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Skowron PM, Łubkowska B, Sobolewski I, Zylicz-Stachula A, Šimoliūnienė M, Šimoliūnas E. Bacteriophages of Thermophilic ' Bacillus Group' Bacteria-A Systematic Review, 2023 Update. Int J Mol Sci 2024; 25:3125. [PMID: 38542099 PMCID: PMC10969951 DOI: 10.3390/ijms25063125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 04/05/2024] Open
Abstract
Bacteriophages associated with thermophiles are gaining increased attention due to their pivotal roles in various biogeochemical and ecological processes, as well as their applications in biotechnology and bionanotechnology. Although thermophages are not suitable for controlling bacterial infections in humans or animals, their individual components, such as enzymes and capsid proteins, can be employed in molecular biology and significantly contribute to the enhancement of human and animal health. Despite their significance, thermophages still remain underrepresented in the known prokaryotic virosphere, primarily due to limited in-depth investigations. However, due to their unique properties, thermophages are currently attracting increasing interest, as evidenced by several newly discovered phages belonging to this group. This review offers an updated compilation of thermophages characterized to date, focusing on species infecting the thermophilic bacilli. Moreover, it presents experimental findings, including novel proteomic data (39 proteins) concerning the model TP-84 bacteriophage, along with the first announcement of 6 recently discovered thermophages infecting Geobacillus thermodenitrificans: PK5.2, PK2.1, NIIg10.1, NIIg2.1, NIIg2.2, and NIIg2.3. This review serves as an update to our previous publication in 2021.
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Affiliation(s)
- Piotr M. Skowron
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (I.S.); (A.Z.-S.)
| | - Beata Łubkowska
- Faculty of Health and Life Sciences, Gdansk University of Physical Education and Sport, K. Gorskiego 1, 80-336 Gdansk, Poland;
- Department of Life and Environmental Sciences, University of Cagliari, 09124 Cagliari, Italy
| | - Ireneusz Sobolewski
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (I.S.); (A.Z.-S.)
| | - Agnieszka Zylicz-Stachula
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (I.S.); (A.Z.-S.)
| | - Monika Šimoliūnienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio Av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (E.Š.)
| | - Eugenijus Šimoliūnas
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio Av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (E.Š.)
- Department of Microbiology and Biotechnology, Institute of Bioscience, Life Sciences Center, Vilnius University, Sauletekio Av. 7, LT-10257 Vilnius, Lithuania
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2
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Marks TJ, Rowland IR. The Diversity of Bacteriophages in Hot Springs. Methods Mol Biol 2024; 2738:73-88. [PMID: 37966592 DOI: 10.1007/978-1-0716-3549-0_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Bacteriophages are ubiquitous in all environments that support microbial life. This includes hot springs, which can range in temperatures between 40 and 98 °C and pH levels between 1 and 9. Bacteriophages that survive in the higher temperatures of hot springs are known as thermophages. Thermophages have developed distinct adaptations allowing for thermostability in these extreme environments, including increased G + C DNA percentages, reliance upon the pentose phosphate metabolic pathway to avoid oxidative stress, and a codon preference for those with a GNA sequence leading to increased hydrophobic interactions and disulfide bonds. In this review, we discuss the diversity of characterized thermophages in hot spring environments that span five viral families: Myoviridae, Siphoviridae, Tectiviridae, Sphaerolipoviridae, and Inoviridae. Potential industrial and medicinal applications of thermophages will also be addressed.
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Affiliation(s)
- Timothy J Marks
- Department of Pharmaceutical and Clinical Sciences, Campbell University, Buies Creek, NC, USA.
| | - Isabella R Rowland
- Department of Pharmaceutical and Clinical Sciences, Campbell University, Buies Creek, NC, USA
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Šimoliūnas E, Šimoliūnienė M, Laskevičiūtė G, Kvederavičiūtė K, Skapas M, Kaupinis A, Valius M, Meškys R, Kuisienė N. Geobacillus Bacteriophages from Compost Heaps: Representatives of Three New Genera within Thermophilic Siphoviruses. Viruses 2023; 15:1691. [PMID: 37632033 PMCID: PMC10459684 DOI: 10.3390/v15081691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023] Open
Abstract
We report a detailed characterization of five thermophilic bacteriophages (phages) that were isolated from compost heaps in Vilnius, Lithuania using Geobacillus thermodenitrificans strains as the hosts for phage propagation. The efficiency of plating experiments revealed that phages formed plaques from 45 to 80 °C. Furthermore, most of the phages formed plaques surrounded by halo zones, indicating the presence of phage-encoded bacterial exopolysaccharide (EPS)-degrading depolymerases. Transmission Electron Microscopy (TEM) analysis revealed that all phages were siphoviruses characterized by an isometric head (from ~63 nm to ~67 nm in diameter) and a non-contractile flexible tail (from ~137 nm to ~150 nm in length). The genome sequencing resulted in genomes ranging from 38,161 to 39,016 bp. Comparative genomic and phylogenetic analysis revealed that all the isolated phages had no close relatives to date, and potentially represent three new genera within siphoviruses. The results of this study not only improve our knowledge about poorly explored thermophilic bacteriophages but also give new insights for further investigation of thermophilic and/or thermostable enzymes of bacterial viruses.
