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Blau K, Gallert C. Prophage Carriage and Genetic Diversity within Environmental Isolates of Clostridioides difficile. Int J Mol Sci 2023; 25:2. [PMID: 38203173 PMCID: PMC10778935 DOI: 10.3390/ijms25010002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/12/2023] [Accepted: 12/16/2023] [Indexed: 01/12/2024] Open
Abstract
Clostridioides difficile is an important human pathogen causing antibiotic-associated diarrhoea worldwide. Besides using antibiotics for treatment, the interest in bacteriophages as an alternative therapeutic option has increased. Prophage abundance and genetic diversity are well-documented in clinical strains, but the carriage of prophages in environmental strains of C. difficile has not yet been explored. Thus, the prevalence and genetic diversity of integrated prophages in the genomes of 166 environmental C. difficile isolates were identified. In addition, the clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems were determined in the genomes of prophage regions. Predicted prophages and CRISPR-Cas systems were identified by using the PHASTER web server and CRISPRCasFinder, respectively. Phylogenetic relationships among predicated prophages were also constructed based on phage-related genes, terminase large (TerL) subunits and LysM. Among 372 intact prophages, the predominant prophages were phiCDHM1, phiCDHM19, phiMMP01, phiCD506, phiCD27, phiCD211, phiMMP03, and phiC2, followed by phiMMP02, phiCDKM9, phiCD6356, phiCDKM15, and phiCD505. Two newly discovered siphoviruses, phiSM101- and phivB_CpeS-CP51-like Clostridium phages, were identified in two C. difficile genomes. Most prophages were found in sequence types (STs) ST11, ST3, ST8, ST109, and ST2, followed by ST6, ST17, ST4, ST5, ST44, and ST58. An obvious correlation was found between prophage types and STs/ribotypes. Most predicated prophages carry CRISPR arrays. Some prophages carry several gene products, such as accessory gene regulator (Agr), putative spore protease, and abortive infection (Abi) systems. This study shows that prophage carriage, along with genetic diversity and their CRISPR arrays, may play a role in the biology, lifestyle, and fitness of their host strains.
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Affiliation(s)
| | - Claudia Gallert
- Department of Microbiology–Biotechnology, Faculty of Technology, University of Applied Sciences Emden/Leer, 26723 Emden, Germany;
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2
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Ávila M, Sánchez C, Calzada J, Mayer MJ, Berruga MI, López-Díaz TM, Narbad A, Garde S. Isolation and characterization of new bacteriophages active against Clostridium tyrobutyricum and their role in preventing the late blowing defect of cheese. Food Res Int 2023; 163:112222. [PMID: 36596151 DOI: 10.1016/j.foodres.2022.112222] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 11/17/2022] [Accepted: 11/20/2022] [Indexed: 11/25/2022]
Abstract
Lytic bacteriophages (phages) offer a great potential as biocontrol agents for spoilage Clostridium tyrobutyricum, responsible for butyric acid fermentation in semi-hard and hard ripened cheeses, resulting in late gas blowing defect. With this aim, we have isolated, identified and characterized new lytic phages of C. tyrobutyricum, and have evaluated their efficacy to control cheese late blowing by adding them to manufacture milk. Silage, soil, milk and cheese from dairy farms were screened for anti-clostridial phages, obtaining 96 isolates active against C. tyrobutyricum. According to host range, source and plaque morphology, we obtained 20 phage profiles, 8 of them (represented by phages FA3, FA21, FA29, FA52, FA58, FA67, FA70 and FA88) showing a wider host range and high quality lysis, which were further characterized. Selected isolates showed a non-contractile tail, belonging to the Siphoviridae family, and were grouped into 3 restriction profiles. Viable phages were detected after storage in sodium-magnesium buffer (SM buffer), skim milk and acidified skim milk (pH 5) for 7 d at 4 °C, 12 °C and 37 °C, although a decline in infectivity was observed in some cases. Good phage survival was also detected during semi-hard cheese manufacture and ripening (60 d), and cheese lactococci counts, pH, dry matter values, and volatile compounds were not affected by phage addition. In semi-hard cheese, phage FA67 impaired the early germination of C. tyrobutyricum spores and caused a significant decrease in clostridial vegetative cells counts at 14 d of ripening, delaying by 2 weeks the consumption of lactic acid, formation of butyric acid and appearance of late blowing symptoms, compared to the spoilt control cheese without the phage. This is the first report on the application of phage to control C. tyrobutyricum in cheese.
