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Sreedharan DK, Alias H, Makhtar MMZ, Shun TJ, Mokhtar AMA, Shukor H, Siddiqui MR, Alam M, Kapoor RT, Rafatullah M. Screening of different growth conditions of Bacillus subtilis isolated from membrane-less microbial fuel cell toward antimicrobial activity profiling. Open Life Sci 2024; 19:20220809. [PMID: 38283116 PMCID: PMC10811530 DOI: 10.1515/biol-2022-0809] [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: 07/27/2023] [Revised: 09/20/2023] [Accepted: 11/23/2023] [Indexed: 01/30/2024] Open
Abstract
Bacteriocins produced by Bacillus subtilis have gained recognition for their safe use in humans. In this study, we aimed to assess the inhibitory activity of an antimicrobial peptide synthesized by the wild-type strain of B. subtilis against the notorious pathogen Pseudomonas aeruginosa. Our investigation employed the broth microdilution method to evaluate the inhibitory potential of this peptide. Among the four different pathogen strains tested, P. aeruginosa exhibited the highest susceptibility, with an inhibition rate of 29.62%. In parallel, we explored the cultivation conditions of B. subtilis, recognizing the potential of this versatile bacterium for applications beyond antimicrobial production. The highest inhibitory activity was achieved at pH 8, with an inhibition rate of 20.18%, indicating the potential for optimizing pH conditions for enhanced antimicrobial peptide production. For the kinetics of peptide production, the study explored different incubation periods and agitation levels. Remarkably, the highest activity of B. subtilis was observed at 24 h of incubation, with an inhibition rate of 44.93%. Finally, the study focused on the isolation of the antimicrobial peptide from the cell-free supernatant of B. subtilis using ammonium sulfate precipitation at various concentrations. The highest recorded activity was an impressive 89.72% achieved at an 80% concentration.
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Affiliation(s)
- Dharni Kuhan Sreedharan
- Bioprocess Technology Division, School of Industrial Technology, Universiti Sains Malaysia, Penang 11800, Malaysia
| | - Hartini Alias
- Centre for Innovation and Consultation, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Muaz Mohd Zaini Makhtar
- Bioprocess Technology Division, School of Industrial Technology, Universiti Sains Malaysia, Penang 11800, Malaysia
- Centre for Innovation and Consultation, Universiti Sains Malaysia, 11800 Penang, Malaysia
- Renewable Biomass Transformation Cluster, School of Industrial Technology, Universiti Sains Malaysia, Penang 11800, Malaysia
| | - Tan Joo Shun
- Bioprocess Technology Division, School of Industrial Technology, Universiti Sains Malaysia, Penang 11800, Malaysia
- Renewable Biomass Transformation Cluster, School of Industrial Technology, Universiti Sains Malaysia, Penang 11800, Malaysia
| | - Ana Masara Ahmad Mokhtar
- Bioprocess Technology Division, School of Industrial Technology, Universiti Sains Malaysia, Penang 11800, Malaysia
- Renewable Biomass Transformation Cluster, School of Industrial Technology, Universiti Sains Malaysia, Penang 11800, Malaysia
| | - Hafiza Shukor
- Centre of Excellence for Biomass Utilization, Faculty of Chemical Engineering Technology, Universiti Malaysia Perlis, 02600Arau, Perlis, Malaysia
| | - Masoom Raza Siddiqui
- Chemistry Department, College of Science, King Saud University, Riyadh11451, Saudi Arabia
| | - Mahboob Alam
- Division of Chemistry and Biotechnology, Dongguk University, 123, Dongdaero, Gyeongju-si, 780714, Republic of Korea
| | - Riti Thapar Kapoor
- Centre for Plant and Environmental Biotechnology, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, 201 313, Uttar Pradesh, India
| | - Mohd Rafatullah
- Renewable Biomass Transformation Cluster, School of Industrial Technology, Universiti Sains Malaysia, Penang 11800, Malaysia
- Environmental Technology Division, School of Industrial Technology, Universiti Sains Malaysia, Penang 11800, Malaysia
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Du R, Xiong W, Xu L, Xu Y, Wu Q. Metagenomics reveals the habitat specificity of biosynthetic potential of secondary metabolites in global food fermentations. MICROBIOME 2023; 11:115. [PMID: 37210545 DOI: 10.1186/s40168-023-01536-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 03/28/2023] [Indexed: 05/22/2023]
Abstract
BACKGROUND Fermented foods are considered to be beneficial for human health. Secondary metabolites determined by biosynthetic gene clusters (BGCs) are precious bioactive compounds with various biological activities. However, the diversity and distribution of the biosynthetic potential of secondary metabolites in global food fermentations remain largely unknown. In this study, we performed a large-scale and comprehensive investigation for the BGCs in global food fermentations by metagenomics analysis. RESULTS We recovered 653 bacterial metagenome-assembled genomes (MAGs) from 367 metagenomic sequencing datasets covering 15 general food fermentation types worldwide. In total, 2334 secondary metabolite BGCs, including 1003 novel BGCs, were identified in these MAGs. Bacillaceae, Streptococcaceae, Streptomycetaceae, Brevibacteriaceae and Lactobacillaceae contained high abundances of novel BGCs (≥ 60 novel BGCs). Among 2334 BGCs, 1655 were habitat-specific, originating from habitat-specific species (80.54%) and habitat-specific genotypes within multi-habitat species (19.46%) in different food fermentation types. Biological activity analysis suggested that 183 BGC-producing secondary metabolites exhibited high probabilities of antibacterial activity (> 80%). These 183 BGCs were distributed across all 15 food fermentation types, and cheese fermentation contained the most BGC number. CONCLUSIONS This study demonstrates that food fermentation systems are an untapped reservoir of BGCs and bioactive secondary metabolites, and it provides novel insights into the potential human health benefits of fermented foods. Video Abstract.
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Affiliation(s)
- Rubing Du
- Lab of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, People's Republic of China
| | - Wu Xiong
- Laboratory of Bio-Interactions and Crop Health, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Lei Xu
- Lab of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, People's Republic of China
| | - Yan Xu
- Lab of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, People's Republic of China
| | - Qun Wu
- Lab of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, People's Republic of China.
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Helfrich M, Entian KD, Stein T. Antibiotic profiling of wild-type bacilli led to the discovery of new lanthipeptide subtilin-producing Bacillus spizizenii strains whose 16S rDNA sequences differ from the B. spizizenii typing strain. INTERNATIONAL MICROBIOLOGY : THE OFFICIAL JOURNAL OF THE SPANISH SOCIETY FOR MICROBIOLOGY 2022; 25:839-850. [PMID: 35902452 PMCID: PMC9526687 DOI: 10.1007/s10123-022-00266-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 06/12/2022] [Accepted: 07/06/2022] [Indexed: 11/25/2022]
Abstract
Two dozen field-collected Bacillus and a dozen Bacillus spizizenii wild-type strains from strain collections were selected on the basis of their antagonistic properties against the Gram-positive strain Micrococcus luteus. Based on their genetic and antibiotic profiles, they were characterized (subtilin encoding spaS gene sequences, mass spectrometric, and quantitative-reversed phase liquid chromatographic analyses, as well as the presence of the lanthionine cyclase protein SpaC by western blotting), seven novel producers of the lanthipeptide subtilin. Phylogenetic analyses of the subtilin-producing wild-type strains based on their 16S rRNA sequences showed that all seven strains could be classified as B. spizizenii: The field-collected strains HS and N5, as well as strains DSM 618, 1087, 6395, 6405, and 8439 from the German Collection of Microorganisms and Cell Cultures. To the best of our knowledge, all B. spizizenii strains described so far are characterized by the fact that they can produce a lanthipeptide of the subtilin family. Both the lanthipeptide structures and the organization and sequences of the 16S rRNA-encoding genes suggest a subdivision of B. spizizenii into subspecies: The subtilin-producing B. spizizenii strains are distinctly different from the entianin-producing B. spizizenii typing strain TU-B-10 T (DSM 15029 T).
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Affiliation(s)
- Markus Helfrich
- Life Sciences, Johann Wolfgang-Goethe-University, Max v. Laue Str. 9, 60439, Frankfurt/Main, Germany
- Jennewein Biotechnologie GmbH, Maarweg 32, 53619, Rheinbreitbach, Germany
| | - Karl-Dieter Entian
- Life Sciences, Johann Wolfgang-Goethe-University, Max v. Laue Str. 9, 60439, Frankfurt/Main, Germany
| | - Torsten Stein
- Life Sciences, Johann Wolfgang-Goethe-University, Max v. Laue Str. 9, 60439, Frankfurt/Main, Germany.
- Chemistry & Molecular Biotechnology, Aalen University, Beethovenstraße 1, 73430, Aalen, Germany.
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Tenea GN, Gonzalez GL, Moreno JL. Probiotic Characteristics and Antimicrobial Potential of a Native Bacillus subtilis Strain Fa17.2 Rescued from Wild Bromelia sp. Flowers. Microorganisms 2022; 10:microorganisms10050860. [PMID: 35630306 PMCID: PMC9145066 DOI: 10.3390/microorganisms10050860] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/11/2022] [Accepted: 04/18/2022] [Indexed: 12/10/2022] Open
Abstract
In the present study, we identified the Bacillus subtilis strain annotated Fa17.2 isolated from Bromelia flower inflorescences collected from the subtropical humid mesothermal region, Santo Domingo de Los Tsachilas Province, Ecuador. The probiotic capacity and antimicrobial potential against four foodborne pathogens were assessed. The cell culture of Fa17.2 is highly resistant to synthetic gastric acid (pH 2.5, 3.0, and 3.5), bile salts (0.3%), tolerating different sodium chloride concentrations (1, 3, and 5%), and growth conditions (15 °C and 45 °C), suggesting its potential probiotic features. The isolate showed no antibiotic resistance and was considered safe as no hemolysis was detected on sheep blood agar. The optimum medium for bacterial growth and the release of antimicrobial compounds was MRS with 10% glucose. The active components released in the neutralized crude extract (NCE) were insensitive to organic solvents, surfactants, and nonproteolytic enzymes and sensitive to proteolytic enzymes suggesting their proteinaceous nature. The antimicrobial activity was enhanced by heat and maintained active over a wide range of pH (2.0–8.0). Moreover, the crude extract (CE) showed inhibitory activity against several Gram-negative and Gram-positive bacteria. The molecular weight of partially purified precipitated bacteriocin-like substances (BLISs) was about 14 kDa in 20% Tricine-SDS-PAGE. The CE obtained from Fa17.2 inhibits the growth of four foodborne pathogens, Staphylococcus aureus, Escherichia coli, Kosaconia cowanii, and Shigella dysenteriae, which implies its potential as an antimicrobial producer strain.