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Affiliation(s)
- Eugenijus Šimoliūnas
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio Av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (G.L.); (R.M.)
- Department of Microbiology and Biotechnology, Institute of Bioscience, Life Sciences Center, Vilnius University, Saulėtekio Av. 7, LT-10257 Vilnius, Lithuania;
| | - Monika Šimoliūnienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio Av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (G.L.); (R.M.)
| | - Gintarė Laskevičiūtė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio Av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (G.L.); (R.M.)
| | - Kotryna Kvederavičiūtė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio Av. 7, LT-10257 Vilnius, Lithuania;
| | - Martynas Skapas
- Department of Characterisation of Materials Structure, Center for Physical Sciences and Technology, Sauletekio Av. 3, LT-10257 Vilnius, Lithuania;
| | - Algirdas Kaupinis
- Proteomics Centre, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio Av. 7, LT-10257 Vilnius, Lithuania; (A.K.); (M.V.)
| | - Mindaugas Valius
- Proteomics Centre, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio Av. 7, LT-10257 Vilnius, Lithuania; (A.K.); (M.V.)
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio Av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (G.L.); (R.M.)
| | - Nomeda Kuisienė
- Department of Microbiology and Biotechnology, Institute of Bioscience, Life Sciences Center, Vilnius University, Saulėtekio Av. 7, LT-10257 Vilnius, Lithuania;
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4
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Liu H, Kheirvari M, Tumban E. Potential Applications of Thermophilic Bacteriophages in One Health. Int J Mol Sci 2023; 24:8222. [PMID: 37175929 PMCID: PMC10179064 DOI: 10.3390/ijms24098222] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/26/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
Bacteriophages have a wide range of applications such as combating antibiotic resistance, preventing food contamination for food safety, and as biomarkers to indirectly assess the quality of water. Additionally, bacteriophage components (endolysins and coat proteins) have a lot of applications in food processing, vaccine design, and the delivery of cargo to the body. Therefore, bacteriophages/components have a multitude of applications in human, plant/veterinary, and environmental health (One Health). Despite their versatility, bacteriophage/component use is mostly limited to temperatures within 4-40 °C. This limits their applications (e.g., in food processing conditions, pasteurization, and vaccine design). Advances in thermophilic bacteriophage research have uncovered novel thermophilic endolysins (e.g., ΦGVE2 amidase and MMPphg) that can be used in food processing and in veterinary medicine. The endolysins are thermostable at temperatures > 65 °C and have broad antimicrobial activities. In addition to thermophilic endolysins, enzymes (DNA polymerase and ligases) derived from thermophages have different applications in molecular biology/biotechnology: to generate DNA libraries and develop diagnostics for human and animal pathogens. Furthermore, coat proteins from thermophages are being explored to develop virus-like particle platforms with versatile applications in human and animal health. Overall, bacteriophages, especially those that are thermophilic, have a plethora of applications in One Health.
