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Otto SJ, Teichmann L, Fante N, Crauwels P, Grünberger A, Neddermann T, Riedel CU. High-throughput detection of potential bacteriocin producers in a large strain library using live fluorescent biosensors. Front Bioeng Biotechnol 2024; 12:1405202. [PMID: 39144483 PMCID: PMC11321961 DOI: 10.3389/fbioe.2024.1405202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 07/03/2024] [Indexed: 08/16/2024] Open
Abstract
The global increase in antibiotic resistances demands for additional efforts to identify novel antimicrobials such as bacteriocins. These antimicrobial peptides of bacterial origin are already used widely in food preservation and promising alternatives for antibiotics in animal feed and some clinical setting. Identification of novel antimicrobials is facilitated by appropriate high throughput screening (HTS) methods. Previously, we have described a rapid, simple and cost-efficient assay based on live biosensor bacteria for detection of antimicrobial compounds that act on membrane integrity using the ratiometric pH-dependent fluorescent protein pHluorin2 (pHin2). Here, we use these biosensors to develop an integrated pipeline for high-throughput identification of bacteriocin producers and their biosynthetic gene clusters. We extend the existing portfolio of biosensors by generating pHin2 expressing strains of Escherichia coli, Bacillus cereus, Staphylococcus epidermidis, and methicillin-resistant Staphylococcus aureus. These strains were characterized, and control experiments were performed to assess heterogeneity of these biosensors in response to known bacteriocins and develop a robust HTS system. To allow detection of compounds that inhibit target bacteria by inhibiting growth without disturbing membrane integrity, the HTS system was extended with a growth-dependent readout. Using this HTS system, we screened supernatants of a total of 395 strains of a collection of lactic acid bacteria. After two rounds of screening 19 strains of the collection were identified that produced antimicrobial activity against Listeria innocua and Listeria monocytogenes. Genomes of confirmed hits were sequenced and annotated. In silico analysis revealed that the identified strains encode between one and six biosynthetic gene clusters (BGCs) for bacteriocins. Our results suggest that pHin2 biosensors provides a flexible, cheap, fast, robust and easy to handle HTS system for identification of potential bacteriocins and their BGCs in large strain collections.
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Affiliation(s)
| | | | - Niklas Fante
- Multiscale Bioengineering, Technical Faculty, Bielefeld University, Bielefeld, Germany
| | | | - Alexander Grünberger
- Multiscale Bioengineering, Technical Faculty, Bielefeld University, Bielefeld, Germany
- Microsystems in Bioprocess Engineering, Institute of Process Engineering in Life Sciences, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
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Steier V, Osthege M, Helleckes LM, Siska M, von Lieres E, Wiechert W, Reich SJ, Riedel CU, Oldiges M. Quantification of nisin concentration from fluorescence-based antimicrobial activity assay using Bayesian calibration. Biotechnol Prog 2024:e3495. [PMID: 39056486 DOI: 10.1002/btpr.3495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 06/24/2024] [Accepted: 07/07/2024] [Indexed: 07/28/2024]
Abstract
Bacteriocins are ribosomally synthesized peptides with the innate ability to kill or inhibit growth of other bacteria. In recent years, bacteriocins have received increased interest, as their antimicrobial activity enhances food safety and shelf life by combatting pathogens such as Listeria monocytogenes. They also have application potential as an active pharmaceutical compound to combat multidrug-resistant pathogens. As new bacteriocins continue to be discovered, accelerated workflows for screening, identification, and process development have been developed. However, antimicrobial activity measurement is often still limited with regards to quantification and throughput. Here, we present the use of a non-linear calibration model to infer nisin concentrations in cultivation supernatants of Lactococcus lactis ssp. lactis B1629 using readouts of pHluorin2 fluorescence-based antimicrobial activity assays.