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High-throughput discovery of novel lanthipeptides and producers by metagenomic mining of isolates population (MMIP) from Chinese spicy cabbage. Food Res Int 2022; 154:110991. [DOI: 10.1016/j.foodres.2022.110991] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 01/13/2022] [Accepted: 01/28/2022] [Indexed: 12/22/2022]
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6
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Characterization of dual bacteriocins producing Bacillus subtilis SC3.7 isolated from fermented food. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2021.112854] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Geraldi A, Famunghui M, Abigail M, Siona Saragih CF, Febitania D, Elmarthenez H, Putri CA, Putri Merdekawati UAS, Sadila AY, Wijaya NH. Screening of antibacterial activities of Bacillus spp. isolated from the Parangkusumo coastal sand dunes, Indonesia. BIO INTEGRATION 2022. [DOI: 10.15212/bioi-2022-0005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Background: The emergence of multidrug-resistant bacteria because of poor understanding of the issue and the misuse of antibiotics has become global health concern. Therefore, the discovery of novel antibacterial drugs is urgently needed. New antibacterial compounds may be found in the Bacillus species, which are abundant in sand dune ecosystems. Herein, we examined samples from the Parangkusumo coastal sand dunes in Indonesia.Methods: Samples were collected from three areas in the sand dunes (the area closest to the sea, the core area of sand dunes, and the area farthest from the sea). The samples were inoculated on Luria Bertani agar. Morphological and molecular identification was performed on the basis of 16S rRNA. The samples’ antimicrobial activity was evaluated with the disc diffusion method and compared with that of opportunistic pathogenic bacteria.Results: Five species of Bacillus were successfully isolated from the Parangkusumo coastal sand dunes. To our knowledge, this is the first report of the isolation of Bacillus aryabhattai in Indonesia. All samples showed antimicrobial activity against pathogenic bacteria. B. velezensis and B. subtilis showed antibacterial activity against Gram-positive bacteria, whereas B. aryabhattai and B. megaterium showed antibacterial activity against Gram-negative bacteria, and B. spizizenii showed antibacterial activity toward Gram-positive and Gram-negative bacteria.Conclusion: Five Bacillus species were successfully isolated from the Parangkusumo coastal sand dunes, Indonesia, and all samples showed antimicrobial activity toward opportunistic pathogenic bacteria. The crude antimicrobial compounds from B. megaterium, B. aryabhattai, B. subtilis, and B. spizizenii showed the highest growth-inhibition activity against E. coli, P. aeruginosa, B. cereus, and S. aureus, respectively.
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Affiliation(s)
- Almando Geraldi
- University-Center of Excellence-Research Center for Bio-Molecule Engineering, Universitas Airlangga, Surabaya 60115, Indonesia
- Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya 60115, Indonesia
| | - Margareth Famunghui
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung 40132, Indonesia
| | - Mercyana Abigail
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung 40132, Indonesia
| | | | - Devina Febitania
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung 40132, Indonesia
| | - Henrietta Elmarthenez
- Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya 60115, Indonesia
| | - Cinantya Aulia Putri
- Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya 60115, Indonesia
| | | | - Aliffa Yusti Sadila
- Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya 60115, Indonesia
| | - Nabilla Hapsari Wijaya
- Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya 60115, Indonesia
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Sharma BR, Jayant D, Rajshee K, Singh Y, Halami PM. Distribution and Diversity of Nisin Producing LAB in Fermented Food. Curr Microbiol 2021; 78:3430-3438. [PMID: 34255153 DOI: 10.1007/s00284-021-02593-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 06/11/2021] [Indexed: 10/20/2022]
Abstract
An attempt was made, to characterize natural antibiotics or lantibiotics from unconventional sources and its antibacterial spectrum against food borne pathogens and drug resistant bacteria. Six different traditional fermented foods i.e., fermented fish, fermented soybeans, Soibum (fermented bamboo shoots), milk, idly and dosa batter were used for the isolation of bacteriocin producing Lactic acid bacteria (LAB). Among all bacterial cultures isolated from the various sources, 129 cultures have found to produce antimicrobial compounds. Nisin specific reporter bacteria was utilized as biosensor to identify the Nisin like bacteriocin, where 10 cultures found to be positive Nisin producer. Identified Nisin like bacteriocin was partially concentrated by using ammonium sulphate followed by butanol extraction. Minimum inhibitory concentration (MIC) was analyzed against food borne pathogen and drug resistant bacteria. MIC of partially purified Nisin (pp-Nisin) of all the LAB isolates against food-borne pathogens are ranged between 0.5 and 92 µg/ml respected to various Gram-positive bacteria. Similarly, the drug resistant bacteria were also inhibited by pp-Nisin (MIC ranged between 15 and 175 µg/ml). All samples of ppnisin exhibited auto induction ability. Taxonomic identification of the nisin producers was done by whole genome sequencing which reveals that cultures belongs to Lactococcus lactis ssp. lactis. Also it was found that Lactococcus lactis ssp. lactis C2d and Lactococcus lactis ssp. lactis SP2C4 harbor nisA gene and Lactococcus lactis ssp. lactis FS2 (L. lactis FS2) harbor nisQ gene. The finding of this study highlights the first case of L. lactis FS2 isolated from fermented fish harbor nisQ gene. Antibacterial activity of pp-Nisin against drug resistant LAB is also reported.
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Affiliation(s)
- Basista Rabina Sharma
- Microbiology and Fermentation Technology Department, CSIR-Central Food Technological Research Institute, Mysore, 570020, India
| | - Dharana Jayant
- Microbiology and Fermentation Technology Department, CSIR-Central Food Technological Research Institute, Mysore, 570020, India
| | - Kumari Rajshee
- Microbiology and Fermentation Technology Department, CSIR-Central Food Technological Research Institute, Mysore, 570020, India
| | - Yashika Singh
- Microbiology and Fermentation Technology Department, CSIR-Central Food Technological Research Institute, Mysore, 570020, India
| | - Prakash M Halami
- Microbiology and Fermentation Technology Department, CSIR-Central Food Technological Research Institute, Mysore, 570020, India.
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Structure, Biosynthesis, and Biological Activity of Succinylated Forms of Bacteriocin BacSp222. Int J Mol Sci 2021; 22:ijms22126256. [PMID: 34200765 PMCID: PMC8230399 DOI: 10.3390/ijms22126256] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/04/2021] [Accepted: 06/07/2021] [Indexed: 01/21/2023] Open
Abstract
BacSp222 is a multifunctional peptide produced by Staphylococcus pseudintermedius 222. This 50-amino acid long peptide belongs to subclass IId of bacteriocins and forms a four-helix bundle molecule. In addition to bactericidal functions, BacSp222 possesses also features of a virulence factor, manifested in immunomodulatory and cytotoxic activities toward eukaryotic cells. In the present study, we demonstrate that BacSp222 is produced in several post-translationally modified forms, succinylated at the ε-amino group of lysine residues. Such modifications have not been previously described for any bacteriocins. NMR and circular dichroism spectroscopy studies have shown that the modifications do not alter the spatial structure of the peptide. At the same time, succinylation significantly diminishes its bactericidal and cytotoxic potential. We demonstrate that the modification of the bacteriocin is an effect of non-enzymatic reaction with a highly reactive intracellular metabolite, i.e., succinyl-coenzyme A. The production of succinylated forms of the bacteriocin depends on environmental factors and on the access of bacteria to nutrients. Our study indicates that the production of succinylated forms of bacteriocin occurs in response to the changing environment, protects producer cells against the autotoxicity of the excreted peptide, and limits the pathogenicity of the strain.
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10
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Vaca J, Ortiz A, Sansinenea E. Bacillus sp. Bacteriocins: Natural Weapons against Bacterial Enemies. Curr Med Chem 2021; 29:2093-2108. [PMID: 34047258 DOI: 10.2174/0929867328666210527093041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/08/2021] [Accepted: 04/13/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Currently, antibiotic-resistant pathogenic bacteria are emerging as an important health problem worldwide. The search for new compounds with antibiotic characteristics is the most promising alternative. Bacteriocins are natural compounds that are inhibitory against pathogens, and Bacillus species are the major producers of these compounds, which have shown antimicrobial activity against clinically important bacteria. These peptides not only have potential in the pharmaceutical industry but also in food and agricultural sectors. OBJECTIVE We provide an overview of the recent bacteriocins isolated from different species of Bacillus including their applications and the older bacteriocins. RESULTS In this review, we have revised some works about the improvements carried out in the production of bacteriocins. CONCLUSION These applications make bacteriocins very promising compounds that need to study for industrial production.
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Affiliation(s)
- Jessica Vaca
- Facultad De Ciencias Químicas, Benemérita Universidad Autónoma De Puebla, 72590 Puebla; Pue, Mexico
| | - Aurelio Ortiz
- Facultad De Ciencias Químicas, Benemérita Universidad Autónoma De Puebla, 72590 Puebla; Pue, Mexico
| | - Estibaliz Sansinenea
- Facultad De Ciencias Químicas, Benemérita Universidad Autónoma De Puebla, 72590 Puebla; Pue, Mexico
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11
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Benítez-Chao DF, León-Buitimea A, Lerma-Escalera JA, Morones-Ramírez JR. Bacteriocins: An Overview of Antimicrobial, Toxicity, and Biosafety Assessment by in vivo Models. Front Microbiol 2021; 12:630695. [PMID: 33935991 PMCID: PMC8083986 DOI: 10.3389/fmicb.2021.630695] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 03/08/2021] [Indexed: 12/13/2022] Open
Abstract
The world is facing a significant increase in infections caused by drug-resistant infectious agents. In response, various strategies have been recently explored to treat them, including the development of bacteriocins. Bacteriocins are a group of antimicrobial peptides produced by bacteria, capable of controlling clinically relevant susceptible and drug-resistant bacteria. Bacteriocins have been studied to be able to modify and improve their physicochemical properties, pharmacological effects, and biosafety. This manuscript focuses on the research being developed on the biosafety of bacteriocins, which is a topic that has not been addressed extensively in previous reviews. This work discusses the studies that have tested the effect of bacteriocins against pathogens and assess their toxicity using in vivo models, including murine and other alternative animal models. Thus, this work concludes the urgency to increase and advance the in vivo models that both assess the efficacy of bacteriocins as antimicrobial agents and evaluate possible toxicity and side effects, which are key factors to determine their success as potential therapeutic agents in the fight against infections caused by multidrug-resistant microorganisms.
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Affiliation(s)
- Diego Francisco Benítez-Chao
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Mexico.,Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Parque de Investigación e Innovación Tecnológica, Universidad Autónoma de Nuevo León, Apodaca, Mexico
| | - Angel León-Buitimea
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Mexico.,Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Parque de Investigación e Innovación Tecnológica, Universidad Autónoma de Nuevo León, Apodaca, Mexico
| | - Jordy Alexis Lerma-Escalera
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Mexico.,Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Parque de Investigación e Innovación Tecnológica, Universidad Autónoma de Nuevo León, Apodaca, Mexico
| | - José Rubén Morones-Ramírez
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Mexico.,Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Parque de Investigación e Innovación Tecnológica, Universidad Autónoma de Nuevo León, Apodaca, Mexico
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12
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Wei Z, Shan C, Zhang L, Ge D, Wang Y, Xia X, Liu X, Zhou J. A novel subtilin-like lantibiotics subtilin JS-4 produced by Bacillus subtilis JS-4, and its antibacterial mechanism against Listeria monocytogenes. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.110993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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13
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Sandvang D, Skjoet-Rasmussen L, Cantor MD, Mathis GF, Lumpkins BS, Blanch A. Effects of feed supplementation with 3 different probiotic Bacillus strains and their combination on the performance of broiler chickens challenged with Clostridium perfringens. Poult Sci 2021; 100:100982. [PMID: 33647715 PMCID: PMC7921869 DOI: 10.1016/j.psj.2021.01.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 12/07/2020] [Accepted: 01/01/2021] [Indexed: 12/27/2022] Open
Abstract
The application of probiotics in broiler feed, to alleviate performance deficiencies due to mild infections by coccidia and Clostridium perfringens, is of increasing interest for the poultry industry. Therefore, our objective was to evaluate the capacity of 3 Bacillus strains and their combination as probiotics in vitro and in vivo. Thus, protein and carbohydrate degradation and C. perfringens growth inhibition capabilities were assessed by colometry measurement and an agar diffusion bioassay, respectively. A total of 2,250 1-day-old male broiler chicks were assigned to 5 dietary treatments: 1) non-probiotic-supplemented control (control); 2) control + DSM 32324 at 0.8 × 106 cfu/g of feed; 3) control + DSM 32325 at 0.5 × 106 cfu/g of feed; 4) control + DSM 25840 at 0.3 × 106 cfu/g of feed; and 5) control + DSM 32324 + DSM 32325 + DSM 25840 at 1.6 × 106 cfu/g of feed. A pathogenic field strain of C. perfringens was used to induce the necrotic enteritis challenge on day 19, 20, and 21. All birds and remaining feed were weighed on pen basis on day 0, 21, 35, and 42, to calculate BW gain and mortality-adjusted feed conversion. Mortality and mortality due to necrotic enteritis were recorded daily. On day 21, 45 birds per treatment were evaluated for macroscopic intestinal necrotic enteritis lesions. Performance data were statistically analyzed using an ANOVA and subjected to a least significant difference comparison. Necrotic enteritis lesion scores were statistically analyzed using nonparametric Kruskal-Wallis test. Dunn's test was used for treatment comparison. The tested strains showed different abilities of degrading protein and carbohydrates and inhibiting C. perfringens growth in vitro. The birds fed the multi-train combination presented significantly better performance and lower necrotic enteritis lesion score than those in the control group. Dietary supplementation with probiotics resulted in significantly lower necrotic enteritis mortality. The results demonstrate the suitability of the evaluated Bacillus multistrain combination as an effective probiotic in C. perfringens-challenged chickens.