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Affiliation(s)
| | | | - Ebenezer Tumban
- School of Veterinary Medicine, Texas Tech University, Amarillo, TX 79106, USA
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Xu C, Zhang R, Duan M, Zhou Y, Bao J, Lu H, Wang J, Hu M, Hu Z, Zhou F, Zhu W. A polygenic stacking classifier revealed the complicated platelet transcriptomic landscape of adult immune thrombocytopenia. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 28:477-487. [PMID: 35505964 PMCID: PMC9046129 DOI: 10.1016/j.omtn.2022.04.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 04/01/2022] [Indexed: 01/19/2023]
Abstract
Immune thrombocytopenia (ITP) is an autoimmune disease with the typical symptom of a low platelet count in blood. ITP demonstrated age and sex biases in both occurrences and prognosis, and adult ITP was mainly induced by the living environments. The current diagnosis guideline lacks the integration of molecular heterogenicity. This study recruited the largest cohort of platelet transcriptome samples. A comprehensive procedure of feature selection, feature engineering, and stacking classification was carried out to detect the ITP biomarkers using RNA sequencing (RNA-seq) transcriptomes. The 40 detected biomarkers were loaded to train the final ITP detection model, with an overall accuracy 0.974. The biomarkers suggested that ITP onset may be associated with various transcribed components, including protein-coding genes, long intergenic non-coding RNA (lincRNA) genes, and pseudogenes with apparent transcriptions. The delivered ITP detection model may also be utilized as a complementary ITP diagnosis tool. The code and the example dataset is freely available on http://www.healthinformaticslab.org/supp/resources.php
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Affiliation(s)
- Chengfeng Xu
- Department of Hematology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, 110 Ganhe Road, Hongkou District, Shanghai 200437, China
| | - Ruochi Zhang
- College of Computer Science and Technology, Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China
| | - Meiyu Duan
- College of Computer Science and Technology, Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China
| | - Yongming Zhou
- Department of Hematology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, 110 Ganhe Road, Hongkou District, Shanghai 200437, China
| | - Jizhang Bao
- Department of Hematology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, 110 Ganhe Road, Hongkou District, Shanghai 200437, China
| | - Hao Lu
- Department of Hematology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, 110 Ganhe Road, Hongkou District, Shanghai 200437, China
| | - Jie Wang
- Department of Hematology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, 110 Ganhe Road, Hongkou District, Shanghai 200437, China
| | - Minghui Hu
- Department of Hematology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, 110 Ganhe Road, Hongkou District, Shanghai 200437, China
| | - Zhaoyang Hu
- Fun-Med Pharmaceutical Technology (Shanghai) Co., Ltd., RM. A310, 115 Xinjunhuan Road, Minhang District, Shanghai 201100, China
- Corresponding author Zhaoyang Hu, PhD, Fengneng Pharmaceutical Technology (Shanghai) Co., Ltd., RM. A310, 115 Xinjunhuan Road, Minhang District, Shanghai 201100, China.
| | - Fengfeng Zhou
- College of Computer Science and Technology, Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China
- Corresponding author Fengfeng Zhou, PhD, College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China.
| | - Wenwei Zhu
- Department of Hematology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, 110 Ganhe Road, Hongkou District, Shanghai 200437, China
- Corresponding author Wenwei Zhu, PhD, Department of Hematology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, 110 Ganhe Road, Hongkou District, Shanghai 200437, China.
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Fayad N, Koné KM, Gillis A, Mahillon J. Bacillus cytotoxicus Genomics: Chromosomal Diversity and Plasmidome Versatility. Front Microbiol 2021; 12:789929. [PMID: 34992589 PMCID: PMC8725734 DOI: 10.3389/fmicb.2021.789929] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 11/17/2021] [Indexed: 11/16/2022] Open
Abstract
Bacillus cytotoxicus is the thermotolerant representative of the Bacillus cereus group. This group, also known as B. cereus sensu lato, comprises both beneficial and pathogenic members and includes psychrotolerant and thermotolerant species. Bacillus cytotoxicus was originally recovered from a fatal outbreak in France in 1998. This species forms a remote cluster from the B. cereus group members and reliably contains the cytk-1 gene, coding for a cytotoxic variant of cytotoxin K. Although this species was originally thought to be homogenous, intra-species diversity has been recently described with four clades, six random amplified polymorphic DNA (RAPD) patterns, and 11 plasmids profiles. This study aimed to get new insights into the genomic diversity of B. cytotoxicus and to decipher the underlying chromosomal and plasmidial variations among six representative isolates through whole genome sequencing (WGS). Among the six sequenced strains, four fitted the previously described genomic clades A and D, while the remaining two constituted new distinct branches. As for the plasmid content of these strains, three large plasmids were putatively conjugative and three small ones potentially mobilizable, harboring coding genes for putative leaderless bacteriocins. Mobile genetic elements, such as prophages, Insertion Sequences (IS), and Bacillus cereus repeats (bcr) greatly contributed to the B. cytotoxicus diversity. As for IS elements and bcr, IS3 and bcr1 were the most abundant elements and, along with the group II intron B.c.I8, were found in all analyzed B. cytotoxicus strains. When compared to other B. cytotoxicus strains, the type-strain NVH 391-98 displayed a relatively low number of IS. Our results shed new light on the contribution of mobile genetic elements to the genome plasticity of B. cytotoxicus and their potential role in horizontal gene transfer.