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Affiliation(s)
- Marta Ávila
- Departamento de Tecnología de Alimentos, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Carretera de La Coruña km 7, 28040 Madrid, Spain.
| | - Carmen Sánchez
- Departamento de Tecnología de Alimentos, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Carretera de La Coruña km 7, 28040 Madrid, Spain.
| | - Javier Calzada
- Departamento de Tecnología de Alimentos, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Carretera de La Coruña km 7, 28040 Madrid, Spain.
| | - Melinda J Mayer
- Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Colney, Norwich NR4 7UA, UK.
| | - M Isabel Berruga
- Food Quality Research Group, Institute for Regional Development (IDR), Universidad de Castilla-La Mancha, 02071 Albacete, Spain.
| | - Teresa M López-Díaz
- Department of Food Hygiene and Food Technology, Veterinary Faculty, Universidad de León, Campus de Vegazana s/n, 24071, León, Spain.
| | - Arjan Narbad
- Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Colney, Norwich NR4 7UA, UK.
| | - Sonia Garde
- Departamento de Tecnología de Alimentos, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Carretera de La Coruña km 7, 28040 Madrid, Spain.
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3
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Thomas P, Abdel-Glil MY, Subbaiyan A, Busch A, Eichhorn I, Wieler LH, Neubauer H, Pletz M, Seyboldt C. First Comparative Analysis of Clostridium septicum Genomes Provides Insights Into the Taxonomy, Species Genetic Diversity, and Virulence Related to Gas Gangrene. Front Microbiol 2021; 12:771945. [PMID: 34956133 PMCID: PMC8696124 DOI: 10.3389/fmicb.2021.771945] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 11/16/2021] [Indexed: 11/13/2022] Open
Abstract
Clostridium septicum is a Gram-positive, toxin-producing, and spore-forming bacterium that is recognized, together with C. perfringens, as the most important etiologic agent of progressive gas gangrene. Clostridium septicum infections are almost always fatal in humans and animals. Despite its clinical and agricultural relevance, there is currently limited knowledge of the diversity and genome structure of C. septicum. This study presents the complete genome sequence of C. septicum DSM 7534T type strain as well as the first comparative analysis of five C. septicum genomes. The taxonomy of C. septicum, as revealed by 16S rRNA analysis as well as by genomic wide indices such as protein-based phylogeny, average nucleotide identity, and digital DNA–DNA hybridization indicates a stable clade. The composition and presence of prophages, CRISPR elements and accessory genetic material was variable in the investigated genomes. This is in contrast to the limited genetic variability described for the phylogenetically and phenotypically related species Clostridium chauvoei. The restriction-modification (RM) systems between two C. septicum genomes were heterogeneous for the RM types they encoded. C. septicum has an open pangenome with 2,311 genes representing the core genes and 1,429 accessory genes. The core genome SNP divergence between genome pairs varied up to 4,886 pairwise SNPs. A vast arsenal of potential virulence genes was detected in the genomes studied. Sequence analysis of these genes revealed that sialidase, hemolysin, and collagenase genes are conserved compared to the α-toxin and hyaluronidase genes. In addition, a conserved gene found in all C. septicum genomes was predicted to encode a leucocidin homolog (beta-channel forming cytolysin) similar (71.10% protein identity) to Clostridium chauvoei toxin A (CctA), which is a potent toxin. In conclusion, our results provide first, valuable insights into strain relatedness and genomic plasticity of C. septicum and contribute to our understanding of the virulence mechanisms of this important human and animal pathogen.