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Affiliation(s)
- Valentin Steier
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Michael Osthege
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Laura M Helleckes
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Maximilian Siska
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University, Aachen, Germany
| | - Eric von Lieres
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University, Aachen, Germany
| | - Wolfgang Wiechert
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University, Aachen, Germany
| | | | | | - Marco Oldiges
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
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Fante N, Desiderato CK, Riedel CU, Grünberger A. Time-resolved cell-to-cell heterogeneity of Listeria innocua after nisin exposure. Front Bioeng Biotechnol 2024; 12:1408652. [PMID: 38933537 PMCID: PMC11199691 DOI: 10.3389/fbioe.2024.1408652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 05/13/2024] [Indexed: 06/28/2024] Open
Abstract
The use of bacteriocins is a promising approach for addressing the immense threat of food-borne and drug-resistant pathogens. In recent years screening platforms for novel bacteriocins using whole-cell biosensors have been established. During screening cell-to-cell heterogeneity is currently neglected but might play a crucial role in signal development of the whole-cell biosensor after bacteriocin exposure. In this study, we explored the temporal dynamics of the signal heterogeneity of the biosensor Listeria innocua LMG2785/pNZpHin2 Lm after nisin exposure using microfluidic single-cell analysis. The results provided novel and detailed insights into the dynamics of cell-to-cell heterogeneity in L. innocua LMG2785/pNZpHin2 Lm at different nisin concentrations with a high spatio-temporal resolution. Furthermore, the formation of subpopulations during bacteriocin exposure was observed. In-depth single-cell tracking even revealed the regeneration of disrupted cells and recovery of pH homeostasis in rare instances. These findings are highly important for the future design and execution of bacteriocin assays and for the interpretation of fluorescence signal development at the population level after exposure to different concentrations of bacteriocins (here, nisin), as well as for obtaining deeper insights into single-cell persistence strategies to quantify the efficacy and efficiency of novel bacteriocins.
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Affiliation(s)
- Niklas Fante
- Multiscale Bioengineering, Technical Faculty, Bielefeld University, Bielefeld, Germany
| | | | | | - Alexander Grünberger
- Multiscale Bioengineering, Technical Faculty, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
- Institute of Process Engineering in Life Sciences: Microsystems in Bioprocess Engineering, Karlsruhe Institute of Technology, Karlsruhe, Germany
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Steier V, Prigolovkin L, Reiter A, Neddermann T, Wiechert W, Reich SJ, Riedel CU, Oldiges M. Automated workflow for characterization of bacteriocin production in natural producers Lactococcus lactis and Latilactobacillus sakei. Microb Cell Fact 2024; 23:74. [PMID: 38433206 PMCID: PMC10910668 DOI: 10.1186/s12934-024-02349-6] [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: 11/02/2023] [Accepted: 02/25/2024] [Indexed: 03/05/2024] Open
Abstract
BACKGROUND Lactic acid bacteria are commonly used as protective starter cultures in food products. Among their beneficial effects is the production of ribosomally synthesized peptides termed bacteriocins that kill or inhibit food-spoiling bacteria and pathogens, e.g., members of the Listeria species. As new bacteriocins and producer strains are being discovered rapidly, modern automated methods for strain evaluation and bioprocess development are required to accelerate screening and development processes. RESULTS In this study, we developed an automated workflow for screening and bioprocess optimization for bacteriocin producing lactic acid bacteria, consisting of microcultivation, sample processing and automated antimicrobial activity assay. We implemented sample processing workflows to minimize bacteriocin adsorption to producer cells via addition of Tween 80 and divalent cations to the cultivation media as well as acidification of culture broth prior to cell separation. Moreover, we demonstrated the applicability of the automated workflow to analyze influence of media components such as MES buffer or yeast extract for bacteriocin producers Lactococcus lactis B1629 and Latilactobacillus sakei A1608. CONCLUSIONS Our automated workflow provides advanced possibilities to accelerate screening and bioprocess optimization for natural bacteriocin producers. Based on its modular concept, adaptations for other strains, bacteriocin products and applications are easily carried out and a unique tool to support bacteriocin research and bioprocess development is provided.