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Affiliation(s)
- Nancy Fayad
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Louvain-la-Neuve, Belgium
- School of Pharmacy, Lebanese American University, Byblos, Lebanon
| | - Klèma Marcel Koné
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Louvain-la-Neuve, Belgium
| | - Annika Gillis
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Louvain-la-Neuve, Belgium
| | - Jacques Mahillon
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Louvain-la-Neuve, Belgium
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7
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Łubkowska B, Jeżewska-Frąckowiak J, Sobolewski I, Skowron PM. Bacteriophages of Thermophilic ' Bacillus Group' Bacteria-A Review. Microorganisms 2021; 9:1522. [PMID: 34361957 PMCID: PMC8303945 DOI: 10.3390/microorganisms9071522] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/03/2021] [Accepted: 07/12/2021] [Indexed: 11/17/2022] Open
Abstract
Bacteriophages of thermophiles are of increasing interest owing to their important roles in many biogeochemical, ecological processes and in biotechnology applications, including emerging bionanotechnology. However, due to lack of in-depth investigation, they are underrepresented in the known prokaryotic virosphere. Therefore, there is a considerable potential for the discovery of novel bacteriophage-host systems in various environments: marine and terrestrial hot springs, compost piles, soil, industrial hot waters, among others. This review aims at providing a reference compendium of thermophages characterized thus far, which infect the species of thermophilic 'Bacillus group' bacteria, mostly from Geobacillus sp. We have listed 56 thermophages, out of which the majority belong to the Siphoviridae family, others belong to the Myoviridae and Podoviridae families and, apparently, a few belong to the Sphaerolipoviridae, Tectiviridae or Corticoviridae families. All of their genomes are composed of dsDNA, either linear, circular or circularly permuted. Fourteen genomes have been sequenced; their sizes vary greatly from 35,055 bp to an exceptionally large genome of 160,590 bp. We have also included our unpublished data on TP-84, which infects Geobacillus stearothermophilus (G. stearothermophilus). Since the TP-84 genome sequence shows essentially no similarity to any previously characterized bacteriophage, we have defined TP-84 as a new species in the newly proposed genus Tp84virus within the Siphoviridae family. The information summary presented here may be helpful in comparative deciphering of the molecular basis of the thermophages' biology, biotechnology and in analyzing the environmental aspects of the thermophages' effect on the thermophile community.
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Affiliation(s)
- Beata Łubkowska
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (J.J.-F.); (I.S.); (P.M.S.)
- The High School of Health in Gdansk, Pelplinska 7, 80-335 Gdansk, Poland
| | - Joanna Jeżewska-Frąckowiak
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (J.J.-F.); (I.S.); (P.M.S.)
| | - Ireneusz Sobolewski
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (J.J.-F.); (I.S.); (P.M.S.)
| | - Piotr M. Skowron
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (J.J.-F.); (I.S.); (P.M.S.)
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8
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Abstract
Thermophilic microbes are an attractive bioproduction platform due to their inherently lower contamination risk and their ability to perform thermostable enzymatic processes which may be required for biomass processing and other industrial applications. The engineering of microbes for industrial scale processes requires a suite of genetic engineering tools to optimize existing biological systems as well as to design and incorporate new metabolic pathways within strains. Yet, such tools are often lacking and/or inadequate for novel microbes, especially thermophiles. This chapter focuses on genetic tool development and engineering strategies, in addition to challenges, for thermophilic microbes. We provide detailed instructions and techniques for tool development for an anaerobic thermophile, Caldanaerobacter subterraneus subsp. tengcongensis, including culturing, plasmid construction, transformation, and selection. This establishes a foundation for advanced genetic tool development necessary for the metabolic engineering of this microbe and potentially other thermophilic organisms.
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A novel thermophilic Aeribacillus bacteriophage AP45 isolated from the Valley of Geysers, Kamchatka: genome analysis suggests the existence of a new genus within the Siphoviridae family. Extremophiles 2019; 23:599-612. [PMID: 31376001 DOI: 10.1007/s00792-019-01119-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 07/21/2019] [Indexed: 12/12/2022]
Abstract
A novel thermophilic bacteriophage AP45 and its host strain Aeribacillus sp. CEMTC656 were isolated from the Valley of Geysers, Kamchatka Peninsula, Russia. Bacteriophage AP45 was identified as a member of the Siphoviridae family by electron microscopy. It showed high thermostability and had a slow cycle of reproduction. The AP45 genome had 51,606 base pairs (bp) and contained 71 open reading frames (ORFs), 40 of them encoding proteins of predicted function. Genes encoding DNA and RNA polymerases were not identified, indicating that AP45 used host polymerases. Based on the ORF65 encoding putative endolysin, the recombinant protein rAP45Lys was developed and its peptidoglycan-hydrolyzing activity was demonstrated. The AP45 genome exhibited limited identity to other phage sequences; the highest identity, 36%, was with the genome of the thermophilic Geobacillus myovirus D6E. The majority of putative proteins encoded by the AP45 genome had higher similarity to proteins from bacteria belonging to the Bacillaceae family, than to bacteriophages. In addition, more than half of the putative ORFs in the AP45 genome were highly similar to prophage sequences of A. pallidus strain 8m3, which was isolated in north-east China. The AP45 phage and revealed prophages might be members of a new genus belonging to the Siphoviridae family.