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Affiliation(s)
- Prasad Thomas
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
- Division of Bacteriology and Mycology, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Mostafa Y. Abdel-Glil
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
- Institute for Infectious Diseases and Infection Control, Jena University Hospital – Friedrich Schiller University, Jena, Germany
- Department of Pathology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
- *Correspondence: Mostafa Y. Abdel-Glil,
| | - Anbazhagan Subbaiyan
- Division of Bacteriology and Mycology, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Anne Busch
- Department of Anaesthesiology and Intensive Care Medicine, University Hospital Jena, Jena, Germany
| | - Inga Eichhorn
- Department of Veterinary Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Lothar H. Wieler
- Department of Veterinary Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
- Robert Koch Institute, Berlin, Germany
| | - Heinrich Neubauer
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Mathias Pletz
- Institute for Infectious Diseases and Infection Control, Jena University Hospital – Friedrich Schiller University, Jena, Germany
| | - Christian Seyboldt
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
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4
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Bonilla E, Costa AR, van den Berg DF, van Rossum T, Hagedoorn S, Walinga H, Xiao M, Song W, Haas PJ, Nobrega FL, Brouns SJJ. Genomic characterization of four novel bacteriophages infecting the clinical pathogen Klebsiella pneumoniae. DNA Res 2021; 28:6352498. [PMID: 34390569 PMCID: PMC8386662 DOI: 10.1093/dnares/dsab013] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 08/12/2021] [Indexed: 12/19/2022] Open
Abstract
Bacteriophages are an invaluable source of novel genetic diversity. Sequencing of phage genomes can reveal new proteins with potential uses as biotechnological and medical tools, and help unravel the diversity of biological mechanisms employed by phages to take over the host during viral infection. Aiming to expand the available collection of phage genomes, we have isolated, sequenced, and assembled the genome sequences of four phages that infect the clinical pathogen Klebsiella pneumoniae: vB_KpnP_FBKp16, vB_KpnP_FBKp27, vB_KpnM_FBKp34, and Jumbo phage vB_KpnM_FBKp24. The four phages show very low (0–13%) identity to genomic phage sequences deposited in the GenBank database. Three of the four phages encode tRNAs and have a GC content very dissimilar to that of the host. Importantly, the genome sequences of the phages reveal potentially novel DNA packaging mechanisms as well as distinct clades of tubulin spindle and nucleus shell proteins that some phages use to compartmentalize viral replication. Overall, this study contributes to uncovering previously unknown virus diversity, and provides novel candidates for phage therapy applications against antibiotic-resistant K. pneumoniae infections.
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Affiliation(s)
- Estrada Bonilla
- Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, The Netherlands.,Kavli Institute of Nanoscience, Delft, The Netherlands.,Fagenbank, Delft, The Netherlands
| | - Ana Rita Costa
- Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, The Netherlands.,Kavli Institute of Nanoscience, Delft, The Netherlands.,Fagenbank, Delft, The Netherlands
| | - Daan F van den Berg
- Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, The Netherlands.,Kavli Institute of Nanoscience, Delft, The Netherlands
| | - Teunke van Rossum
- Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, The Netherlands.,Kavli Institute of Nanoscience, Delft, The Netherlands.,Fagenbank, Delft, The Netherlands
| | - Stefan Hagedoorn
- Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, The Netherlands
| | - Hielke Walinga
- Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, The Netherlands
| | - Minfeng Xiao
- BGI-Shenzhen, Shenzhen 518083, China.,Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China
| | - Wenchen Song
- BGI-Shenzhen, Shenzhen 518083, China.,Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China
| | - Pieter-Jan Haas
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Franklin L Nobrega