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Affiliation(s)
| | | | | | - Greg F Mathis
- Southern Poultry Feed and Research, Inc. 30607-3153 Georgia, USA
| | - Brett S Lumpkins
- Southern Poultry Feed and Research, Inc. 30607-3153 Georgia, USA
| | - Alfred Blanch
- Addimus, Providing Trust, S.L., 08012 Barcelona, Spain
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14
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Bacteriocin isolated from the natural inhabitant of Allium cepa against Staphylococcus aureus. World J Microbiol Biotechnol 2021; 37:20. [PMID: 33427970 DOI: 10.1007/s11274-020-02989-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 12/22/2020] [Indexed: 12/19/2022]
Abstract
Extensive usage of antibiotics has led to the emergence of drug-resistant strains of pathogens and hence, there is an urgent need for alternative antimicrobial agents. Antimicrobial Peptides (AMPs) of bacterial origin have shown the potential to replace some conventional antibiotics. In the present study, an AMP was isolated from Bacillus subtilis subsp. spizizenii strain Ba49 present on the Allium cepa, the common onion and named as peptide-Ba49. The isolated AMP was purified and characterized. The purified peptide-Ba49, having a molecular weight of ~ 3.3 kDa as determined using mass spectroscopy, was stable up to 121 °C and in the pH range of 5-10. Its interaction with protein degrading enzymes confirmed the peptide nature of the molecule. The peptide exhibited low minimum inhibitory concentration (MIC) against Staphylococcus aureus and its (Methicillin-resistant Staphylococcus aureus) MRSA strains (MIC, 2-16 µM/mL). Further, time kill kinetic assay was performed and analysis of the results of membrane depolarization and permeabilization assays (TEM, DiBAC4 (3) and PI) suggested peptide-Ba49 to be acting through the change in membrane potential leading to disruption of S. aureus membrane. Additionally, cytotoxicity studies of peptide-Ba49, carried out using three mammalian cell lines viz. HEK 293T, RAW 264.7, and L929, showed limited cytotoxicity on these cell lines at a concentration much higher than its MIC values. All these studies suggested that the AMP isolated from strain Ba49 (peptide-Ba49) has the potential to be an alternative to antibiotics in terms of eradicating the pathogenic as well as drug-resistant microorganisms.
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16
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Lajis AFB. Biomanufacturing process for the production of bacteriocins from Bacillaceae family. BIORESOUR BIOPROCESS 2020. [DOI: 10.1186/s40643-020-0295-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
AbstractMembers of Bacillaceae family are of major interest in medical industry due to vast antimicrobial peptides they produce as therapeutic agents. For decades, synthetic and natural occurring antibiotics have been used to treat infectious diseases, but heavy dependence on these drugs has led to significant drawbacks which propel continuous development of new antibiotics generation. Recent findings have shown several bacteriocins of Bacillaceae as promising alternatives to the conventional drugs to combat the emergence of new drug-resistant pathogens. In this present review, Bacillaceae bacteriocins’ classification such as lantibiotics and thiazole/oxazole-modified microcins as well as their biochemical characterization such as sensitivity to enzymes, temperature, pH and chemicals are described. This article enlightens on the medical application of several Bacillaceae bacteriocins emphasizing those that underwent and on-going preclinical trials. This review also discusses the development of Bacillaceae bacteriocins production, focusing strains selection and fermentation factors such as inocula size, medium (carbon, nitrogen, minerals sources), temperature, pH, agitation and aeration rate, dissolved oxygen tension (DOT), fermentation time, inducers and mode of operation via various statistical methods for their optimization. It also highlights recent advance in the production of bioengineered and recombinant bacteriocins in bioreactors system which are rarely disclosed in literature.
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Ibrahim S, Azab El-Liethy M, Abia ALK, Abdel-Gabbar M, Mahmoud Al Zanaty A, Mohamed Kamel M. Design of a bioaugmented multistage biofilter for accelerated municipal wastewater treatment and deactivation of pathogenic microorganisms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 703:134786. [PMID: 31731155 DOI: 10.1016/j.scitotenv.2019.134786] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 09/02/2019] [Accepted: 10/01/2019] [Indexed: 06/10/2023]
Abstract
Biological treatment of municipal wastewater for reuse in irrigation is highly required, especially with the current global financial and water shortage crises. Bioaugmentation is a simple and cost-effective technology which could be a useful tool in alleviating this challenge. Thus, this study aimed to enhance the biological treatment of municipal wastewater using a bioaugmented substance supplemented in a three-stages bio-filter consisting of a sedimentation step followed by gravel biofiltration and then sand biofiltration at a laboratory scale. Also, a toxicity assay, the antimicrobial effect of the bioaugmented substance against pathogenic microorganisms, and identification of the synergistic effect of the bacterial consortium involved in the bioaugmented substance were studied. The bioaugmented substance was nontoxic and had an antimicrobial effect against the tested potentially pathogenic microorganisms (Escherichia coli, Pseudomonas aeruginosa, Listeria monocytogenes, Staphylococcus aureus, and Candida albicans). The minimum effective concentration of the bioaugmented substance for organic, inorganic and microbial pollutants removal from high strength wastewater was 2.5 ppm with a contact time of 6-8 h. The removal efficiencies of H2S, COD, BOD5, total solids (TS), total dissolved solids, total suspended solids, ammonia, nitrate, phosphorus, and oil and grease reached 85, 93.4, 83.5, 37, 49.2, 93.4, 100, 55.7, 76.6 and 76.6%, respectively in the treated effluent after sand biofiltration. The physicochemical parameters of the treated wastewater effluent were below the Egyptian recommended limits (Law 84/1984) for use in irrigation. However, COD and BOD values were 90.33 and 38.46 mgO2/L, respectively, and were still above the regulations (COD ≤60 and BOD ≤20). The high fecal coliforms count in the wastewater influent (8.4 × 108 MPN-index/100 mL) were 95.1% removed after the sedimentation stage, and 99.99% removal was achieved after gravel and sand biofiltration. Thus, this study successfully designed a bioaugmented multistage biofiltration system for the effective removal of pollutants from wastewater, especially in resource-limited areas.
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Affiliation(s)
- Salma Ibrahim
- Water and Wastewater Company, Fayoum Governorate, Egypt
| | - Mohamed Azab El-Liethy
- Environmental Microbiology Lab., Water Pollution Research Department, National Research Centre, Dokki, Giza 12622, Egypt.
| | - Akebe Luther King Abia
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, X54001 Durban, South Africa.
| | - Mohammed Abdel-Gabbar
- Biochemistry Department, Faculty of Science, Beni-Suef University, BeniSuef Governorate, Egypt
| | - Ali Mahmoud Al Zanaty
- Biochemistry Department, Faculty of Science, Beni-Suef University, BeniSuef Governorate, Egypt
| | - Mohamed Mohamed Kamel
- Environmental Microbiology Lab., Water Pollution Research Department, National Research Centre, Dokki, Giza 12622, Egypt
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18
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Antimicrobial secondary metabolites from agriculturally important bacteria as next-generation pesticides. Appl Microbiol Biotechnol 2019; 104:1013-1034. [PMID: 31858191 DOI: 10.1007/s00253-019-10300-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/25/2019] [Accepted: 12/03/2019] [Indexed: 10/25/2022]
Abstract
The whole organisms can be packaged as biopesticides, but secondary metabolites secreted by microorganisms can also have a wide range of biological activities that either protect the plant against pests and pathogens or act as plant growth promotors which can be beneficial for the agricultural crops. In this review, we have compiled information about the most important secondary metabolites of three important bacterial genera currently used in agriculture pest and disease management.
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19
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Geiger C, Korn SM, Häsler M, Peetz O, Martin J, Kötter P, Morgner N, Entian KD. LanI-Mediated Lantibiotic Immunity in Bacillus subtilis: Functional Analysis. Appl Environ Microbiol 2019; 85:e00534-19. [PMID: 30952662 PMCID: PMC6532034 DOI: 10.1128/aem.00534-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 03/26/2019] [Indexed: 01/09/2023] Open
Abstract
Lantibiotics subtilin and nisin are produced by Bacillus subtilis and Lactococcus lactis, respectively. To prevent toxicity of their own lantibiotic, both bacteria express specific immunity proteins, called SpaI and NisI. In addition, ABC transporters SpaFEG and NisFEG prevent lantibiotic toxicity by transporting the respective peptides to the extracellular space. Although the three-dimensional structures of SpaI and NisI have been solved, very little is known about the molecular function of either lipoprotein. Using laser-induced liquid bead ion desorption (LILBID)-mass spectrometry, we show here that subtilin interacts with SpaI monomers. The expression of either SpaI or NisI in a subtilin-nonproducing B. subtilis strain resulted in the respective strain being more resistant against either subtilin or nisin. Furthermore, pore formation provided by subtilin and nisin was prevented specifically upon the expression of either SpaI or NisI. As shown with a nisin-subtilin hybrid molecule, the C-terminal part of subtilin but not any particular lanthionine ring was needed for SpaI-mediated immunity. With respect to growth, SpaI provided less immunity against subtilin than is provided by the ABC transporter SpaFEG. However, SpaI prevented pore formation much more efficiently than SpaFEG. Taken together, our data show the physiological function of SpaI as a fast immune response to protect the cellular membrane.IMPORTANCE The two lantibiotics nisin and subtilin are produced by Lactococcus lactis and Bacillus subtilis, respectively. Both peptides have strong antimicrobial activity against Gram-positive bacteria, and therefore, appropriate protection mechanisms are required for the producing strains. To prevent toxicity of their own lantibiotic, both bacteria express immunity proteins, called SpaI and NisI, and in addition, ABC transporters SpaFEG and NisFEG. Whereas it has been shown that the ABC transporters protect the producing strains by transporting the toxic peptides to the extracellular space, the exact mode of action and the physiological function of the lipoproteins during immunity are still unknown. Understanding the exact role of lantibiotic immunity proteins is of major importance for improving production rates and for the design of newly engineered peptide antibiotics. Here, we show (i) the specificity of each lipoprotein for its own lantibiotic, (ii) the specific physical interaction of subtilin with its lipoprotein SpaI, (iii) the physiological function of SpaI in protecting the cellular membrane, and (iv) the importance of the C-terminal part of subtilin for its interaction with SpaI.
