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Phillips EK, Cannon JA, Zhou Y, Bonifer KS, Reynolds TB. Conjugation-Mediated Plasmid Transfer Enables Genetic Modification of Diverse Bacillus Species. Microbiol Spectr 2023; 11:e0370022. [PMID: 36975796 PMCID: PMC10101014 DOI: 10.1128/spectrum.03700-22] [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: 09/12/2022] [Accepted: 02/17/2023] [Indexed: 03/29/2023] Open
Abstract
Performing genetic manipulations in Bacillus strains is often hindered by difficulty in identifying conditions appropriate for DNA uptake. This shortcoming limits our understanding of the functional diversity within this genus and the practical application of new strains. We have developed a simple method for increasing the genetic tractability of Bacillus spp. through conjugation-mediated plasmid transfer via a diaminopimelic acid (DAP) auxotrophic Escherichia coli donor strain. We observe transfer into representatives of the Bacillus clades subtilis, cereus, galactosidilyticus, and Priestia megaterium and successfully applied this protocol to 9 out of 12 strains attempted. We utilized the BioBrick 2.0 plasmids pECE743 and pECE750, as well as the CRISPR plasmid pJOE9734.1, to generate a xylose-inducible green-fluorescent protein (GFP)-expressing conjugal vector, pEP011. The use of xylose-inducible GFP ensures ease of confirming transconjugants, which enables users to quickly rule out false positives. Additionally, our plasmid backbone offers the flexibility to be used in other contexts, including transcriptional fusions and overexpression, with only a few modifications. IMPORTANCE Bacillus species are widely used to produce proteins and to understand microbial differentiation. Unfortunately, outside a few lab strains, genetic manipulation is difficult and can prevent thorough dissection of useful phenotypes. We developed a protocol that utilizes conjugation (plasmids that initiate their own transfer) to introduce plasmids into a diverse range of Bacillus spp. This will facilitate a deeper study of wild isolates for both industrial and pure research uses.
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Affiliation(s)
- Elise K. Phillips
- Department of Microbiology, University of Tennessee at Knoxville, Knoxville, Tennessee, USA
| | - Jordan A. Cannon
- Department of Microbiology, University of Tennessee at Knoxville, Knoxville, Tennessee, USA
| | - Yue Zhou
- Department of Microbiology, University of Tennessee at Knoxville, Knoxville, Tennessee, USA
| | - Kyle S. Bonifer
- Department of Microbiology, University of Tennessee at Knoxville, Knoxville, Tennessee, USA
| | - Todd B. Reynolds
- Department of Microbiology, University of Tennessee at Knoxville, Knoxville, Tennessee, USA
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Sheridan PO, Odat MA, Scott KP. Establishing genetic manipulation for novel strains of human gut bacteria. MICROBIOME RESEARCH REPORTS 2023; 2:1. [PMID: 38059211 PMCID: PMC10696588 DOI: 10.20517/mrr.2022.13] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/29/2022] [Accepted: 12/12/2022] [Indexed: 12/08/2023]
Abstract
Recent years have seen the development of high-accuracy and high-throughput genetic manipulation techniques, which have greatly improved our understanding of genetically tractable microbes. However, challenges remain in establishing genetic manipulation techniques in novel organisms, owing largely to exogenous DNA defence mechanisms, lack of selectable markers, lack of efficient methods to introduce exogenous DNA and an inability of genetic vectors to replicate in their new host. In this review, we describe some of the techniques that are available for genetic manipulation of novel microorganisms. While many reviews exist that focus on the final step in genetic manipulation, the editing of recipient DNA, we particularly focus on the first step in this process, the transfer of exogenous DNA into a strain of interest. Examples illustrating the use of these techniques are provided for a selection of human gut bacteria in which genetic tractability has been established, such as Bifidobacterium, Bacteroides and Roseburia. Ultimately, this review aims to provide an information source for researchers interested in developing genetic manipulation techniques for novel bacterial strains, particularly those of the human gut microbiota.
