods to droplet-based microfluidic screening, various novel product-driven high-throughput screening (HTS) methods have pushed the screening speed limit towards a minimum of hundreds of strains per second with single cell resolution.
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Affiliation(s)
- Yue Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
| | - Xuemei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; Haihe Laboratory of Synthetic Biology, Tianjin 300308, China; School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Meng Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
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Vitalis C, Wenzel T. Leveraging interactions in microfluidic droplets for enhanced biotechnology screens. Curr Opin Biotechnol 2023; 82:102966. [PMID: 37390513 DOI: 10.1016/j.copbio.2023.102966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 05/31/2023] [Accepted: 06/05/2023] [Indexed: 07/02/2023]
Abstract
Microfluidic droplet screens serve as an innovative platform for high-throughput biotechnology, enabling significant advancements in discovery, product optimization, and analysis. This review sheds light on the emerging trends of interaction assays in microfluidic droplets, underscoring the unique suitability of droplets for these applications. Encompassing a diverse range of biological entities such as antibodies, enzymes, DNA, RNA, various microbial and mammalian cell types, drugs, and other molecules, these assays demonstrate their versatility and scope. Recent methodological breakthroughs have escalated these screens to novel scales of bioanalysis and biotechnological product design. Moreover, we highlight pioneering advancements that extend droplet-based screens into new domains: cargo delivery within human bodies, application of synthetic gene circuits in natural environments, 3D printing, and the development of droplet structures responsive to environmental signals. The potential of this field is profound and only set to increase.
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Affiliation(s)
- Carolus Vitalis
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Macul 7820244, Santiago, Chile
| | - Tobias Wenzel
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Macul 7820244, Santiago, Chile.
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Wang Y, Li S, Xue N, Wang L, Zhang X, Zhao L, Guo Y, Zhang Y, Wang M. Modulating Sensitivity of an Erythromycin Biosensor for Precise High-Throughput Screening of Strains with Different Characteristics. ACS Synth Biol 2023; 12:1761-1771. [PMID: 37198736 DOI: 10.1021/acssynbio.3c00059] [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: 05/19/2023]
Abstract
Genetically encoded biosensors are powerful tools for product-driven high-throughput screening in synthetic biology and metabolic engineering. However, most biosensors can only properly function in a limited concentration cutoff, and the incompatible performance characteristics of biosensors will lead to false positives or failure in screening. The transcription factor (TF)-based biosensors are usually organized in modular architecture and function in a regulator-depended manner, whose performance properties can be fine-tuned by modifying the expression level of the TF. In this study, we modulated the performance characteristics, including sensitivity and operating range, of an MphR-based erythromycin biosensor by fine-adjusting regulator expression levels via ribosome-binding site (RBS) engineering and obtained a panel of biosensors with varied sensitivities by iterative fluorescence-assisted cell sorting (FACS) in Escherichia coli to accommodate different screening purposes. To exemplify their application potential, two engineered biosensors with 10-fold different sensitivities were employed in the precise high-throughput screening by microfluidic-based fluorescence-activated droplet sorting (FADS) of Saccharopolyspora erythraea mutant libraries with different starting erythromycin productions, and mutants representing as high as 6.8 folds and over 100% of production improvements were obtained starting from the wild-type strain and the high-producing industrial strain, respectively. This work demonstrated a simple strategy to engineer biosensor performance properties, which was significant to stepwise strain engineering and production improvement.
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Affiliation(s)
- Yan Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Haihe Laboratory of Synthetic Biology, Tianjin 300308, China
| | - Shixin Li
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Ning Xue
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Lixian Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xuemei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Longqian Zhao
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yanmei Guo
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yue Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Meng Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
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Zhang Z, Guo Q, Wang Y, Huang H. High-throughput screening of microbial strains in large-scale microfluidic droplets. Front Bioeng Biotechnol 2023; 11:1105277. [PMID: 36970622 PMCID: PMC10037112 DOI: 10.3389/fbioe.2023.1105277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 02/17/2023] [Indexed: 03/12/2023] Open
Abstract
The transformation of engineered microbial cells is a pivotal link in green biomanufacturing. Its distinctive research application involves genetic modification of microbial chassis to impart targeted traits and functions for effective synthesis of the desired products. Microfluidics, as an emerging complementary solution, focuses on controlling and manipulating fluid in channels at the microscopic scale. One of its subcategories is droplet-based microfluidics (DMF), which can generate discrete droplets using immiscible multiphase fluids at kHz frequencies. To date, droplet microfluidics has been successfully applied to a variety of microbes, including bacteria, yeast, and filamentous fungi, and the detection of massive metabolites of strain products, such as polypeptides, enzymes, and lipids, has been realized. In summary, we firmly believe that droplet microfluidics has evolved into a powerful technology that will pave the way for high-throughput screening of engineered microbial strains in the green biomanufacturing industry.