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Gilman J, Singleton C, Tennant RK, James P, Howard TP, Lux T, Parker DA, Love J. Rapid, Heuristic Discovery and Design of Promoter Collections in Non-Model Microbes for Industrial Applications. ACS Synth Biol 2019; 8:1175-1186. [PMID: 30995831 DOI: 10.1021/acssynbio.9b00061] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Well-characterized promoter collections for synthetic biology applications are not always available in industrially relevant hosts. We developed a broadly applicable method for promoter identification in atypical microbial hosts that requires no a priori understanding of cis-regulatory element structure. This novel approach combines bioinformatic filtering with rapid empirical characterization to expand the promoter toolkit and uses machine learning to improve the understanding of the relationship between DNA sequence and function. Here, we apply the method in Geobacillus thermoglucosidasius, a thermophilic organism with high potential as a synthetic biology chassis for industrial applications. Bioinformatic screening of G. kaustophilus, G. stearothermophilus, G. thermodenitrificans, and G. thermoglucosidasius resulted in the identification of 636 100 bp putative promoters, encompassing the genome-wide design space and lacking known transcription factor binding sites. Eighty of these sequences were characterized in vivo, and activities covered a 2-log range of predictable expression levels. Seven sequences were shown to function consistently regardless of the downstream coding sequence. Partition modeling identified sequence positions upstream of the canonical -35 and -10 consensus motifs that were predicted to strongly influence regulatory activity in Geobacillus, and artificial neural network and partial least squares regression models were derived to assess if there were a simple, forward, quantitative method for in silico prediction of promoter function. However, the models were insufficiently general to predict pre hoc promoter activity in vivo, most probably as a result of the relatively small size of the training data set compared to the size of the modeled design space.
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Affiliation(s)
- James Gilman
- The BioEconomy Centre, Biosciences, College of Life and Environmental Sciences, Stocker Road, University of Exeter, Exeter EX4 4QD, U.K
| | - Chloe Singleton
- The BioEconomy Centre, Biosciences, College of Life and Environmental Sciences, Stocker Road, University of Exeter, Exeter EX4 4QD, U.K
| | - Richard K. Tennant
- The BioEconomy Centre, Biosciences, College of Life and Environmental Sciences, Stocker Road, University of Exeter, Exeter EX4 4QD, U.K
| | - Paul James
- The BioEconomy Centre, Biosciences, College of Life and Environmental Sciences, Stocker Road, University of Exeter, Exeter EX4 4QD, U.K
| | - Thomas P. Howard
- School of Natural and Environmental Sciences, Newcastle University, Devonshire Building, Newcastle-upon-Tyne NE1 7RU, U.K
| | - Thomas Lux
- Plant Genome and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Munich 85764, Germany
| | - David A. Parker
- Biodomain, Shell Technology Center Houston, 3333 Highway 6 South, Houston, Texas 77082-3101, United States
| | - John Love
- The BioEconomy Centre, Biosciences, College of Life and Environmental Sciences, Stocker Road, University of Exeter, Exeter EX4 4QD, U.K
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11
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Yasir M, Qureshi AK, Khan I, Bibi F, Rehan M, Khan SB, Azhar EI. Culturomics-Based Taxonomic Diversity of Bacterial Communities in the Hot Springs of Saudi Arabia. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2018; 23:17-27. [PMID: 30589606 DOI: 10.1089/omi.2018.0176] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Hot springs are natural habitats for thermophilic microorganisms and provide a significant opportunity for bioprospecting thermostable biomolecules. However, the scientific community has only a fragmented understanding of the microbial diversity and composition in these biotopes. In this study, bacterial diversity in sediment samples from six hot springs of Saudi Arabia was investigated using an improved culture-dependent approach. High-throughput MALDI-TOF MS (matrix assisted laser desorption/ionization mass spectrometry) and 16S rRNA genes sequencing were used for the identification of purified isolates. Most of the hot springs had a neutral pH and a temperature range of 45-89°C. Relatively higher colony-forming units (1.9 ± 0.45 × 104) were observed with 60°C incubation of an 89°C sediment sample from the hot spring at Ain al Harra1. Among the 536 purified isolates, 6 novel candidate species were found, and the remaining isolates represented 139 distinct species. Several species, such as Bacillus cereus, Bacillus subtilis, and Bacillus schlegelii, were ubiquitous in the hot springs sampled, but 102 of the identified species were uniquely distributed among the hot springs. Sixteen of the isolated thermophilic bacteria, including Geobacillus kaustophilus, Thermus oshimai, and Brevibacillus thermoruber, grew at ≥60°C. In addition, 21 species exhibited hydrolytic enzymatic activity. Most of these species belonged to Bacillus and Brevibacillus. Overall, this study contributes to global knowledgebase on bacterial communities by comprehensively profiling culture-based bacterial diversity in the hot springs of Saudi Arabia. Further studies are required for investigating bacteria from hot springs by a metagenomic approach.