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Affiliation(s)
- Paul O. Sheridan
- School of Biological and Chemical Sciences, University of Galway, Galway H91 TK33, Ireland
| | - Ma’en Al Odat
- Gut Health Group, Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, Scotland AB25 2ZD, UK
| | - Karen P. Scott
- Gut Health Group, Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, Scotland AB25 2ZD, UK
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Goswami G, Hazarika DJ, Chowdhury N, Bora SS, Sarmah U, Naorem RS, Boro RC, Barooah M. Proline confers acid stress tolerance to Bacillus megaterium G18. Sci Rep 2022; 12:8875. [PMID: 35614097 PMCID: PMC9133035 DOI: 10.1038/s41598-022-12709-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 04/25/2022] [Indexed: 11/09/2022] Open
Abstract
Proline plays a multifunctional role in several organisms including bacteria in conferring protection under stress conditions. In this paper we report the role of proline in conferring acid tolerance to Bacillus megaterium G18. An acid susceptible mutant of B. megaterium G18 which required proline for its growth under acid stress condition was generated through Tn5 mutagenesis. Further, targeted inactivation of proC involved in osmo-adaptive proline synthesis in B. megaterium G18 resulted in the loss of ability of the bacterium to grow at low pH (pH 4.5). Exogenous supply of proline (1 mM) to the growth medium restored the ability of the mutant cells to grow at pH 4.5 which was not the same in case of other osmoprotectants tested. Proline was produced and secreted to extracellular medium by B. megaterium G18 when growing in low pH condition as evidenced by the use of Escherichia coli proline auxotrophs and HPLC analysis. Further, pHT01 vector based expression of full length proC gene in the ∆proC mutant cells restored the survival capacity of the mutant cells in acidic pH, suggesting that proline production is an important strategy employed by B. megaterium G18 to survive under acid stress induced osmotic stress.
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Affiliation(s)
- Gunajit Goswami
- DBT-North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Dibya Jyoti Hazarika
- DBT-North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Naimisha Chowdhury
- DBT-North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Sudipta Sankar Bora
- DBT-North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Unmona Sarmah
- DBT-North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Romen Singh Naorem
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Robin Chandra Boro
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Madhumita Barooah
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India.
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Kim MS, Kim HR, Jeong DE, Choi SK. Cytosine Base Editor-Mediated Multiplex Genome Editing to Accelerate Discovery of Novel Antibiotics in Bacillus subtilis and Paenibacillus polymyxa. Front Microbiol 2021; 12:691839. [PMID: 34122396 PMCID: PMC8193733 DOI: 10.3389/fmicb.2021.691839] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 04/30/2021] [Indexed: 12/30/2022] Open
Abstract
Genome-based identification of new antibiotics is emerging as an alternative to traditional methods. However, uncovering hidden antibiotics under the background of known antibiotics remains a challenge. To over this problem using a quick and effective genetic approach, we developed a multiplex genome editing system using a cytosine base editor (CBE). The CBE system achieved simultaneous double, triple, quadruple, and quintuple gene editing with efficiencies of 100, 100, 83, and 75%, respectively, as well as the 100% editing efficiency of single targets in Bacillus subtilis. Whole-genome sequencing of the edited strains showed that they had an average of 8.5 off-target single-nucleotide variants at gRNA-independent positions. The CBE system was used to simultaneously knockout five known antibiotic biosynthetic gene clusters to leave only an uncharacterized polyketide biosynthetic gene cluster in Paenibacillus polymyxa E681. The polyketide showed antimicrobial activities against gram-positive bacteria, but not gram-negative bacteria and fungi. Therefore, our findings suggested that the CBE system might serve as a powerful tool for multiplex genome editing and greatly accelerating the unraveling of hidden antibiotics in Bacillus and Paenibacillus species.
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Affiliation(s)
- Man Su Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, South Korea
| | - Ha-Rim Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | - Da-Eun Jeong
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | - Soo-Keun Choi
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, South Korea
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Juhas M, Ajioka JW. T7 RNA polymerase-driven inducible cell lysis for DNA transfer from Escherichia coli to Bacillus subtilis. Microb Biotechnol 2017; 10:1797-1808. [PMID: 28815907 PMCID: PMC5658589 DOI: 10.1111/1751-7915.12843] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 07/15/2017] [Accepted: 07/28/2017] [Indexed: 01/25/2023] Open
Abstract
The majority of the good DNA editing techniques have been developed in Escherichia coli; however, Bacillus subtilis is better host for a plethora of synthetic biology and biotechnology applications. Reliable and efficient systems for the transfer of synthetic DNA between E. coli and B. subtilis are therefore of the highest importance. Using synthetic biology approaches, such as streamlined lambda Red recombineering and Gibson Isothermal Assembly, we integrated genetic circuits pT7L123, Repr‐ts‐1 and pLT7pol encoding the lysis genes of bacteriophages MS2, ΦX174 and lambda, the thermosensitive repressor and the T7 RNA polymerase into the E. coli chromosome. In this system, T7 RNA polymerase regulated by the thermosensitive repressor drives the expression of the phage lysis genes. We showed that T7 RNA polymerase significantly increases efficiency of cell lysis and transfer of the plasmid and bacterial artificial chromosome‐encoded DNA from the lysed E. coli into B. subtilis. The T7 RNA polymerase‐driven inducible cell lysis system is suitable for the efficient cell lysis and transfer of the DNA engineered in E. coli to other naturally competent hosts, such as B. subtilis.