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Affiliation(s)
- Zhidong Zhang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences/ Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, Xinjiang, China
| | - Qi Guo
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Yuetong Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
- *Correspondence: Yuetong Wang, ; He Huang,
| | - He Huang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
- *Correspondence: Yuetong Wang, ; He Huang,
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Chen L, Guo X, Sun X, Zhang S, Wu J, Yu H, Zhang T, Cheng W, Shi Y, Pan L. Porous Structural Microfluidic Device for Biomedical Diagnosis: A Review. MICROMACHINES 2023; 14:547. [PMID: 36984956 PMCID: PMC10051279 DOI: 10.3390/mi14030547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 06/18/2023]
Abstract
Microfluidics has recently received more and more attention in applications such as biomedical, chemical and medicine. With the development of microelectronics technology as well as material science in recent years, microfluidic devices have made great progress. Porous structures as a discontinuous medium in which the special flow phenomena of fluids lead to their potential and special applications in microfluidics offer a unique way to develop completely new microfluidic chips. In this article, we firstly introduce the fabrication methods for porous structures of different materials. Then, the physical effects of microfluid flow in porous media and their related physical models are discussed. Finally, the state-of-the-art porous microfluidic chips and their applications in biomedicine are summarized, and we present the current problems and future directions in this field.
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Affiliation(s)
| | | | - Xidi Sun
- Correspondence: (X.S.); (Y.S.); (L.P.)
| | | | | | | | | | | | - Yi Shi
- Correspondence: (X.S.); (Y.S.); (L.P.)
| | - Lijia Pan
- Correspondence: (X.S.); (Y.S.); (L.P.)
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Ding Q, Ye C. Microbial cell factories based on filamentous bacteria, yeasts, and fungi. Microb Cell Fact 2023; 22:20. [PMID: 36717860 PMCID: PMC9885587 DOI: 10.1186/s12934-023-02025-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 01/20/2023] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Advanced DNA synthesis, biosensor assembly, and genetic circuit development in synthetic biology and metabolic engineering have reinforced the application of filamentous bacteria, yeasts, and fungi as promising chassis cells for chemical production, but their industrial application remains a major challenge that needs to be solved. RESULTS As important chassis strains, filamentous microorganisms can synthesize important enzymes, chemicals, and niche pharmaceutical products through microbial fermentation. With the aid of metabolic engineering and synthetic biology, filamentous bacteria, yeasts, and fungi can be developed into efficient microbial cell factories through genome engineering, pathway engineering, tolerance engineering, and microbial engineering. Mutant screening and metabolic engineering can be used in filamentous bacteria, filamentous yeasts (Candida glabrata, Candida utilis), and filamentous fungi (Aspergillus sp., Rhizopus sp.) to greatly increase their capacity for chemical production. This review highlights the potential of using biotechnology to further develop filamentous bacteria, yeasts, and fungi as alternative chassis strains. CONCLUSIONS In this review, we recapitulate the recent progress in the application of filamentous bacteria, yeasts, and fungi as microbial cell factories. Furthermore, emphasis on metabolic engineering strategies involved in cellular tolerance, metabolic engineering, and screening are discussed. Finally, we offer an outlook on advanced techniques for the engineering of filamentous bacteria, yeasts, and fungi.
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Affiliation(s)
- Qiang Ding
- grid.252245.60000 0001 0085 4987School of Life Sciences, Anhui University, Hefei, 230601 China ,grid.252245.60000 0001 0085 4987Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei, 230601 Anhui China ,Anhui Key Laboratory of Modern Biomanufacturing, Hefei, 230601 Anhui China
| | - Chao Ye
- grid.260474.30000 0001 0089 5711School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023 China
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Cephalosporin C biosynthesis and fermentation in Acremonium chrysogenum. Appl Microbiol Biotechnol 2022; 106:6413-6426. [DOI: 10.1007/s00253-022-12181-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 11/25/2022]
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