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Affiliation(s)
- Muhammad Yasir
- 1 Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Arooj K Qureshi
- 1 Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Imran Khan
- 1 Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,2 State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology Taipa, Macau, China
| | - Fehmida Bibi
- 1 Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohd Rehan
- 3 King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sher Bahadar Khan
- 4 Department of Chemistry, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Esam I Azhar
- 1 Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,5 Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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12
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Zablocki O, van Zyl L, Trindade M. Biogeography and taxonomic overview of terrestrial hot spring thermophilic phages. Extremophiles 2018; 22:827-837. [PMID: 30121708 DOI: 10.1007/s00792-018-1052-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 08/13/2018] [Indexed: 12/11/2022]
Abstract
Bacterial viruses ("phages") play important roles in the regulation and evolution of microbial communities in most ecosystems. Terrestrial hot springs typically contain thermophilic bacterial communities, but the diversity and impacts of its associated viruses ("thermophilic phages") are largely unexplored. Here, we provide a taxonomic overview of phages that have been isolated strictly from terrestrial hot springs around the world. In addition, we placed 17 thermophilic phage genomes in a global phylogenomic context to detect evolutionary patterns. Thermophilic phages have diverse morphologies (e.g., tailed, filamentous), unique virion structures (e.g., extremely long tailed siphoviruses), and span five taxonomic families encompassing strictly thermophilic phage genera. Within the phage proteomic tree, six thermophilic phage-related clades were identified, with evident genomic relatedness between thermophilic phages and archaeal viruses. Moreover, whole proteome analyses showed clustering between phages that infect distinct host phyla, such as Firmicutes and Deinococcus-Thermus. The potential for discovery of novel phage-host systems in terrestrial hot springs remain mostly untapped, thus additional emphasis on thermophilic phages in ecological prospecting is encouraged to gain insights into the microbial population dynamics of these environments.
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Affiliation(s)
- Olivier Zablocki
- Department of Microbiology, The Ohio State University, Columbus, OH, USA.,Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville, South Africa
| | - Leonardo van Zyl
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville, South Africa
| | - Marla Trindade
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville, South Africa.
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13
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Sequence, genome organization, annotation and proteomics of the thermophilic, 47.7-kb Geobacillus stearothermophilus bacteriophage TP-84 and its classification in the new Tp84virus genus. PLoS One 2018; 13:e0195449. [PMID: 29624616 PMCID: PMC5889276 DOI: 10.1371/journal.pone.0195449] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 03/22/2018] [Indexed: 11/19/2022] Open
Abstract
Bacteriophage TP-84 is a well-characterized bacteriophage of historical interest. It is a member of the Siphoviridae, and infects a number of thermophilic Geobacillus (Bacillus) stearothermophilus strains. Its’ 47.7-kbp double-stranded DNA genome revealed the presence of 81 coding sequences (CDSs) coding for polypeptides of 4 kDa or larger. Interestingly, all CDSs are oriented in the same direction, pointing to a dominant transcription direction of one DNA strand. Based on a homology search, a hypothetical function could be assigned to 31 CDSs. No RNA or DNA polymerase-coding genes were found on the bacteriophage genome indicating that TP-84 relies on the host’s transcriptional and replication enzymes. The TP84 genome is tightly packed with CDSs, typically spaced by several-to-tens of bp or often overlapping. The genome contains five putative promoter-like sequences showing similarity to the host promoter consensus sequence and allowing for a 2-bp mismatch. In addition, ten putative rho-independent terminators were detected. Because the genome sequence shows essentially no similarity to any previously characterised bacteriophage, TP-84 should be considered a new species in an undefined genus within the Siphoviridae family. Thus a taxonomic proposal of a new Tp84virus genus has been accepted by the International Committee on Taxonomy of Viruses. The bioinformatics genome analysis was verified by confirmation of 33 TP-84 proteins, which included: a) cloning of a selected CDS in Escherichia coli, coding for a DNA single-stranded binding protein (SSB; gene TP84_63), b) purification and functional assays of the recombinant TP-84 SSB, which has been shown to improve PCR reactions, c) mass spectrometric (MS) analysis of TP-84 bacteriophage capsid proteins, d) purification of TP-84 endolysin activity, e) MS analysis of the host cells from infection time course.