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Affiliation(s)
- Mario Juhas
- Department of Pathology, University of Cambridge, Tennis Court Road, CB2 1QP, Cambridge, UK
| | - James W Ajioka
- Department of Pathology, University of Cambridge, Tennis Court Road, CB2 1QP, Cambridge, UK
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Gerber A, Milhim M, Hartz P, Zapp J, Bernhardt R. Genetic engineering of Bacillus megaterium for high-yield production of the major teleost progestogens 17α,20β-di- and 17α,20β,21α-trihydroxy-4-pregnen-3-one. Metab Eng 2016; 36:19-27. [DOI: 10.1016/j.ymben.2016.02.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 02/01/2016] [Accepted: 02/23/2016] [Indexed: 11/28/2022]
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7
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Jakobs M, Meinhardt F. What renders Bacilli genetically competent? A gaze beyond the model organism. Appl Microbiol Biotechnol 2014; 99:1557-70. [DOI: 10.1007/s00253-014-6316-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 12/08/2014] [Accepted: 12/09/2014] [Indexed: 12/20/2022]
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Dong H, Zhang D. Current development in genetic engineering strategies of Bacillus species. Microb Cell Fact 2014; 13:63. [PMID: 24885003 PMCID: PMC4030025 DOI: 10.1186/1475-2859-13-63] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Accepted: 04/28/2014] [Indexed: 11/28/2022] Open
Abstract
The complete sequencing and annotation of the genomes of industrially-important Bacillus species has enhanced our understanding of their properties, and allowed advances in genetic manipulations in other Bacillus species. Post-genomic studies require simple and highly efficient tools to enable genetic manipulation. Here, we summarize the recent progress in genetic engineering strategies for Bacillus species. We review the available genetic tools that have been developed in Bacillus species, as well as methods developed in other species that may also be applicable in Bacillus. Furthermore, we address the limitations and challenges of the existing methods, and discuss the future research prospects in developing novel and useful tools for genetic modification of Bacillus species.
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Affiliation(s)
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
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A new cytochrome P450 system from Bacillus megaterium DSM319 for the hydroxylation of 11-keto-β-boswellic acid (KBA). Appl Microbiol Biotechnol 2013; 98:1701-17. [DOI: 10.1007/s00253-013-5029-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 05/27/2013] [Accepted: 05/30/2013] [Indexed: 12/11/2022]
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Wemhoff S, Meinhardt F. Generation of biologically contained, readily transformable, and genetically manageable mutants of the biotechnologically important Bacillus pumilus. Appl Microbiol Biotechnol 2013; 97:7805-19. [PMID: 23644770 DOI: 10.1007/s00253-013-4935-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 04/12/2013] [Accepted: 04/15/2013] [Indexed: 11/25/2022]
Abstract
Bacillus pumilus mutants were generated by targeted deletion of a set of genes eventually facilitating genetic handling and assuring biological containment. The well-defined and stable mutants do not form functional endospores due to the deletion of yqfD, an essential sporulation gene; they are affected in DNA repair, as ΔuvrBA rendered them UV hypersensitive and, thus, biologically contained; they are deficient for the uracil phosphoribosyl-transferase (Δupp), allowing for 5-fluorouracil-based counterselection facilitating rapid allelic exchanges; and they are readily transformable due to the deletion of the restrictase encoding locus (ΔhsdR) of a type I restriction modification system. Vegetative growth as well as extracellular enzyme production and secretion are in no case affected. The combination of such gene deletions allows for development of B. pumilus strains suited for industrial use and further improvements.