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Affiliation(s)
- Valentin Steier
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Lisa Prigolovkin
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Alexander Reiter
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | | | - Wolfgang Wiechert
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University, Aachen, Germany
| | | | | | - Marco Oldiges
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany.
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany.
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Desiderato CK, Müller C, Schretzmeier A, Hasenauer KM, Gnannt B, Süpple B, Reiter A, Steier V, Oldiges M, Eikmanns BJ, Riedel CU. Optimized recombinant production of the bacteriocin garvicin Q by Corynebacterium glutamicum. Front Microbiol 2024; 14:1254882. [PMID: 38260893 PMCID: PMC10800739 DOI: 10.3389/fmicb.2023.1254882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 12/12/2023] [Indexed: 01/24/2024] Open
Abstract
Bacteriocins are antimicrobial peptides applied in food preservation and are interesting candidates as alternatives to conventional antibiotics or as microbiome modulators. Recently, we established Corynebacterium glutamicum as a suitable production host for various bacteriocins including garvicin Q (GarQ). Here, we establish secretion of GarQ by C. glutamicum via the Sec translocon achieving GarQ titers of about 7 mg L-1 in initial fermentations. At neutral pH, the cationic peptide is efficiently adsorbed to the negatively charged envelope of producer bacteria limiting availability of the bacteriocin in culture supernatants. A combination of CaCl2 and Tween 80 efficiently reduces GarQ adsorption to C. glutamicum. Moreover, cultivation in minimal medium supplemented with CaCl2 and Tween 80 improves GarQ production by C. glutamicum to about 15 mg L-1 but Tween 80 resulted in reduced GarQ activity at later timepoints. Using a reporter strain and proteomic analyses, we identified HtrA, a protease associated with secretion stress, as another potential factor limiting GarQ production. Transferring production to HtrA-deficient C. glutamicum K9 improves GarQ titers to close to 40 mg L-1. Applying conditions of low aeration prevented loss in activity at later timepoints and improved GarQ titers to about 100 mg L-1. This is about 50-fold higher than previously shown with a C. glutamicum strain employing the native GarQ transporter GarCD for secretion and in the range of levels observed with the native producer Lactococcus petauri B1726. Additionally, we tested several synthetic variants of GarQ and were able to show that exchange of the methionine in position 5 to a phenylalanine (GarQM5F) results in markedly increased activity against Lactococcus lactis and Listeria monocytogenes. In summary, our findings shed light on several aspects of recombinant GarQ production that may also be of relevance for production with natural producers and other bacteriocins.
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Affiliation(s)
- Christian K. Desiderato
- Institute of Molecular Biology and Biotechnology of Prokaryotes, University of Ulm, Ulm, Germany
| | - Carolin Müller
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Alexander Schretzmeier
- Institute of Molecular Biology and Biotechnology of Prokaryotes, University of Ulm, Ulm, Germany
| | - Katharina M. Hasenauer
- Institute of Molecular Biology and Biotechnology of Prokaryotes, University of Ulm, Ulm, Germany
| | - Bruno Gnannt
- Institute of Molecular Biology and Biotechnology of Prokaryotes, University of Ulm, Ulm, Germany
| | - Bastian Süpple
- Institute of Molecular Biology and Biotechnology of Prokaryotes, University of Ulm, Ulm, Germany
| | - Alexander Reiter
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Valentin Steier
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Marco Oldiges
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Bernhard J. Eikmanns
- Institute of Molecular Biology and Biotechnology of Prokaryotes, University of Ulm, Ulm, Germany
| | - Christian U. Riedel
- Institute of Molecular Biology and Biotechnology of Prokaryotes, University of Ulm, Ulm, Germany
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Vogel V, Olari LR, Jachmann M, Reich SJ, Häring M, Kissmann AK, Rosenau F, Riedel CU, Münch J, Spellerberg B. The bacteriocin Angicin interferes with bacterial membrane integrity through interaction with the mannose phosphotransferase system. Front Microbiol 2022; 13:991145. [PMID: 36147850 PMCID: PMC9486217 DOI: 10.3389/fmicb.2022.991145] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 08/17/2022] [Indexed: 12/29/2022] Open