- Fagenbank, Delft, The Netherlands.,School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, UK
| | - Stan J J Brouns
- Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, The Netherlands.,Kavli Institute of Nanoscience, Delft, The Netherlands.,Fagenbank, Delft, The Netherlands
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5
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Benameur Q, Gervasi T, Pellizzeri V, Pľuchtová M, Gruľová D, Cicero N, Meriem-Hind B. Comparison of sensitivity to a commercial Origanum vulgare essential oil between extended-spectrum β-lactamases (ESBL-) and non-ESBL-producing Enterobacteriaceae isolates. Nat Prod Res 2021; 36:2830-2835. [PMID: 34121535 DOI: 10.1080/14786419.2021.1933969] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
This study aimed to evaluate the antibacterial effect of Origanum vulgare essential oil (OVEO) against ESBL- and non-ESBL-producing multidrug-resistant (MDR) Enterobacteriaceae isolates. OVEO composition was determined using Gas chromatograph-mass spectrometer (GC/MS). In the current study, the effect of OVEO was studied on seven MDR Enterobacteriaceae isolates. Antibacterial activity of OVEO was investigated by the disc diffusion assay and twofold serial dilution method. GC/MS analysis identified thymol (78.21%) as the single major component present in the OVEO. This EO showed an unexpectedly high antibacterial activity against all the studied MDR Enterobacteriaceae isolates, with inhibition zone diameters and minimum inhibitory concentration (MIC) values ranging from 28 ± 0.6 to 35 ± 0.6 mm and 0.31 ± 0.0 to 5 ± 0.0 μL/mL, respectively. However, ESBL-producing isolates were more susceptible to OVEO than non-ESBL producing isolates. This study compared, for the first time, the sensitivity to OVEO between ESBL and non-ESBL-producing Enterobacteriaceae isolates.
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Affiliation(s)
- Qada Benameur
- Nursing Department, Faculty of Nature and Life Sciences, University of Abdelhamid Ibn Badis of Mostaganem, Mostaganem, Algeria.,Research Laboratory 'Health and Animal Productions', Higher National Veterinary School, Algiers, Algeria
| | - Teresa Gervasi
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Italy
| | - Vito Pellizzeri
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Italy
| | - Mária Pľuchtová
- Department of Ecology, Faculty of Humanities and Natural Sciences, University of Prešov, Slovakia
| | - Daniela Gruľová
- Department of Ecology, Faculty of Humanities and Natural Sciences, University of Prešov, Slovakia
| | - Nicola Cicero
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Italy
| | - Benmahdi Meriem-Hind
- Research Laboratory 'Health and Animal Productions', Higher National Veterinary School, Algiers, Algeria
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6
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Schüler MA, Stegmann BA, Poehlein A, Daniel R, Dürre P. Genome sequence analysis of the temperate bacteriophage TBP2 of the solvent producer Clostridium saccharoperbutylacetonicum N1-4 (HMT, ATCC 27021). FEMS Microbiol Lett 2020; 367:5866474. [PMID: 32614389 DOI: 10.1093/femsle/fnaa103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 06/23/2020] [Indexed: 11/13/2022] Open
Abstract
The genus Clostridium consists of a diverse group of pathogenic and non-pathogenic bacteria. The non-pathogenic clostridia contain several solventogenic members of industrial importance, such as Clostridium acetobutylicum or C. beijerinckii. In the process of acetone-butanol-ethanol (ABE) fermentation, these strains are used in large scale fermentation plants since almost 100 years. Soon after establishment of the first plants, the fermentation processes suffered from different bacteriophage infections worldwide. A limited set of studies addressing bacteriophages in solventogenic clostridia have been conducted since then. In this study, we present the genome sequence of the temperate bacteriophage TBP2 of the solventogenic strain C. saccharoperbutylacetonicum N1-4 (HMT) that is used for ABE fermentation. The phage genome consists of 38 039 bp and includes 48 open reading frames. Sequence analysis indicates that the genome encloses random parts of the bacterial genome in addition to its own DNA. It represents the first fully sequenced genome of a temperate bacteriophage infecting solventogenic clostridia.