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14
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Parikka KJ, Jacquet S, Colombet J, Guillaume D, Le Romancer M. Abundance and observations of thermophilic microbial and viral communities in submarine and terrestrial hot fluid systems of the French Southern and Antarctic Lands. Polar Biol 2018. [DOI: 10.1007/s00300-018-2288-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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15
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Description of a cryptic thermophilic (pro)phage, CBP1 from Caldibacillus debilis strain GB1. Extremophiles 2018; 22:203-209. [PMID: 29380170 DOI: 10.1007/s00792-017-0988-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 12/08/2017] [Indexed: 10/18/2022]
Abstract
This study characterizes a cryptic (pro)phage-related sequence within the Caldibacillus debilis GB1 genome, designated CBP1.CBP1 is a Siphoviridae-like genome highly related to GBVS1 from Geobacillus sp. 6k51. The CBP1genome is a 37,315 bp region containing 69 putative ORFs with a GC content of 42% flanked on both sides by host DNA integrated into the main bacterial chromosome (contig 16). Bioinformatic analyses identified cassettes of genes within the CBP1 genome that were similar in function, yet distinct in sequence, from genes previously identified in GBVS1. All of CBP1 genes had less than 60% amino acid sequence identity with GBVS1by tBLASTx, with the exception of the TMP repeat gene. CBP1 possessed all the necessary genes to undergo a temperate/lytic phage life cycle, including excision, replication, structural genes, DNA packaging, and cell lyses. Proteomic analysis of CBP1 revealed the expression of 5 proteins. One of the expressed proteins was a transcriptional regulator protein homologous to the bacteriophage λ repressor protein (cI) expressed in high amounts from the CBP1 region, consistent with a lysogenic phage in a repressed state. The CBP1 protein expression profile during host growth provides unique insight into thermophilic Siphoviridae-like phages in the repressed state within their host cells.
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16
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Nagayoshi Y, Kumagae K, Mori K, Tashiro K, Nakamura A, Fujino Y, Hiromasa Y, Iwamoto T, Kuhara S, Ohshima T, Doi K. Physiological Properties and Genome Structure of the Hyperthermophilic Filamentous Phage φOH3 Which Infects Thermus thermophilus HB8. Front Microbiol 2016; 7:50. [PMID: 26941711 PMCID: PMC4763002 DOI: 10.3389/fmicb.2016.00050] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 01/12/2016] [Indexed: 12/11/2022] Open
Abstract
A filamentous bacteriophage, φOH3, was isolated from hot spring sediment in Obama hot spring in Japan with the hyperthermophilic bacterium Thermus thermophilus HB8 as its host. Phage φOH3, which was classified into the Inoviridae family, consists of a flexible filamentous particle 830 nm long and 8 nm wide. φOH3 was stable at temperatures ranging from 70 to 90°C and at pHs ranging from 6 to 9. A one-step growth curve of the phage showed a 60-min latent period beginning immediately postinfection, followed by intracellular virus particle production during the subsequent 40 min. The released virion number of φOH3 was 109. During the latent period, both single stranded DNA (ssDNA) and the replicative form (RF) of phage DNA were multiplied from min 40 onward. During the release period, the copy numbers of both ssDNA and RF DNA increased sharply. The size of the φOH3 genome is 5688 bp, and eight putative open reading frames (ORFs) were annotated. These ORFs were encoded on the plus strand of RF DNA and showed no significant homology with any known phage genes, except ORF 5, which showed 60% identity with the gene VIII product of the Thermus filamentous phage PH75. All the ORFs were similar to predicted genes annotated in the Thermus aquaticus Y51MC23 and Meiothermus timidus DSM 17022 genomes at the amino acid sequence level. This is the first report of the whole genome structure and DNA multiplication of a filamentous T. thermophilus phage within its host cell.