Abstract
In a natural environment, bacteria are members of multispecies communities. To compete with rival species, bacteria produce antimicrobial peptides (AMPs), called bacteriocins. Bacteriocins are small, cationic, ribosomally synthesized peptides, which normally inhibit closely related species of the producing organism. Bacteriocin production is best studied in lactic bacteria (LAB). Streptococcus anginosus, belonging to LAB, produces the potent bacteriocin Angicin, which shows inhibitory activity against other streptococci, Listeria monocytogenes and vancomycin resistant Enterococcus faecium (VRE). Furthermore, Angicin shows a high resistance toward pH changes and heat, rendering it an interesting candidate for food preservation or clinical applications. The inhibitory activity of Angicin depends on the presence of a mannose phosphotransferase system (Man-PTS) in target cells, since L. monocytogenes harboring a deletion in an extracellular loop of this system is no longer sensitive to Angicin. Furthermore, we demonstrated by liposome leakage and pHluorin assays that Angicin destroys membrane integrity but shows only low cytotoxicity against human cell lines. In conclusion, we show that Angicin has a detrimental effect on the membrane of target organisms by using the Man-PTS as a receptor.
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Affiliation(s)
- Verena Vogel
- Institute of Medical Microbiology and Hygiene, Ulm University Medical Center, Ulm, Germany
| | - Lia-Raluca Olari
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Marie Jachmann
- Institute of Medical Microbiology and Hygiene, Ulm University Medical Center, Ulm, Germany
| | - Sebastian J. Reich
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| | - Michelle Häring
- Institute of Pharmaceutical Biotechnology, University of Ulm, Ulm, Germany
| | | | - Frank Rosenau
- Institute of Pharmaceutical Biotechnology, University of Ulm, Ulm, Germany
| | - Christian U. Riedel
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Barbara Spellerberg
- Institute of Medical Microbiology and Hygiene, Ulm University Medical Center, Ulm, Germany
- *Correspondence: Barbara Spellerberg,
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Ovchinnikov KV, Oftedal TF, Reich SJ, Bar NS, Holo H, Skaugen M, Riedel CU, Diep DB. Genome-assisted Identification, Purification, and Characterization of Bacteriocins. Bio Protoc 2022; 12:e4477. [PMID: 35978579 PMCID: PMC9350922 DOI: 10.21769/bioprotoc.4477] [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: 04/19/2022] [Revised: 06/15/2022] [Accepted: 06/20/2022] [Indexed: 12/29/2022] Open
Abstract
Bacteriocins are antimicrobial peptides with activity against antibiotic resistant bacterial pathogens. Here, we describe a set of methods aimed at purifying, identifying, and characterizing new bacteriocins. The purification consists of ammonium sulphate precipitation, cation-exchange chromatography, and reversed-phase chromatography. The yield of the bacteriocin is quantified by bacteriocin antimicrobial activity in a microtiter plate assay after each purification step. The mass of the purified bacteriocin is assessed by MALDI TOF MS analysis of the active fractions after reversed-phase chromatography. The mass is compared with the theoretical mass based on genetic information from the whole genome sequencing of the bacteriocin producer strain. Physicochemical characterization is performed by assessing antimicrobial activity following heat and protease treatments. Fluorescent techniques are used to examine the capacity of the bacteriocin to disrupt membrane integrity. Herein a set of protocols for purification and characterization of the bacteriocin nisin Z is used as a typical example in this paper.
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Affiliation(s)
- Kirill V. Ovchinnikov
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Thomas F. Oftedal
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Sebastian J. Reich
- Institute of Microbiology and Biotechnology, Ulm University, Ulm, Germany
| | - Nadav S. Bar
- Department of Chemical Engineering, Norwegian University of Science and Technology, Trondheim, Norway
| | - Helge Holo
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Morten Skaugen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | | | - Dzung B. Diep
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
,
*For correspondence:
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