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Affiliation(s)
- Miriam A Schüler
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Georg-August University, Grisebachstr. 8, D-37077 Göttingen, Germany
| | - Benjamin A Stegmann
- Institut für Mikrobiologie und Biotechnologie, Universität Ulm, Albert-Einstein-Allee 11, D-89081, Ulm, Germany
| | - Anja Poehlein
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Georg-August University, Grisebachstr. 8, D-37077 Göttingen, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Georg-August University, Grisebachstr. 8, D-37077 Göttingen, Germany
| | - Peter Dürre
- Institut für Mikrobiologie und Biotechnologie, Universität Ulm, Albert-Einstein-Allee 11, D-89081, Ulm, Germany
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7
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8
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Cadieux B, Colavecchio A, Jeukens J, Freschi L, Emond-Rheault JG, Kukavica-Ibrulj I, Levesque RC, Bekal S, Chandler JC, Coleman SM, Bisha B, Goodridge LD. Prophage induction reduces Shiga toxin producing Escherichia coli (STEC) and Salmonella enterica on tomatoes and spinach: A model study. Food Control 2018. [DOI: 10.1016/j.foodcont.2018.02.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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9
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Whole genome analysis reveals the diversity and evolutionary relationships between necrotic enteritis-causing strains of Clostridium perfringens. BMC Genomics 2018; 19:379. [PMID: 29788909 PMCID: PMC5964661 DOI: 10.1186/s12864-018-4771-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 05/09/2018] [Indexed: 11/19/2022] Open
Abstract
Background Clostridium perfringens causes a range of diseases in animals and humans including necrotic enteritis in chickens and food poisoning and gas gangrene in humans. Necrotic enteritis is of concern in commercial chicken production due to the cost of the implementation of infection control measures and to productivity losses. This study has focused on the genomic analysis of a range of chicken-derived C. perfringens isolates, from around the world and from different years. The genomes were sequenced and compared with 20 genomes available from public databases, which were from a diverse collection of isolates from chickens, other animals, and humans. We used a distance based phylogeny that was constructed based on gene content rather than sequence identity. Similarity between strains was defined as the number of genes that they have in common divided by their total number of genes. In this type of phylogenetic analysis, evolutionary distance can be interpreted in terms of evolutionary events such as acquisition and loss of genes, whereas the underlying properties (the gene content) can be interpreted in terms of function. We also compared these methods to the sequence-based phylogeny of the core genome. Results Distinct pathogenic clades of necrotic enteritis-causing C. perfringens were identified. They were characterised by variable regions encoded on the chromosome, with predicted roles in capsule production, adhesion, inhibition of related strains, phage integration, and metabolism. Some strains have almost identical genomes, even though they were isolated from different geographic regions at various times, while other highly distant genomes appear to result in similar outcomes with regard to virulence and pathogenesis. Conclusions The high level of diversity in chicken isolates suggests there is no reliable factor that defines a chicken strain of C. perfringens, however, disease-causing strains can be defined by the presence of netB-encoding plasmids. This study reveals that horizontal gene transfer appears to play a significant role in genetic variation of the C. perfringens chromosome as well as the plasmid content within strains.