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Affiliation(s)
- Christoph Geiger
- Molecular Genetics and Cellular Microbiology, Institute for Molecular Biosciences, University of Frankfurt, Frankfurt, Germany
| | - Sophie Marianne Korn
- Molecular Genetics and Cellular Microbiology, Institute for Molecular Biosciences, University of Frankfurt, Frankfurt, Germany
| | - Michael Häsler
- Molecular Genetics and Cellular Microbiology, Institute for Molecular Biosciences, University of Frankfurt, Frankfurt, Germany
| | - Oliver Peetz
- Institute of Physical and Theoretical Chemistry, Goethe University, Frankfurt, Germany
| | - Janosch Martin
- Institute of Physical and Theoretical Chemistry, Goethe University, Frankfurt, Germany
| | - Peter Kötter
- Molecular Genetics and Cellular Microbiology, Institute for Molecular Biosciences, University of Frankfurt, Frankfurt, Germany
| | - Nina Morgner
- Institute of Physical and Theoretical Chemistry, Goethe University, Frankfurt, Germany
| | - Karl-Dieter Entian
- Molecular Genetics and Cellular Microbiology, Institute for Molecular Biosciences, University of Frankfurt, Frankfurt, Germany
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20
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Horak I, Engelbrecht G, Rensburg PJ, Claassens S. Microbial metabolomics: essential definitions and the importance of cultivation conditions for utilizingBacillusspecies as bionematicides. J Appl Microbiol 2019; 127:326-343. [PMID: 30739384 DOI: 10.1111/jam.14218] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 02/04/2019] [Accepted: 02/04/2019] [Indexed: 01/05/2023]
Affiliation(s)
- I. Horak
- Unit for Environmental Sciences and Management North‐West University Potchefstroom South Africa
| | - G. Engelbrecht
- Unit for Environmental Sciences and Management North‐West University Potchefstroom South Africa
| | | | - S. Claassens
- Unit for Environmental Sciences and Management North‐West University Potchefstroom South Africa
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21
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Qin Y, Wang Y, He Y, Zhang Y, She Q, Chai Y, Li P, Shang Q. Characterization of Subtilin L-Q11, a Novel Class I Bacteriocin Synthesized by Bacillus subtilis L-Q11 Isolated From Orchard Soil. Front Microbiol 2019; 10:484. [PMID: 30930878 PMCID: PMC6429107 DOI: 10.3389/fmicb.2019.00484] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 02/25/2019] [Indexed: 12/25/2022] Open
Abstract
Bacteriocins are peptides or proteins synthesized by bacterial ribosomes that show killing or inhibitory activities against different groups of bacteria. Bacteriocins are considered potential alternatives to traditional antibiotics, preservatives in pharmaceutical and food industries. A strain L-Q11 isolated from orchard soil was phylogenetically characterized as Bacillus subtilis based on 16S rRNA gene sequencing analysis. A novel class I bacteriocin (Subtilin L-Q11), was identified and purified from L-Q11 cell-free supernatant in a four-step procedure, including salt precipitation, cation exchange, gel filtration, and reverse-phase high-performance liquid chromatography (RP-HPLC). The molecular mass (3,552.9 Da) of this novel bacteriocin was determined by Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). The purified Subtilin L-Q11 exhibited optimal features in pH tolerance, thermostability, and sensitivity to proteases. Further, Subtilin L-Q11 showed inhibitory activities against a number of bacteria including some human pathogens and food spoilage bacteria, in particular Staphylococcus aureus. All these important features make this novel bacteriocin a potential candidate for the development of a new antibacterial drug or food preservative in the future.
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Affiliation(s)
- Yuxuan Qin
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, Key Laboratory of Functional Dairy, China Agricultural University, Beijing, China.,Department of Biology, Northeastern University, Boston, MA, United States
| | - Yao Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, Key Laboratory of Functional Dairy, China Agricultural University, Beijing, China
| | - Yinghao He
- Department of Biology, Northeastern University, Boston, MA, United States
| | - Ying Zhang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, Key Laboratory of Functional Dairy, China Agricultural University, Beijing, China
| | - Qianxuan She
- Department of Biology, Northeastern University, Boston, MA, United States
| | - Yunrong Chai
- Department of Biology, Northeastern University, Boston, MA, United States
| | - Pinglan Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, Key Laboratory of Functional Dairy, China Agricultural University, Beijing, China
| | - Qingmao Shang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
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22
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Bacillus subtilis DSM 32315 Supplementation Attenuates the Effects of Clostridium perfringens Challenge on the Growth Performance and Intestinal Microbiota of Broiler Chickens. Microorganisms 2019; 7:microorganisms7030071. [PMID: 30841654 PMCID: PMC6463140 DOI: 10.3390/microorganisms7030071] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 02/23/2019] [Accepted: 03/04/2019] [Indexed: 12/15/2022] Open
Abstract
The objective of this study was to evaluate the effects of the dietary supplementation of Bacillus subtilis DSM 32315 (probiotic) on the performance and intestinal microbiota of broiler chickens infected with Clostridium perfringens (CP). One-day-old broiler chickens were assigned to 3 treatments with 8 replicate pens (50 birds/pen). The treatments were: non-infected control; infected control; and infected supplemented with probiotic (1 × 106 CFU/g of feed). On day of hatch, all birds were sprayed with a coccidia vaccine based on the manufacturer recommended dosage. On d 18–20 the infected birds were inoculated with CP via feed. Necrotic enteritis (NE) lesion score was performed on d 21. Digestive tract of 2 birds/pen was collected on d 21 to analyze the ileal and cecal microbiota by 16S rRNA sequencing. Performance was evaluated on d 28 and 42. On d 21, probiotic supplementation reduced (p < 0.001) the severity of NE related lesion versus infected control birds. On d 28, feed efficiency was improved (p < 0.001) in birds supplemented with probiotic versus infected control birds. On d 42, body weight gain (BW gain) and feed conversion ratio (FCR) were improved (p < 0.001) in probiotic supplemented birds versus infected control birds. The diversity, composition and predictive function of the intestinal microbial digesta changed with the infection but the supplementation of probiotic reduced these variations. Therefore, dietary supplementation of Bacillus subtilis DSM 32315 was beneficial in attenuating the negative effects of CP challenge on the performance and intestinal microbiota of broilers chickens.
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23
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Halami PM. Sublichenin, a new subtilin-like lantibiotics of probiotic bacterium Bacillus licheniformis MCC 2512T with antibacterial activity. Microb Pathog 2019; 128:139-146. [DOI: 10.1016/j.micpath.2018.12.044] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 12/22/2018] [Accepted: 12/26/2018] [Indexed: 11/16/2022]
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24
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Caulier S, Nannan C, Gillis A, Licciardi F, Bragard C, Mahillon J. Overview of the Antimicrobial Compounds Produced by Members of the Bacillus subtilis Group. Front Microbiol 2019; 10:302. [PMID: 30873135 PMCID: PMC6401651 DOI: 10.3389/fmicb.2019.00302] [Citation(s) in RCA: 302] [Impact Index Per Article: 60.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 02/05/2019] [Indexed: 12/19/2022] Open
Abstract
Over the last seven decades, applications using members of the Bacillus subtilis group have emerged in both food processes and crop protection industries. Their ability to form survival endospores and the plethora of antimicrobial compounds they produce has generated an increased industrial interest as food preservatives, therapeutic agents and biopesticides. In the growing context of food biopreservation and biological crop protection, this review suggests a comprehensive way to visualize the antimicrobial spectrum described within the B. subtilis group, including volatile compounds. This classification distinguishes the bioactive metabolites based on their biosynthetic pathways and chemical nature: i.e., ribosomal peptides (RPs), volatile compounds, polyketides (PKs), non-ribosomal peptides (NRPs), and hybrids between PKs and NRPs. For each clade, the chemical structure, biosynthesis and antimicrobial activity are described and exemplified. This review aims at constituting a convenient and updated classification of antimicrobial metabolites from the B. subtilis group, whose complex phylogeny is prone to further development.
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Affiliation(s)
- Simon Caulier
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium.,Laboratory of Phytopathology-Applied Microbiology, Earth and Life Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Catherine Nannan
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Annika Gillis
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Florent Licciardi
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Claude Bragard
- Laboratory of Phytopathology-Applied Microbiology, Earth and Life Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Jacques Mahillon
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium
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25
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Alkhalili RN, Canbäck B. Identification of Putative Novel Class-I Lanthipeptides in Firmicutes: A Combinatorial In Silico Analysis Approach Performed on Genome Sequenced Bacteria and a Close Inspection of Z-Geobacillin Lanthipeptide Biosynthesis Gene Cluster of the Thermophilic Geobacillus sp. Strain ZGt-1. Int J Mol Sci 2018; 19:E2650. [PMID: 30200662 PMCID: PMC6165006 DOI: 10.3390/ijms19092650] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 08/23/2018] [Accepted: 09/04/2018] [Indexed: 01/03/2023] Open
Abstract
Lanthipeptides are ribosomally synthesized and post-translationally modified polycyclic peptides. Lanthipeptides that have antimicrobial activity are known as lantibiotics. Accordingly, the discovery of novel lantibiotics constitutes a possible solution for the problem of antibiotic resistance. We utilized the publicly available genome sequences and the bioinformatic tools tailored for the detection of lanthipeptides. We designed our strategy for screening of 252 firmicute genomes and detecting class-I lanthipeptide-coding gene clusters. The designed strategy resulted in identifying 69 class-I lanthipeptide sequences, of which more than 10% were putative novel. The identified putative novel lanthipeptides have not been annotated on the original or the RefSeq genomes, or have been annotated merely as coding for hypothetical proteins. Additionally, we identified bacterial strains that have not been previously recognized as lanthipeptide-producers. Moreover, we suggest corrections for certain firmicute genome annotations, and recommend lanthipeptide records for enriching the bacteriocin genome mining tool (BAGEL) databases. Furthermore, we propose Z-geobacillin, a putative class-I lanthipeptide coded on the genome of the thermophilic strain Geobacillus sp. ZGt-1. We provide lists of putative novel lanthipeptide sequences and of the previously unrecognized lanthipeptide-producing bacterial strains, so they can be prioritized for experimental investigation. Our results are expected to benefit researchers interested in the in vitro production of lanthipeptides.
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Affiliation(s)
- Rawana N Alkhalili
- Biotechnology, Department of Chemistry, Lund University, SE-221 00 Lund, Sweden.
| | - Björn Canbäck
- Department of Biology, Lund University, SE-221 00 Lund, Sweden.
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26
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Xu B, Aitken EJ, Baker BP, Turner CA, Harvey JE, Stott MB, Power JF, Harris PWR, Keyzers RA, Brimble MA. Genome mining, isolation, chemical synthesis and biological evaluation of a novel lanthipeptide, tikitericin, from the extremophilic microorganism Thermogemmatispora strain T81. Chem Sci 2018; 9:7311-7317. [PMID: 30294420 PMCID: PMC6167946 DOI: 10.1039/c8sc02170h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 08/19/2018] [Indexed: 01/31/2023] Open
Abstract
Tikitericin, a novel lanthipeptide was isolated and characterised together with its first total synthesis.
Genome mining of the New Zealand extremophilic microorganism Thermogemmatispora strain T81 indicated the presence of biosynthetic machinery to produce several different peptidic natural products. Solid-phase culture of T81 led to the isolation of tikitericin 1, a new lanthipeptide characterised by four (methyl)lanthionine bridges. The mass-guided isolation and structural elucidation of tikitericin 1 is described together with its total synthesis via Fmoc-solid-phase peptide synthesis (SPPS). The key non-canonical (methyl)lanthionine residues were synthesised in solution phase via an improved synthetic route and subsequently assembled to construct the peptide backbone using Fmoc-SPPS. N-Terminal truncated analogues of tikitericin (2–5) were also prepared in order to evaluate the contribution of each sequential ring of the polycyclic lanthipeptide to the antibacterial activity.