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Affiliation(s)
- Stephanie Wemhoff
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 3, 48149, Münster, Germany
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Korneli C, David F, Biedendieck R, Jahn D, Wittmann C. Getting the big beast to work--systems biotechnology of Bacillus megaterium for novel high-value proteins. J Biotechnol 2012; 163:87-96. [PMID: 22750448 DOI: 10.1016/j.jbiotec.2012.06.018] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Revised: 06/18/2012] [Accepted: 06/20/2012] [Indexed: 12/31/2022]
Abstract
The high industrial relevance of the soil bacterium Bacillus megaterium as host for recombinant proteins is driving systems-wide analyses of its metabolic and regulatory networks. The present review highlights novel systems biology tools available to unravel the various cellular components on the level of metabolic and regulatory networks. These provide a rational platform for systems metabolic engineering of B. megaterium. In line, a number of interesting studies have particularly focused on studying recombinant B. megaterium in its industrial bioprocess environment thus integrating systems metabolic engineering with systems biotechnology and providing the full picture toward optimal processes.
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Affiliation(s)
- Claudia Korneli
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
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Borgmeier C, Biedendieck R, Hoffmann K, Jahn D, Meinhardt F. Transcriptome profiling of degU expression reveals unexpected regulatory patterns in Bacillus megaterium and discloses new targets for optimizing expression. Appl Microbiol Biotechnol 2011; 92:583-96. [PMID: 21935588 DOI: 10.1007/s00253-011-3575-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Revised: 08/17/2011] [Accepted: 09/08/2011] [Indexed: 11/24/2022]
Abstract
The first whole transcriptome assessment of a Bacillus megaterium strain provides unanticipated insights into the degSU regulon considered to be of central importance for exo-enzyme production. Regulatory patterns as well as the transcription of degSU itself deviate from the model organism Bacillus subtilis; the number of DegU-regulated secretory enzymes is rather small. Targets for productivity optimization, besides degSU itself, arise from the unexpected DegU-dependent induction of the transition-state regulator AbrB during exponential growth. Induction of secretion-assisting factors, such as the translocase subunit SecY or the signal peptidase SipM, promote hypersecretion. B. megaterium DegSU transcriptional control is advantageous for production purposes, since the degU32 constitutively active mutant conferred hypersecretion of a heterologous Bacillus amyloliquefaciens amylase without the detrimental rise, as for B. subtilis and Bacillus licheniformis, in extracellular proteolytic activities.
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Affiliation(s)
- Claudia Borgmeier
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms Universität, Corrensstrasse 3, 48149, Münster, Germany
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Functional analysis of the response regulator DegU in Bacillus megaterium DSM319 and comparative secretome analysis of degSU mutants. Appl Microbiol Biotechnol 2011; 91:699-711. [DOI: 10.1007/s00253-011-3302-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Revised: 04/01/2011] [Accepted: 04/01/2011] [Indexed: 10/18/2022]
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Biedendieck R, Borgmeier C, Bunk B, Stammen S, Scherling C, Meinhardt F, Wittmann C, Jahn D. Systems biology of recombinant protein production using Bacillus megaterium. Methods Enzymol 2011; 500:165-95. [PMID: 21943898 DOI: 10.1016/b978-0-12-385118-5.00010-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The Gram-negative bacterium Escherichia coli is the most widely used production host for recombinant proteins in both academia and industry. The Gram-positive bacterium Bacillus megaterium represents an increasingly used alternative for high yield intra- and extracellular protein synthesis. During the past two decades, multiple tools including gene expression plasmids and production strains have been developed. Introduction of free replicating and integrative plasmids into B. megaterium is possible via protoplasts transformation or transconjugation. Using His(6)- and StrepII affinity tags, the intra- or extracellular produced proteins can easily be purified in one-step procedures. Different gene expression systems based on the xylose controlled promoter P(xylA) and various phage RNA polymerase (T7, SP6, K1E) driven systems enable B. megaterium to produce up to 1.25g of recombinant protein per liter. Biomass concentrations of up to 80g/l can be achieved by high cell density cultivations in bioreactors. Gene knockouts and gene replacements in B. megaterium are possible via an optimized gene disruption system. For a safe application in industry, sporulation and protease-deficient as well as UV-sensitive mutants are available. With the help of the recently published B. megaterium genome sequence, it is possible to characterize bottle necks in the protein production process via systems biology approaches based on transcriptome, proteome, metabolome, and fluxome data. The bioinformatical platform (Megabac, http://www.megabac.tu-bs.de) integrates obtained theoretical and experimental data.
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Affiliation(s)
- Rebekka Biedendieck
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstrasse 7, Braunschweig, Germany
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