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10
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Gervasi T, Pellizzeri V, Benameur Q, Gervasi C, Santini A, Cicero N, Dugo G. Valorization of raw materials from agricultural industry for astaxanthin and β-carotene production by Xanthophyllomyces dendrorhous. Nat Prod Res 2017; 32:1554-1561. [DOI: 10.1080/14786419.2017.1385024] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Teresa Gervasi
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Polo Universitario Annunziata, Messina, Italy
| | - Vito Pellizzeri
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Polo Universitario Annunziata, Messina, Italy
| | - Qada Benameur
- Faculty of Natural Sciences and Life, Nursing Department, University of Mostaganem, Mostaganem, Algeria
| | - Claudio Gervasi
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Polo Universitario Annunziata, Messina, Italy
| | - Antonello Santini
- Dipartimento di Farmacia, Università di Napoli Federico II, Napoli, Italy
| | - Nicola Cicero
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Polo Universitario Annunziata, Messina, Italy
- Science4Life, Spin Off Company, University of Messina, Messina, Italy
| | - Giacomo Dugo
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Polo Universitario Annunziata, Messina, Italy
- Science4Life, Spin Off Company, University of Messina, Messina, Italy
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11
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Gervasi T, Pellizzeri V, Calabrese G, Di Bella G, Cicero N, Dugo G. Production of single cell protein (SCP) from food and agricultural waste by using Saccharomyces cerevisiae. Nat Prod Res 2017; 32:648-653. [DOI: 10.1080/14786419.2017.1332617] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Teresa Gervasi
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy
| | - Vito Pellizzeri
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy
| | - Giorgio Calabrese
- Department of Pharmacy, Università degli Studi di Napoli Federico II, Napoli, Italy
| | - Giuseppa Di Bella
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy
| | - Nicola Cicero
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy
- Department of Pharmacy, Università degli Studi di Napoli Federico II, Napoli, Italy
| | - Giacomo Dugo
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy
- Science4Life, Spin Off Company, University of Messina, Messina, Italy
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12
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Pyne ME, Liu X, Moo-Young M, Chung DA, Chou CP. Genome-directed analysis of prophage excision, host defence systems, and central fermentative metabolism in Clostridium pasteurianum. Sci Rep 2016; 6:26228. [PMID: 27641836 PMCID: PMC5027557 DOI: 10.1038/srep26228] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 04/29/2016] [Indexed: 11/09/2022] Open
Abstract
Clostridium pasteurianum is emerging as a prospective host for the production of biofuels and chemicals, and has recently been shown to directly consume electric current. Despite this growing biotechnological appeal, the organism’s genetics and central metabolism remain poorly understood. Here we present a concurrent genome sequence for the C. pasteurianum type strain and provide extensive genomic analysis of the organism’s defence mechanisms and central fermentative metabolism. Next generation genome sequencing produced reads corresponding to spontaneous excision of a novel phage, designated φ6013, which could be induced using mitomycin C and detected using PCR and transmission electron microscopy. Methylome analysis of sequencing reads provided a near-complete glimpse into the organism’s restriction-modification systems. We also unveiled the chief C. pasteurianum Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) locus, which was found to exemplify a Type I-B system. Finally, we show that C. pasteurianum possesses a highly complex fermentative metabolism whereby the metabolic pathways enlisted by the cell is governed by the degree of reductance of the substrate. Four distinct fermentation profiles, ranging from exclusively acidogenic to predominantly alcohologenic, were observed through redox consideration of the substrate. A detailed discussion of the organism’s central metabolism within the context of metabolic engineering is provided.
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Affiliation(s)
- Michael E Pyne
- Department of Chemical Engineering, University of Waterloo, Waterloo, Ontario, Canada
| | - Xuejia Liu
- Department of Chemical Engineering, University of Waterloo, Waterloo, Ontario, Canada
| | - Murray Moo-Young
- Department of Chemical Engineering, University of Waterloo, Waterloo, Ontario, Canada
| | - Duane A Chung
- Department of Chemical Engineering, University of Waterloo, Waterloo, Ontario, Canada.,Department of Pathology and Molecular Medicine, McMaster University, Ontario, Canada.,Algaeneers Inc. and Neemo Inc., Hamilton, Ontario, Canada
| | - C Perry Chou
- Department of Chemical Engineering, University of Waterloo, Waterloo, Ontario, Canada
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13
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Delesalle VA, Tanke NT, Vill AC, Krukonis GP. Testing hypotheses for the presence of tRNA genes in mycobacteriophage genomes. BACTERIOPHAGE 2016; 6:e1219441. [PMID: 27738556 DOI: 10.1080/21597081.2016.1219441] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 07/27/2016] [Accepted: 07/28/2016] [Indexed: 10/21/2022]
Abstract
The presence of tRNA genes in bacteriophages has been explained on the basis of codon usage (tRNA genes are retained in the phage genome if they correspond to codons more common in the phage than in its host) or amino acid usage (independent of codon, the amino acid corresponding to the retained tRNA gene is more common in the phage genome than in the bacterial host). The existence of a large database of sequenced mycobacteriophages, isolated on the common host Mycobacterium smegmatis, allows us to test the above hypotheses as well as explore other hypotheses for the presence of tRNA genes. Our analyses suggest that amino acid rather than codon usage better explains the presence of tRNA genes in mycobacteriophages. However, closely related phages that differ in the presence of tRNA genes in their genomes are capable of lysing the common bacterial host and do not differ in codon or amino acid usage. This suggests that the benefits of having tRNA genes may be associated with either growth in the host or the ability to infect more hosts (i.e., host range) rather than simply infecting a particular host.