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Affiliation(s)
- Buzhe Xu
- School of Chemical Sciences , 23 Symonds Street , Auckland 1010 , New Zealand . ; Tel: +64 9 9238259.,Maurice Wilkins Centre for Molecular Biodiscovery , The University of Auckland , Private Bag 92019 , Auckland 1142 , New Zealand . ; Tel: +64 4 4635117
| | - Emma J Aitken
- School of Chemical & Physical Sciences , The Centre for Biodiscovery , Victoria University of Wellington , PO Box 600 , Wellington 6140 , New Zealand
| | - Benjamin P Baker
- School of Chemical & Physical Sciences , The Centre for Biodiscovery , Victoria University of Wellington , PO Box 600 , Wellington 6140 , New Zealand
| | - Claire A Turner
- School of Chemical & Physical Sciences , The Centre for Biodiscovery , Victoria University of Wellington , PO Box 600 , Wellington 6140 , New Zealand
| | - Joanne E Harvey
- Maurice Wilkins Centre for Molecular Biodiscovery , The University of Auckland , Private Bag 92019 , Auckland 1142 , New Zealand . ; Tel: +64 4 4635117.,School of Chemical & Physical Sciences , The Centre for Biodiscovery , Victoria University of Wellington , PO Box 600 , Wellington 6140 , New Zealand
| | - Matthew B Stott
- School of Biological Sciences , University of Canterbury , Private Bag 4800 , Christchurch 8140 , New Zealand.,GNS Science , Private Bag 2000 , Taupō 3352 , New Zealand
| | - Jean F Power
- GNS Science , Private Bag 2000 , Taupō 3352 , New Zealand
| | - Paul W R Harris
- School of Chemical Sciences , 23 Symonds Street , Auckland 1010 , New Zealand . ; Tel: +64 9 9238259.,Maurice Wilkins Centre for Molecular Biodiscovery , The University of Auckland , Private Bag 92019 , Auckland 1142 , New Zealand . ; Tel: +64 4 4635117.,School of Biological Sciences , 23 Symonds Street , Auckland 1010 , New Zealand
| | - Robert A Keyzers
- Maurice Wilkins Centre for Molecular Biodiscovery , The University of Auckland , Private Bag 92019 , Auckland 1142 , New Zealand . ; Tel: +64 4 4635117.,School of Chemical & Physical Sciences , The Centre for Biodiscovery , Victoria University of Wellington , PO Box 600 , Wellington 6140 , New Zealand
| | - Margaret A Brimble
- School of Chemical Sciences , 23 Symonds Street , Auckland 1010 , New Zealand . ; Tel: +64 9 9238259.,Maurice Wilkins Centre for Molecular Biodiscovery , The University of Auckland , Private Bag 92019 , Auckland 1142 , New Zealand . ; Tel: +64 4 4635117.,School of Biological Sciences , 23 Symonds Street , Auckland 1010 , New Zealand
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27
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Schouw A, Vulcano F, Roalkvam I, Hocking WP, Reeves E, Stokke R, Bødtker G, Steen IH. Genome Analysis of Vallitalea guaymasensis Strain L81 Isolated from a Deep-Sea Hydrothermal Vent System. Microorganisms 2018; 6:E63. [PMID: 29973550 PMCID: PMC6163223 DOI: 10.3390/microorganisms6030063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 06/28/2018] [Accepted: 06/29/2018] [Indexed: 12/21/2022] Open
Abstract
Abyssivirga alkaniphila strain L81T, recently isolated from a black smoker biofilm at the Loki’s Castle hydrothermal vent field, was previously described as a mesophilic, obligately anaerobic heterotroph able to ferment carbohydrates, peptides, and aliphatic hydrocarbons. The strain was classified as a new genus within the family Lachnospiraceae. Herein, its genome is analyzed and A. alkaniphila is reassigned to the genus Vallitalea as a new strain of V. guaymasensis, designated V. guaymasensis strain L81. The 6.4 Mbp genome contained 5651 protein encoding genes, whereof 4043 were given a functional prediction. Pathways for fermentation of mono-saccharides, di-saccharides, peptides, and amino acids were identified whereas a complete pathway for the fermentation of n-alkanes was not found. Growth on carbohydrates and proteinous compounds supported methane production in co-cultures with Methanoplanus limicola. Multiple confurcating hydrogen-producing hydrogenases, a putative bifurcating electron-transferring flavoprotein—butyryl-CoA dehydrogenase complex, and a Rnf-complex form a basis for the observed hydrogen-production and a putative reverse electron-transport in V. guaymasensis strain L81. Combined with the observation that n-alkanes did not support growth in co-cultures with M. limicola, it seemed more plausible that the previously observed degradation patterns of crude-oil in strain L81 are explained by unspecific activation and may represent a detoxification mechanism, representing an interesting ecological function. Genes encoding a capacity for polyketide synthesis, prophages, and resistance to antibiotics shows interactions with the co-occurring microorganisms. This study enlightens the function of the fermentative microorganisms from hydrothermal vents systems and adds valuable information on the bioprospecting potential emerging in deep-sea hydrothermal systems.
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Affiliation(s)
- Anders Schouw
- Department of Biological Sciences and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
| | - Francesca Vulcano
- Department of Biological Sciences and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
| | - Irene Roalkvam
- Department of Biological Sciences and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
| | - William Peter Hocking
- Department of Biological Sciences and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
| | - Eoghan Reeves
- Department of Earth Science and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
| | - Runar Stokke
- Department of Biological Sciences and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
| | - Gunhild Bødtker
- Centre for Integrated Petroleum Research (CIPR), Uni Research AS, Nygårdsgaten 112, N-5008 Bergen, Norway.
| | - Ida Helene Steen
- Department of Biological Sciences and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
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Grant A, Gay CG, Lillehoj HS. Bacillus spp. as direct-fed microbial antibiotic alternatives to enhance growth, immunity, and gut health in poultry. Avian Pathol 2018; 47:339-351. [PMID: 29635926 DOI: 10.1080/03079457.2018.1464117] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The increasing occurrence of antibiotic-resistant bacteria combined with regulatory pressure and consumer demands for foods produced without antibiotics has caused the agricultural industry to restrict its practice of using antibiotic growth promoters (AGP) in food animals. The poultry industry is not immune to this trend, and has been actively seeking natural alternatives to AGP that will improve the health and growth performance of commercial poultry flocks. Bacillus probiotics have been gaining in popularity in recent years as an AGP alternative because of their health-promoting benefits and ability to survive the harsh manufacturing conditions of chicken feed production. This review provides an overview of several modes of action of some Bacillus direct-fed microbials as probiotics. Among the benefits of these direct-fed microbials are their production of naturally synthesized antimicrobial peptides, gut flora modulation to promote beneficial microbiota along the gastrointestinal tract, and various immunological and gut morphological alterations. The modes of action for increased performance are not well defined, and growth promotion is not equal across all Bacillus species or within strains. Appropriate screening and characterization of Bacillus isolates prior to commercialization are necessary to maximize poultry growth to meet the ultimate goal of eliminating AGP usage in animal husbandry.
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Affiliation(s)
- Ar'Quette Grant
- a Animal Biosciences and Biotechnology Laboratory, Agricultural Research Service , US Department of Agriculture , Beltsville , MD , USA
| | - Cyril G Gay
- b National Program Staff - Animal Health, Agricultural Research Service , US Department of Agriculture , Beltsville , MD , USA
| | - Hyun S Lillehoj
- a Animal Biosciences and Biotechnology Laboratory, Agricultural Research Service , US Department of Agriculture , Beltsville , MD , USA
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CerR, a Single-Domain Regulatory Protein of the LuxR Family, Promotes Cerecidin Production and Immunity in Bacillus cereus. Appl Environ Microbiol 2018; 84:AEM.02245-17. [PMID: 29247062 DOI: 10.1128/aem.02245-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 12/12/2017] [Indexed: 12/14/2022] Open
Abstract
Cerecidins are small lantibiotics from Bacillus cereus that were obtained using a semi-in vitro biosynthesis strategy and showed prominent antimicrobial activities against certain Gram-positive bacteria. However, the parental strain B. cereus As 1.1846 is incapable of producing cerecidins, most probably due to the transcriptional repression of the cerecidin gene cluster. Located in the cerecidin gene cluster, cerR encodes a putative response regulator protein that belongs to the LuxR family transcriptional regulators. CerR (84 amino acids) contains only a conserved DNA binding domain and lacks a conventional phosphorylation domain, which is rarely found in lantibiotic gene clusters. To investigate its function in cerecidin biosynthesis, cerR was constitutively expressed in B. cereus As 1.1846. Surprisingly, Constitutive expression of cerR enabled the production of cerecidins and enhanced self-immunity of B. cereus toward cerecidins. Reverse transcription-PCR analysis and electrophoresis mobility shift assays indicated, respectively, that the cer cluster was transcribed in two transcripts (cerAM and cerRTPFE) and that CerR regulated the cerecidin gene cluster directly by binding to the two predicted promoter regions of cerA and cerR DNase I footprinting experiments further confirmed that CerR specifically bound to the two promoter regions at a conserved inverted repeat sequence that was designated a CerR binding motif (cerR box). The present study demonstrated that CerR, as the first single-domain LuxR family transcriptional regulator, serves as a transcriptional activator in cerecidin biosynthesis and activates the cerecidin gene cluster, which was otherwise cryptic in B. cereusIMPORTANCE Lantibiotics with intriguing and prominent bioactivities are potential peptide antibiotics that could be applied in many areas, including food and pharmaceutical industries. The biosynthesis of lantibiotics is generally controlled by two-component regulatory systems consisting of histidine kinases and response regulators, while some unique and interesting regulatory systems are also revealed with the ever-increasing discovery of lantibiotic gene clusters among diverse microorganisms. Dissection of diverse lantibiotic regulation machineries would permit deep understanding of the biological functions of lantibiotics in different niches and even enable genetic activation of lantibiotic gene clusters that are otherwise cryptic. The significance of our study is to illuminate the regulatory mechanism of a special single-domain protein, CerR, in regulating cerecidin biosynthesis in Bacillus cereus, providing a possible novel approach to activate cryptic lantibiotic clusters.
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Chromatography of Quorum Sensing Peptides: An Important Functional Class of the Bacterial Peptidome. Chromatographia 2017. [DOI: 10.1007/s10337-017-3411-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Specificity of Subtilin-Mediated Activation of Histidine Kinase SpaK. Appl Environ Microbiol 2017; 83:AEM.00781-17. [PMID: 28710266 DOI: 10.1128/aem.00781-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 07/11/2017] [Indexed: 12/29/2022] Open
Abstract
Autoinduction via two-component systems is a widespread regulatory mechanism that senses environmental and metabolic changes. Although the lantibiotics nisin and subtilin are closely related and share the same lanthionine ring structure, they autoinduce their biosynthesis in a highly specific manner. Subtilin activates only the two-component system SpaRK of Bacillus subtilis, whereas nisin activates solely the two-component system NisRK of Lactococcus lactis To identify components that determine the specificity of subtilin autoinduction, several variants of the respective lantibiotics were analyzed for their autoinductive capacities. Here, we show that amino acid position 20 is crucial for SpaK activation, as an engineered nisin molecule with phenylalanine at position 20 (nisin N20F) was able to activate SpaK in a specific manner. In combination with the N-terminal tryptophan of subtilin (nisin I1W/N20F), SpaK autoinduction reached almost the level of subtilin-mediated autoinduction. Furthermore, the overall structure of subtilin is also important for its association with the histidine kinase. The destruction of the second lanthionine ring (subtilin C11A, ring B), as well as mutations that interfere with the flexibility of the hinge region located between lanthionine rings C and D (subtilin L21P/Q22P), abolished SpaK autoinduction. Although the C-terminal part of subtilin is needed for efficient SpaK autoinduction, the destruction of lanthionine rings D and E had no measurable impact. Based on these findings, a model for the interaction of subtilin with histidine kinase SpaK was established.IMPORTANCE Although two-component systems are important regulatory systems that sense environmental changes, very little information on the molecular mechanism of sensing or the interaction of the sensor with its respective kinase is available. The strong specificity of linear lantibiotics such as subtilin and nisin for their respective kinases provides an excellent model system to unravel the structural needs of these lantibiotics for activating histidine kinases in a specific manner. More than that, the biosyntheses of lantibiotics are autoinduced via two-component systems. Therefore, an understanding of their interactions with histidine kinases is needed for the biosynthesis of newly engineered peptide antibiotics. Using a Bacillus subtilis-based reporter system, we were able to identify the molecular constraints that are necessary for specific SpaK activation and to provide SpaK specificity to nisin with just two point mutations.
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Assis LM, Nedeljković M, Dessen A. New strategies for targeting and treatment of multi-drug resistant Staphylococcus aureus. Drug Resist Updat 2017; 31:1-14. [PMID: 28867240 DOI: 10.1016/j.drup.2017.03.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 02/07/2017] [Accepted: 03/23/2017] [Indexed: 12/17/2022]
Abstract
Staphylococcus aureus is a major cause of bacterial infection in humans, and has been notoriously able to acquire resistance to a variety of antibiotics. An example is methicillin-resistant S. aureus (MRSA), which despite having been initially associated with clinical settings, now is one of the key causative agents of community-acquired infections. Antibiotic resistance in S. aureus involves mechanisms ranging from drug efflux to increased expression or mutation of target proteins, and this has required innovative approaches to develop novel treatment methodologies. This review provides an overview of the major mechanisms of antibiotic resistance developed by S. aureus, and describes the emerging alternatives being sought to circumvent infection and proliferation, including new generations of classic antibiotics, synergistic approaches, antibodies, and targeting of virulence factors.
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Affiliation(s)
- L Mayrink Assis
- Brazilian National Laboratory for Biosciences (LNBio), CNPEM, Campinas, São Paulo, Brazil
| | - M Nedeljković
- Institut de Biologie Structurale (IBS), Univ Grenoble Alpes, CEA, CNRS, Bacterial Pathogenesis Group, 38044 Grenoble, France
| | - A Dessen
- Brazilian National Laboratory for Biosciences (LNBio), CNPEM, Campinas, São Paulo, Brazil; Institut de Biologie Structurale (IBS), Univ Grenoble Alpes, CEA, CNRS, Bacterial Pathogenesis Group, 38044 Grenoble, France.
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Shafi J, Tian H, Ji M. Bacillus species as versatile weapons for plant pathogens: a review. BIOTECHNOL BIOTEC EQ 2017. [DOI: 10.1080/13102818.2017.1286950] [Citation(s) in RCA: 132] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Affiliation(s)
- Jamil Shafi
- Department of Pesticide Science, Plant Protection College, Shenyang Agricultural University, Shenyang, Liaoning, P. R. China
| | - Hui Tian
- Department of Pesticide Science, Plant Protection College, Shenyang Agricultural University, Shenyang, Liaoning, P. R. China
| | - Mingshan Ji
- Department of Pesticide Science, Plant Protection College, Shenyang Agricultural University, Shenyang, Liaoning, P. R. China
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Zhao X, Kuipers OP. Identification and classification of known and putative antimicrobial compounds produced by a wide variety of Bacillales species. BMC Genomics 2016; 17:882. [PMID: 27821051 PMCID: PMC5100339 DOI: 10.1186/s12864-016-3224-y] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Accepted: 10/27/2016] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Gram-positive bacteria of the Bacillales are important producers of antimicrobial compounds that might be utilized for medical, food or agricultural applications. Thanks to the wide availability of whole genome sequence data and the development of specific genome mining tools, novel antimicrobial compounds, either ribosomally- or non-ribosomally produced, of various Bacillales species can be predicted and classified. Here, we provide a classification scheme of known and putative antimicrobial compounds in the specific context of Bacillales species. RESULTS We identify and describe known and putative bacteriocins, non-ribosomally synthesized peptides (NRPs), polyketides (PKs) and other antimicrobials from 328 whole-genome sequenced strains of 57 species of Bacillales by using web based genome-mining prediction tools. We provide a classification scheme for these bacteriocins, update the findings of NRPs and PKs and investigate their characteristics and suitability for biocontrol by describing per class their genetic organization and structure. Moreover, we highlight the potential of several known and novel antimicrobials from various species of Bacillales. CONCLUSIONS Our extended classification of antimicrobial compounds demonstrates that Bacillales provide a rich source of novel antimicrobials that can now readily be tapped experimentally, since many new gene clusters are identified.
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Affiliation(s)
- Xin Zhao
- Department of Molecular Genetics, University of Groningen, Nijenborgh 7, Groningen, 9747AG, The Netherlands.,School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Oscar P Kuipers
- Department of Molecular Genetics, University of Groningen, Nijenborgh 7, Groningen, 9747AG, The Netherlands.
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Haloalkaliphilic Bacillus species from solar salterns: an ideal prokaryote for bioprospecting studies. ANN MICROBIOL 2016. [DOI: 10.1007/s13213-016-1221-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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Yan ZY, Ai XX, Su YL, Liu XY, Shan XH, Wu SM. Intracellular Biosynthesis of Fluorescent CdSe Quantum Dots in Bacillus subtilis: A Strategy to Construct Signaling Bacterial Probes for Visually Detecting Interaction Between Bacillus subtilis and Staphylococcus aureus. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2016; 22:13-21. [PMID: 26687198 DOI: 10.1017/s1431927615015548] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
In this work, fluorescent Bacillus subtilis (B. subtilis) cells were developed as probes for imaging applications and to explore behaviorial interaction between B. subtilis and Staphylococcus aureus (S. aureus). A novel biological strategy of coupling intracellular biochemical reactions for controllable biosynthesis of CdSe quantum dots by living B. subtilis cells was demonstrated, through which highly luminant and photostable fluorescent B. subtilis cells were achieved with good uniformity. With the help of the obtained fluorescent B. subtilis cells probes, S. aureus cells responded to co-cultured B. subtilis and to aggregate. The degree of aggregation was calculated and nonlinearly fitted to a polynomial model. Systematic investigations of their interactions implied that B. subtilis cells inhibit the growth of neighboring S. aureus cells, and this inhibition was affected by both the growth stage and the amount of surrounding B. subtilis cells. Compared to traditional methods of studying bacterial interaction between two species, such as solid culture medium colony observation and imaging mass spectrometry detection, the procedures were more simple, vivid, and photostable due to the efficient fluorescence intralabeling with less influence on the cells' surface, which might provide a new paradigm for future visualization of microbial behavior.
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Affiliation(s)
- Zheng-Yu Yan
- 1Department of Analytical Chemistry,China Pharmaceutical University,24 Tongjia Lane,Gulou District,Nanjing 210009,China
| | - Xiao-Xia Ai
- 1Department of Analytical Chemistry,China Pharmaceutical University,24 Tongjia Lane,Gulou District,Nanjing 210009,China
| | - Yi-Long Su
- 1Department of Analytical Chemistry,China Pharmaceutical University,24 Tongjia Lane,Gulou District,Nanjing 210009,China
| | - Xin-Ying Liu
- 1Department of Analytical Chemistry,China Pharmaceutical University,24 Tongjia Lane,Gulou District,Nanjing 210009,China
| | - Xiao-Hui Shan
- 3Laizhou Entry-Exit Inspection and Quarantine Bureau,Laizhou 261400,China
| | - Sheng-Mei Wu
- 1Department of Analytical Chemistry,China Pharmaceutical University,24 Tongjia Lane,Gulou District,Nanjing 210009,China
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Monaci L, Quintieri L, Caputo L, Visconti A, Baruzzi F. Rapid profiling of antimicrobial compounds characterising B. subtilis TR50 cell-free filtrate by high-performance liquid chromatography coupled to high-resolution Orbitrap™ mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:45-53. [PMID: 26661969 DOI: 10.1002/rcm.7408] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 09/23/2015] [Accepted: 09/23/2015] [Indexed: 06/05/2023]
Abstract
RATIONALE Several Bacillus strains, typically isolated from different food sources, represent renowned producers of a multitude of low and high molecular weight compounds, including lipopeptides and macrolactones, with an importance for their antimicrobial activity. The high homology shared by many of these compounds also occurring as closely related isoforms poses a challenge in their prompt detection. METHODS Identification and structural elucidation is generally achieved by matrix-assisted laser desorption/ionization (MALDI) or liquid chromatography (LC) coupled to mass spectrometry (MS) after a pre-fractionation and/or purification step of the extract. In this paper we report the application of a method based on LC separation and high-resolution Orbitrap™-based MS for the rapid screening of raw filtrate of the strain Bacillus subtilis TR50 endowed with antimicrobial activity, without requiring any sample pre-treatment. RESULTS Upon direct analysis of the cell-free filtrate of Bacillus subtilis TR50 by high-resolution mass spectrometry (HRMS), different compounds families, that proved to exert a remarked antimicrobial activity against several foodborne pathogens, can be readily displayed along the chromatographic run. Among them, three different classes were identified and characterized belonging to the iturin, fengycin and surfactin groups. The high resolving power and accurate mass accuracy provided by the HRMS system in use ensured an enhanced selectivity compared to other mass spectrometers. In addition, after activation of the HCD cell, the HR-MS/MS spectra can provide insights in the structural elucidation of several compounds. CONCLUSIONS The acquisition of HRMS spectra of raw filtrates of subtilis strains allows untargeted analysis of the major classes of compounds produced to be performed, thus facilitating identification of other unknown bioactive molecules after retrospective analysis. These features make this approach a fast tool applicable to the rapid screening and further identification of antimicrobial compounds released by Bacillus strains in raw filtrates.
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Affiliation(s)
- Linda Monaci
- Institute of Sciences of Food Production, National Research Council of Italy (ISPA-CNR), Via Amendola 122/O, 70126, Bari, Italy
| | - Laura Quintieri
- Institute of Sciences of Food Production, National Research Council of Italy (ISPA-CNR), Via Amendola 122/O, 70126, Bari, Italy
| | - Leonardo Caputo
- Institute of Sciences of Food Production, National Research Council of Italy (ISPA-CNR), Via Amendola 122/O, 70126, Bari, Italy
| | - Angelo Visconti
- Institute of Sciences of Food Production, National Research Council of Italy (ISPA-CNR), Via Amendola 122/O, 70126, Bari, Italy
| | - Federico Baruzzi
- Institute of Sciences of Food Production, National Research Council of Italy (ISPA-CNR), Via Amendola 122/O, 70126, Bari, Italy
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Hacker C, Christ NA, Duchardt-Ferner E, Korn S, Göbl C, Berninger L, Düsterhus S, Hellmich UA, Madl T, Kötter P, Entian KD, Wöhnert J. The Solution Structure of the Lantibiotic Immunity Protein NisI and Its Interactions with Nisin. J Biol Chem 2015; 290:28869-86. [PMID: 26459561 PMCID: PMC4661402 DOI: 10.1074/jbc.m115.679969] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 09/25/2015] [Indexed: 12/21/2022] Open
Abstract
Many Gram-positive bacteria produce lantibiotics, genetically encoded and posttranslationally modified peptide antibiotics, which inhibit the growth of other Gram-positive bacteria. To protect themselves against their own lantibiotics these bacteria express a variety of immunity proteins including the LanI lipoproteins. The structural and mechanistic basis for LanI-mediated lantibiotic immunity is not yet understood. Lactococcus lactis produces the lantibiotic nisin, which is widely used as a food preservative. Its LanI protein NisI provides immunity against nisin but not against structurally very similar lantibiotics from other species such as subtilin from Bacillus subtilis. To understand the structural basis for LanI-mediated immunity and their specificity we investigated the structure of NisI. We found that NisI is a two-domain protein. Surprisingly, each of the two NisI domains has the same structure as the LanI protein from B. subtilis, SpaI, despite the lack of significant sequence homology. The two NisI domains and SpaI differ strongly in their surface properties and function. Additionally, SpaI-mediated lantibiotic immunity depends on the presence of a basic unstructured N-terminal region that tethers SpaI to the membrane. Such a region is absent from NisI. Instead, the N-terminal domain of NisI interacts with membranes but not with nisin. In contrast, the C-terminal domain specifically binds nisin and modulates the membrane affinity of the N-terminal domain. Thus, our results reveal an unexpected structural relationship between NisI and SpaI and shed light on the structural basis for LanI mediated lantibiotic immunity.