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Affiliation(s)
| | - Natalie T Tanke
- Department of Biology, Gettysburg College , Gettysburg, PA, USA
| | - Albert C Vill
- Department of Biology, Gettysburg College , Gettysburg, PA, USA
| | - Greg P Krukonis
- Department of Biology, Bucknell University , Lewisburg, PA, USA
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Luang-In V, Narbad A, Cebeci F, Bennett M, Rossiter JT. Identification of Proteins Possibly Involved in Glucosinolate Metabolism in L. agilis R16 and E. coli VL8. Protein J 2016; 34:135-46. [PMID: 25805049 DOI: 10.1007/s10930-015-9607-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This study was aimed to identify sinigrin-induced bacterial proteins potentially involved in the metabolism of glucosinolate in two glucosinolate-metabolising bacteria Lactobacillus agilis R16 and Escherichia coli VL8. Sinigrin (2 mM) was used to induce the proteins in both bacteria under anaerobic incubation for 8 h at 30 °C for L. agilis R16 and 37 °C for E. coli VL8 and the controls without sinigrin were performed. Allyl isothiocyanate and allyl nitrile as two degradation products of sinigrin were detected in sinigrin-induced cultures of L. agilis R16 (27% total products) and E. coli VL8 (38% total products) from a complete sinigrin degradation in 8 h for both bacteria. 2D gel electrophoresis was conducted to identify induced proteins with at least twofold increased abundance. Sinigrin-induced L. agilis R16 and the control produced 1561 and 1543 protein spots, respectively. For E. coli VL8, 1363 spots were detected in sinigrin-induced and 1354 spots in the control. A combination of distinct proteins and upregulated proteins of 32 and 35 spots in L. agilis R16 and E. coli VL8, respectively were detected upon sinigrin induction. Of these, 12 and 16 spots from each bacterium respectively were identified by LC-MS/MS. In both bacteria most of the identified proteins are involved in carbohydrate metabolism, oxidoreduction system and sugar transport while the minority belong to purine metabolism, hydrolysis, and proteolysis. This indicated that sinigrin induction led to the expressions of proteins with similar functions in both bacteria and these proteins may play a role in bacterial glucosinolate metabolism.
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Affiliation(s)
- Vijitra Luang-In
- Natural Antioxidant Research Unit, Department of Biotechnology, Faculty of Technology, Mahasarakham University, Mahasarakham, 44150, Thailand,
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15
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Caly DL, D'Inca R, Auclair E, Drider D. Alternatives to Antibiotics to Prevent Necrotic Enteritis in Broiler Chickens: A Microbiologist's Perspective. Front Microbiol 2015; 6:1336. [PMID: 26648920 PMCID: PMC4664614 DOI: 10.3389/fmicb.2015.01336] [Citation(s) in RCA: 143] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 11/16/2015] [Indexed: 12/20/2022] Open
Abstract
Since the 2006 European ban on the use of antibiotics as growth promoters in animal feed, numerous studies have been published describing alternative strategies to prevent diseases in animals. A particular focus has been on prevention of necrotic enteritis in poultry caused by Clostridium perfringens by the use of microbes or microbe-derived products. Microbes produce a plethora of molecules with antimicrobial properties and they can also have beneficial effects through interactions with their host. Here we review recent developments in novel preventive treatments against C. perfringens-induced necrotic enteritis in broiler chickens that employ yeasts, bacteria and bacteriophages or secondary metabolites and other microbial products in disease control.