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Affiliation(s)
- Carolin Hacker
- From the Institute for Molecular Biosciences and the Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University, 60438 Frankfurt am Main, Germany
| | - Nina A Christ
- From the Institute for Molecular Biosciences and the Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University, 60438 Frankfurt am Main, Germany
| | - Elke Duchardt-Ferner
- From the Institute for Molecular Biosciences and the Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University, 60438 Frankfurt am Main, Germany
| | - Sophie Korn
- From the Institute for Molecular Biosciences and
| | - Christoph Göbl
- the Department of Chemistry, Center for Integrated Protein Science Munich, Technical University München, Lichtenbergstraße 4, 85748 Garching, Germany, the Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | | | | | - Ute A Hellmich
- the Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University, 60438 Frankfurt am Main, Germany, the Institute of Pharmacy and Biochemistry, Gutenberg University, 55128 Mainz, Germany
| | - Tobias Madl
- the Department of Chemistry, Center for Integrated Protein Science Munich, Technical University München, Lichtenbergstraße 4, 85748 Garching, Germany, the Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany, the Institute of Molecular Biology & Biochemistry, Center of Molecular Medicine, Medical University of Graz, 8010 Graz, Austria, and the Omics Center Graz, BioTechMed Graz, 8010 Graz, Austria
| | - Peter Kötter
- From the Institute for Molecular Biosciences and
| | | | - Jens Wöhnert
- From the Institute for Molecular Biosciences and the Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University, 60438 Frankfurt am Main, Germany,
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Barbosa J, Caetano T, Mendo S. Class I and Class II Lanthipeptides Produced by Bacillus spp. JOURNAL OF NATURAL PRODUCTS 2015; 78:2850-2866. [PMID: 26448102 DOI: 10.1021/np500424y] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The increasing number of multidrug-resistant pathogens, along with the small number of new antimicrobials under development, leads to an increased need for novel alternatives. Class I and class II lanthipeptides (also known as lantibiotics) have been considered promising alternatives to classical antibiotics. In addition to their relevant medical applications, they are used as probiotics, prophylactics, preservatives, and additives in cosmetics and personal-care products. The genus Bacillus is a prolific source of bioactive compounds including ribosomally and nonribosomally synthesized antibacterial peptides. Accordingly, there is significant interest in the biotechnological potential of members of the genus Bacillus as producers of antimicrobial lanthipeptides. The present review focuses on aspects of the biosynthesis, gene cluster organization, structure, antibacterial spectrum, and bioengineering approaches of lanthipeptides produced by Bacillus strains. Their efficacy and potency against some clinically relevant strains, including MRSA and VRE, are also discussed. Although no lanthipeptides are currently in clinical use, the information herein highlights the potential of these compounds.
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Affiliation(s)
- Joana Barbosa
- Department of Biology & Centre for Environmental and Marine Studies (CESAM), University of Aveiro , 3810-193 Aveiro, Portugal
| | - Tânia Caetano
- Department of Biology & Centre for Environmental and Marine Studies (CESAM), University of Aveiro , 3810-193 Aveiro, Portugal
| | - Sónia Mendo
- Department of Biology & Centre for Environmental and Marine Studies (CESAM), University of Aveiro , 3810-193 Aveiro, Portugal
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40
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Spieß T, Korn SM, Kötter P, Entian KD. Autoinduction Specificities of the Lantibiotics Subtilin and Nisin. Appl Environ Microbiol 2015; 81:7914-23. [PMID: 26341212 PMCID: PMC4616960 DOI: 10.1128/aem.02392-15] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 09/01/2015] [Indexed: 12/23/2022] Open
Abstract
The biosynthesis of the lantibiotics subtilin and nisin is regulated by autoinduction via two-component systems. Although subtilin is structurally closely related to nisin and contains the same lanthionine ring structure, both lantibiotics specifically autoinduce their biosynthesis. Subtilin and also the subtilin-like lantibiotics entianin and ericin autoinduce the two-component system SpaRK of Bacillus subtilis, whereas the biosynthesis of nisin is autoinduced via the two-component system NisRK of Lactococcus lactis. Autoinduction is highly specific for the respective lantibiotic and therefore of major importance for the functional expression of genetically engineered subtilin-like lantibiotics. To identify the structural features required for subtilin autoinduction, subtilin-nisin hybrids and specific point mutations of amino acid position 1 were generated. For subtilin autoinduction, the N-terminal tryptophan is the most important for full SpaK activation. The failure of subtilin to autoinduce the histidine kinase NisK mainly depends on the N-terminal tryptophan, as its single exchange to the aliphatic amino acid residues isoleucine, leucine, and valine provided NisK autoinduction. In addition, the production of subtilin variants which did not autoinduce their own biosynthesis could be rescued upon heterologous coexpression in B. subtilis DSM15029 by the autoinducing subtilin-like lantibiotic entianin.
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Affiliation(s)
- Tobias Spieß
- Institute for Molecular Biosciences, Goethe University, Frankfurt, Germany
| | | | - Peter Kötter
- Institute for Molecular Biosciences, Goethe University, Frankfurt, Germany
| | - Karl-Dieter Entian
- Institute for Molecular Biosciences, Goethe University, Frankfurt, Germany
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Walsh CJ, Guinane CM, Hill C, Ross RP, O'Toole PW, Cotter PD. In silico identification of bacteriocin gene clusters in the gastrointestinal tract, based on the Human Microbiome Project's reference genome database. BMC Microbiol 2015; 15:183. [PMID: 26377179 PMCID: PMC4573289 DOI: 10.1186/s12866-015-0515-4] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 09/08/2015] [Indexed: 01/12/2023] Open
Abstract
Background The human gut microbiota comprises approximately 100 trillion microbial cells which significantly impact many aspects of human physiology - including metabolism, nutrient absorption and immune function. Disturbances in this population have been implicated in many conditions and diseases, including obesity, type-2 diabetes and inflammatory bowel disease. This suggests that targeted manipulation or shaping of the gut microbiota, by bacteriocins and other antimicrobials, has potential as a therapeutic tool for the prevention or treatment of these conditions. With this in mind, several studies have used traditional culture-dependent approaches to successfully identify bacteriocin-producers from the mammalian gut. In silico-based approaches to identify novel gene clusters are now also being utilised to take advantage of the vast amount of data currently being generated by next generation sequencing technologies. In this study, we employed an in silico screening approach to mine potential bacteriocin clusters in genome-sequenced isolates from the gastrointestinal tract (GIT). More specifically, the bacteriocin genome-mining tool BAGEL3 was used to identify potential bacteriocin producers in the genomes of the GIT subset of the Human Microbiome Project’s reference genome database. Each of the identified gene clusters were manually annotated and potential bacteriocin-associated genes were evaluated. Results We identified 74 clusters of note from 59 unique members of the Firmicutes, Bacteroidetes, Actinobacteria, Fusobacteria and Synergistetes. The most commonly identified class of bacteriocin was the >10 kDa class, formerly known as bacteriolysins, followed by lantibiotics and sactipeptides. Conclusions Multiple bacteriocin gene clusters were identified in a dataset representative of the human gut microbiota. Interestingly, many of these were associated with species and genera which are not typically associated with bacteriocin production. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0515-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Calum J Walsh
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland. .,School of Microbiology, University College Cork, Cork, Ireland.
| | | | - Colin Hill
- APC Microbiome Institute, University College Cork, Cork, Ireland. .,School of Microbiology, University College Cork, Cork, Ireland.
| | - R Paul Ross
- APC Microbiome Institute, University College Cork, Cork, Ireland. .,School of Microbiology, University College Cork, Cork, Ireland.
| | - Paul W O'Toole
- APC Microbiome Institute, University College Cork, Cork, Ireland. .,School of Microbiology, University College Cork, Cork, Ireland.
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland. .,APC Microbiome Institute, University College Cork, Cork, Ireland.
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Activation of Histidine Kinase SpaK Is Mediated by the N-Terminal Portion of Subtilin-Like Lantibiotics and Is Independent of Lipid II. Appl Environ Microbiol 2015; 81:5335-43. [PMID: 26025904 DOI: 10.1128/aem.01368-15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 05/21/2015] [Indexed: 12/11/2022] Open
Abstract
The biosynthesis of the lantibiotic subtilin is autoinduced in a quorum-sensing mechanism via histidine kinase SpaK. Subtilin-like lantibiotics, such as entianin, ericin S, and subtilin, specifically activated SpaK in a comparable manner, whereas the structurally similar nisin did not provide the signal for SpaK activation at nontoxic concentrations. Surprisingly, nevertheless, nisin if applied together with entianin partly quenched SpaK activation. The N-terminal entianin1-20 fragment (comprising N-terminal amino acids 1 to 20) was sufficient for SpaK activation, although higher concentrations were needed. The N-terminal nisin1-20 fragment also interfered with entianin-mediated activation of SpaK and, remarkably, at extremely high concentrations also activated SpaK. Our data show that the N-terminal entianin1-20 fragment is sufficient for SpaK activation. However, if present, the C-terminal part of the molecule further strongly enhances the activation, possibly by its interference with the cellular membrane. As shown by using lipid II-interfering substances and a lipid II-deficient mutant strain, lipid II is not needed for the sensing mechanism.
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Torres MJ, Petroselli G, Daz M, Erra-Balsells R, Audisio MC. Bacillus subtilis subsp. subtilis CBMDC3f with antimicrobial activity against Gram-positive foodborne pathogenic bacteria: UV-MALDI-TOF MS analysis of its bioactive compounds. World J Microbiol Biotechnol 2015; 31:929-40. [PMID: 25820813 DOI: 10.1007/s11274-015-1847-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 03/21/2015] [Indexed: 02/07/2023]
Abstract
In this work a new Bacillus sp. strain, isolated from honey, was characterized phylogenetically. Its antibacterial activity against three relevant foodborne pathogenic bacteria was studied; the main bioactive metabolites were analyzed using ultraviolet matrix assisted laser desorption-ionization mass spectrometry (UV-MALDI MS). Bacillus CBMDC3f was phylogenetically characterized as Bacillus subtilis subsp. subtilis after rRNA analysis of the 16S subunit and the gyrA gene (access codes Genbank JX120508 and JX120516, respectively). Its antibacterial potential was evaluated against Listeria monocytogenes (9 strains), B. cereus (3 strains) and Staphylococcus aureus ATCC29213. Its cell suspension and cell-free supernatant (CFS) exerted significant anti-Listeria and anti-S. aureus activities, while the lipopeptides fraction (LF) also showed anti-B. cereus effect. The UV-MALDI-MS analysis revealed surfactin, iturin and fengycin in the CFS, whereas surfactin predominated in the LF. The CFS from CBMDC3f contained surfactin, iturin and fengycin with four, two and four homologues per family, respectively, whereas four surfactin, one iturin and one fengycin homologues were identified in the LF. For some surfactin homologues, their UV-MALDI-TOF/TOF (MS/MS; Laser Induced Decomposition method, LID) spectra were also obtained. Mass spectrometry analysis contributed with relevant information about the type of lipopeptides that Bacillus strains can synthesize. From our results, surfactin would be the main metabolite responsible for the antibacterial effect.
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Affiliation(s)
- M J Torres
- Instituto de Investigaciones para la Industria Química (INIQUI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Salta, Av.Bolivia 5150, 4400, Salta, Argentina
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Sandiford SK. Perspectives on lantibiotic discovery - where have we failed and what improvements are required? Expert Opin Drug Discov 2015; 10:315-20. [PMID: 25697059 DOI: 10.1517/17460441.2015.1016496] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The increasing resistance of bacteria to conventional antimicrobial therapy within both the nosocomial and community environment has enforced the urgent requirement for the discovery of novel agents. This has stimulated increased research efforts within the field of lantibiotic discovery. Lantibiotics are ribosomally synthesised, post-translationally modified antimicrobial peptides that exhibit antimicrobial activity against a range of multi-drug-resistant (MDR) bacteria. The success of these agents as a novel treatment of MDR infections is exemplified by: the clinical development of MU1140 (mutacin 1140) and NAI-107 (microbisporicin), which are in late pre-clinical trials against gram-positive bacteria; NVB302 that has completed Phase I clinical trials for the treatment of Clostridium difficile infections and; duramycin that has completed Phase II clinical trials in the treatment of cystic fibrosis. Despite these potential successes, the traditional method of lantibiotic discovery involving the induction, production and identification is often an inefficient, time-consuming process creating a barrier to the efficient discovery of novel lantibiotics. The introduction of novel and innovative identification methods, including the application of probes and the ability to improve the stability and activity of agents via mutagenesis offer encouraging new areas to explore. The rapid expansion of available genome sequences of a wide variety of bacteria has revealed multiple interesting lantibiotic clusters that have the potential to be effective antimicrobials. However, due to the inefficient expression, screening and production methods currently employed, they are being assessed inefficiently and not rapidly enough to keep up with the ever-increasing demand for new agents.
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Affiliation(s)
- Stephanie Kate Sandiford
- Institute of Pharmaceutical Sciences, King's College London , Britannia House, 7 Trinity Street, SE1 1DB London , UK
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Sumi CD, Yang BW, Yeo IC, Hahm YT. Antimicrobial peptides of the genus Bacillus: a new era for antibiotics. Can J Microbiol 2014; 61:93-103. [PMID: 25629960 DOI: 10.1139/cjm-2014-0613] [Citation(s) in RCA: 193] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The rapid onset of resistance reduces the efficacy of most conventional antimicrobial drugs and is a general cause of concern for human well-being. Thus, there is great demand for a continuous supply of novel antibiotics to combat this problem. Bacteria-derived antimicrobial peptides (AMPs) have long been used as food preservatives; moreover, prior to the development of conventional antibiotics, these AMPs served as an efficient source of antibiotics. Recently, peptides produced by members of the genus Bacillus were shown to have a broad spectrum of antimicrobial activity against pathogenic microbes. Bacillus-derived AMPs can be synthesized both ribosomally and nonribosomally and can be classified according to peptide biosynthesis, structure, and molecular weight. The precise mechanism of action of these AMPs is not yet clear; however, one proposed mechanism is that these AMPs kill bacteria by forming channels in and (or) disrupting the bacterial cell wall. Bacillus-derived AMPs have potential in the pharmaceutical industry, as well as the food and agricultural sectors. Here, we focus on Bacillus-derived AMPs as a novel alternative approach to antibacterial drug development. We also provide an overview of the biosynthesis, mechanisms of action, applications, and effectiveness of different AMPs produced by members of the Bacillus genus, including several recently identified novel AMPs.
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Affiliation(s)
- Chandra Datta Sumi
- a Department of Systems Biotechnology, Chung-Ang University, 72-1 Nae-Ri, Daeduk-Myun, Anseong-Si, Gyeonggi-Do 456-756, South Korea
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Synthesis and succinylation of subtilin-like lantibiotics are strongly influenced by glucose and transition state regulator AbrB. Appl Environ Microbiol 2014; 81:614-22. [PMID: 25381239 DOI: 10.1128/aem.02579-14] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Subtilin and the closely related entianin are class I lantibiotics produced by different subspecies of Bacillus subtilis. Both molecules are ribosomally synthesized peptide antibiotics with unusual ring structures. Subtilin-like lantibiotics develop strong antibiotic activities against various Gram-positive organisms with an efficiency similar to that of nisin from Lactococcus lactis. In contrast to nisin, subtilin-like lantibiotics partially undergo an additional posttranslational modification, where the N-terminal tryptophan residue becomes succinylated, resulting in drastically reduced antibiotic activities. A highly sensitive high-performance liquid chromatography (HPLC)-based quantification method enabled us to determine entianin and succinylated entianin (S-entianin) concentrations in the supernatant during growth. We show that entianin synthesis and the degree of succinylation drastically change with culture conditions. In particular, increasing glucose concentrations resulted in higher entianin amounts and lower proportions of S-entianin in Landy-based media. In contrast, no succinylation was observed in medium A with 10% glucose. Interestingly, glucose retarded the expression of entianin biosynthesis genes. Furthermore, deletion of the transition state regulator AbrB resulted in a 6-fold increased entianin production in medium A with 10% glucose. This shows that entianin biosynthesis in B. subtilis is strongly influenced by glucose, in addition to its regulation by the transition state regulator AbrB. Our results suggest that the mechanism underlying the succinylation of subtilin-like lantibiotics is enzymatically catalyzed and occurs in the extracellular space or at the cellular membrane.
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Blin K, Kazempour D, Wohlleben W, Weber T. Improved lanthipeptide detection and prediction for antiSMASH. PLoS One 2014; 9:e89420. [PMID: 24586765 PMCID: PMC3930743 DOI: 10.1371/journal.pone.0089420] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 01/21/2014] [Indexed: 11/18/2022] Open
Abstract
Lanthipeptides are a class of ribosomally synthesised and post-translationally modified peptide (RiPP) natural products from the bacterial secondary metabolism. Their name is derived from the characteristic lanthionine or methyl-lanthionine residues contained in the processed peptide. Lanthipeptides that possess an antibacterial activity are called lantibiotics. Whereas multiple tools exist to identify lanthipeptide gene clusters from genomic data, no programs are available to predict the post-translational modifications of lanthipeptides, such as the proteolytic cleavage of the leader peptide part or tailoring modifications based on the analysis of the gene cluster sequence. antiSMASH is a software pipeline for the identification of secondary metabolite biosynthetic clusters from genomic input and the prediction of products produced by the identified clusters. Here we present a novel antiSMASH module using a rule-based approach to combine signature motifs for biosynthetic enzymes and lanthipeptide-specific cleavage site motifs to identify lanthipeptide clusters in genomic data, assign the specific lanthipeptide class, predict prepeptide cleavage, tailoring reactions, and the processed molecular weight of the mature peptide products.
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Affiliation(s)
- Kai Blin
- Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, Eberhard-Karls-University of Tübingen, Tübingen, Germany
- German Centre for Infection Research, Tübingen, Germany
| | - Daniyal Kazempour
- Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, Eberhard-Karls-University of Tübingen, Tübingen, Germany
| | - Wolfgang Wohlleben
- Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, Eberhard-Karls-University of Tübingen, Tübingen, Germany
- German Centre for Infection Research, Tübingen, Germany
| | - Tilmann Weber
- Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, Eberhard-Karls-University of Tübingen, Tübingen, Germany
- German Centre for Infection Research, Tübingen, Germany
- * E-mail:
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Cerecidins, novel lantibiotics from Bacillus cereus with potent antimicrobial activity. Appl Environ Microbiol 2014; 80:2633-43. [PMID: 24532070 DOI: 10.1128/aem.03751-13] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lantibiotics are ribosomally synthesized and posttranslationally modified antimicrobial peptides that are widely produced by Gram-positive bacteria, including many species of the Bacillus group. In the present study, one novel gene cluster coding lantibiotic cerecidins was unveiled in Bacillus cereus strain As 1.1846 through genomic mining and PCR screening. The designated cer locus is different from that of conventional class II lantibiotics in that it included seven tandem precursor cerA genes, one modification gene (cerM), two processing genes (cerT and cerP), one orphan regulator gene (cerR), and two immunity genes (cerF and cerE). In addition, one unprecedented quorum sensing component, comQXPA, was inserted between cerM and cerR. The expression of cerecidins was not detected in this strain of B. cereus, which might be due to repressed transcription of cerM. We constitutively coexpressed cerA genes and cerM in Escherichia coli, and purified precerecidins were proteolytically processed with the endoproteinase GluC and a truncated version of putative serine protease CerP. Thus, two natural variants of cerecidins A1 and A7 were obtained which contained two terminal nonoverlapping thioether rings rarely found in lantibiotics. Both cerecidins A1 and A7 were active against a broad spectrum of Gram-positive bacteria. Cerecidin A7, especially its mutant Dhb13A, showed remarkable efficacy against multidrug-resistant Staphylococcus aureus (MDRSA), vancomycin-resistant Enterococcus faecalis (VRE), and even Streptomyces.
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Arguelles Arias A, Ongena M, Devreese B, Terrak M, Joris B, Fickers P. Characterization of amylolysin, a novel lantibiotic from Bacillus amyloliquefaciens GA1. PLoS One 2013; 8:e83037. [PMID: 24349428 PMCID: PMC3857288 DOI: 10.1371/journal.pone.0083037] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 10/30/2013] [Indexed: 11/18/2022] Open
Abstract
Background Lantibiotics are heat-stable peptides characterized by the presence of thioether amino acid lanthionine and methyllanthionine. They are capable to inhibit the growth of Gram-positive bacteria, including Listeria monocytogenes, Staphylococcus aureus or Bacillus cereus, the causative agents of food-borne diseases or nosocomial infections. Lantibiotic biosynthetic machinery is encoded by gene cluster composed by a structural gene that codes for a pre-lantibiotic peptide and other genes involved in pre-lantibiotic modifications, regulation, export and immunity. Methodology/Findings Bacillus amyloliquefaciens GA1 was found to produce an antimicrobial peptide, named amylolysin, active on an array of Gram-positive bacteria, including methicillin resistant S. aureus. Genome characterization led to the identification of a putative lantibiotic gene cluster that comprises a structural gene (amlA) and genes involved in modification (amlM), transport (amlT), regulation (amlKR) and immunity (amlFE). Disruption of amlA led to loss of biological activity, confirming thus that the identified gene cluster is related to amylolysin synthesis. MALDI-TOF and LC-MS analysis on purified amylolysin demonstrated that this latter corresponds to a novel lantibiotic not described to date. The ability of amylolysin to interact invitro with the lipid II, the carrier of peptidoglycan monomers across the cytoplasmic membrane and the presence of a unique modification gene suggest that the identified peptide belongs to the group B lantibiotic. Amylolysin immunity seems to be driven by only two AmlF and AmlE proteins, which is uncommon within the Bacillus genus. Conclusion/Significance Apart from mersacidin produced by Bacillus amyloliquefaciens strains Y2 and HIL Y-85,544728, reports on the synthesis of type B-lantibiotic in this species are scarce. This study reports on a genetic and structural characterization of another representative of the type B lantibiotic in B. amyloliquefaciens.
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Affiliation(s)
- Anthony Arguelles Arias
- Centre d'Ingénierie des Protéines, Bacterial Physiology and Genetics, Université de Liège, Liège, Belgium
| | - Marc Ongena
- Centre Wallon de Biologie Industrielle, Unité de Bioindustrie, Faculté de Sciences Agronomique de Gembloux, Gembloux, Belgium
| | - Bart Devreese
- Laboratorium voor Eiwitbiochemie en Eiwitengineering, Universiteit-Gent, Gent, Belgium
| | - Mohammed Terrak
- Centre d'Ingénierie des Protéines, Bacterial Physiology and Genetics, Université de Liège, Liège, Belgium
| | - Bernard Joris
- Centre d'Ingénierie des Protéines, Bacterial Physiology and Genetics, Université de Liège, Liège, Belgium
| | - Patrick Fickers
- Unité de Biotechnologies et Bioprocédés, Université Libre de Bruxelles, Brussels, Belgium
- * E-mail:
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