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Affiliation(s)
- Delphine L. Caly
- Université Lille, INRA, ISA, Université Artois, Université Littoral Côte d'Opale, Institut Charles ViolletteLille, France
| | - Romain D'Inca
- Société Industrielle Lesaffre, Phileo Lesaffre Animal CareMarcq-en-Baroeul, France
| | - Eric Auclair
- Société Industrielle Lesaffre, Phileo Lesaffre Animal CareMarcq-en-Baroeul, France
| | - Djamel Drider
- Université Lille, INRA, ISA, Université Artois, Université Littoral Côte d'Opale, Institut Charles ViolletteLille, France
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16
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Frey J, Falquet L. Patho-genetics of Clostridium chauvoei. Res Microbiol 2014; 166:384-92. [PMID: 25445013 DOI: 10.1016/j.resmic.2014.10.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 10/24/2014] [Accepted: 10/26/2014] [Indexed: 11/30/2022]
Abstract
The genomic sequence of Clostridium chauvoei, the etiological agent of blackleg, a severe disease of ruminants with high mortality specified by a myonecrosis reveals a chromosome of 2.8 million base-pairs and a cryptic plasmid of 5.5 kilo base-pairs. The chromosome contains the main pathways like glycolysis/gluconeogenesis, sugar metabolism, purine and pyrimidine metabolisms, but the notable absence of genes of the citric acid cycle and deficient or partially deficient amino acid metabolism for Histidine, Tyrosine, Phenylalanine, and Tryptophan. These essential amino acids might be acquired from host tissue damage caused by various toxins and by protein metabolism that includes 57 genes for peptidases, and several ABC transporters for amino acids import.
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Affiliation(s)
- Joachim Frey
- Institute of Veterinary Bacteriology, University of Bern, Länggasstrasse 122, 3001 Bern, Switzerland.
| | - Laurent Falquet
- Biochemistry Unit, Dept. of Biology, University of Fribourg and Swiss Institute of Bioinformatics, Fribourg, Switzerland
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17
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Gervasi T, Horn N, Wegmann U, Dugo G, Narbad A, Mayer MJ. Expression and delivery of an endolysin to combat Clostridium perfringens. Appl Microbiol Biotechnol 2013; 98:2495-505. [PMID: 23942878 PMCID: PMC3936119 DOI: 10.1007/s00253-013-5128-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 07/02/2013] [Accepted: 07/13/2013] [Indexed: 12/29/2022]
Abstract
Clostridium perfringens is a cause for increasing concern due to its responsibility for severe infections both in humans and animals, especially poultry. To find new control strategies to treat C. perfringens infection, we investigated the activity and delivery of a bacteriophage endolysin. We identified a new endolysin, designated CP25L, which shows similarity to an N-acetylmuramoyl-l-alanine amidase domain and is distinct from other C. perfringens endolysins whose activity has been demonstrated in vitro. The cp25l gene was cloned and expressed in Escherichia coli, and the gene product demonstrated lytic activity against all 25 C. perfringens strains tested. The probiotic strain Lactobacillus johnsonii FI9785 was engineered to deliver the endolysin to the gastrointestinal tract. The integration of the nisRK two-component regulatory system from the Lactococcus lactis nisin A biosynthesis operon into the chromosome of L. johnsonii allowed constitutive expression of the endolysin under the control of the nisA promoter (PnisA), while the use of a signal peptide (SLPmod) led to successful secretion of the active endolysin to the surrounding media. The high specificity and activity of the endolysin suggest that it may be developed as an effective tool to enhance the control of C. perfringens by L. johnsonii in the gastrointestinal tract.
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Affiliation(s)
- Teresa Gervasi
- Gut Health and Food Safety Programme, Institute of Food Research, Colney, Norwich, NR4 7UA, UK
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