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Affiliation(s)
- Yuko Nagayoshi
- Faculty of Agriculture, Institute of Genetic Resources, Kyushu University Fukuoka, Japan
| | - Kenta Kumagae
- Faculty of Agriculture, Institute of Genetic Resources, Kyushu University Fukuoka, Japan
| | - Kazuki Mori
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University Fukuoka, Japan
| | - Kosuke Tashiro
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University Fukuoka, Japan
| | - Ayano Nakamura
- Faculty of Agriculture, Institute of Genetic Resources, Kyushu University Fukuoka, Japan
| | - Yasuhiro Fujino
- Faculty of Arts and Science, Kyushu University Fukuoka, Japan
| | - Yasuaki Hiromasa
- Faculty of Agriculture, Attached Promotive Center for International Education and Research of Agriculture, Kyushu University Fukuoka, Japan
| | - Takeo Iwamoto
- Core Research Facilities, Research Center for Medical Sciences, Jikei University School of Medicine Tokyo, Japan
| | - Satoru Kuhara
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University Fukuoka, Japan
| | - Toshihisa Ohshima
- Department of Biomedical Engineering, Faculty of Engineering, Osaka Institute of Technology Osaka, Japan
| | - Katsumi Doi
- Faculty of Agriculture, Institute of Genetic Resources, Kyushu University Fukuoka, Japan
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17
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van Zyl LJ, Sunda F, Taylor MP, Cowan DA, Trindade MI. Identification and characterization of a novel Geobacillus thermoglucosidasius bacteriophage, GVE3. Arch Virol 2015; 160:2269-82. [PMID: 26123922 DOI: 10.1007/s00705-015-2497-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 06/12/2015] [Indexed: 11/25/2022]
Abstract
The study of extremophilic phages may reveal new phage families as well as different mechanisms of infection, propagation and lysis to those found in phages from temperate environments. We describe a novel siphovirus, GVE3, which infects the thermophile Geobacillus thermoglucosidasius. The genome size is 141,298 bp (G+C 29.6%), making it the largest Geobacillus spp-infecting phage known. GVE3 appears to be most closely related to the recently described Bacillus anthracis phage vB_BanS_Tsamsa, rather than Geobacillus-infecting phages described thus far. Tetranucleotide usage deviation analysis supports this relationship, showing that the GVE3 genome sequence correlates best with B. anthracis and Bacillus cereus genome sequences, rather than Geobacillus spp genome sequences.
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Affiliation(s)
- Leonardo Joaquim van Zyl
- Institute for Microbial Biotechnology and Metagenomics (IMBM), University of the Western Cape, Robert Sobukwe Road, Bellville, Cape Town, South Africa,
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18
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Lossouarn J, Nesbø CL, Mercier C, Zhaxybayeva O, Johnson MS, Charchuck R, Farasin J, Bienvenu N, Baudoux AC, Michoud G, Jebbar M, Geslin C. ‘Ménage à trois’: a selfish genetic element uses a virus to propagate withinThermotogales. Environ Microbiol 2015; 17:3278-88. [DOI: 10.1111/1462-2920.12783] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 01/13/2015] [Accepted: 01/13/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Julien Lossouarn
- Université de Bretagne Occidentale (UBO, UEB); Institut Universitaire Européen de la Mer (IUEM) - UMR 6197; Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); rue Dumont d'Urville; F-29280 Plouzané France
- CNRS; IUEM - UMR 6197; Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); rue Dumont d'Urville; F-29280 Plouzané France
- Ifremer; UMR 6197; Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); Technopôle Pointe du diablea; F-29280 Plouzané France
| | - Camilla L. Nesbø
- CEES; Department of Biology; University of Oslo; Oslo 0316 Norway
- Department of Biological Sciences; University of Alberta; Edmonton AB T6G2R3 Canada
| | - Coraline Mercier
- Université de Bretagne Occidentale (UBO, UEB); Institut Universitaire Européen de la Mer (IUEM) - UMR 6197; Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); rue Dumont d'Urville; F-29280 Plouzané France
- CNRS; IUEM - UMR 6197; Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); rue Dumont d'Urville; F-29280 Plouzané France
- Ifremer; UMR 6197; Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); Technopôle Pointe du diablea; F-29280 Plouzané France
| | - Olga Zhaxybayeva
- Department of Biological Sciences; Dartmouth College; Hanover NH 03755 USA
| | - Milo S. Johnson
- Department of Biological Sciences; Dartmouth College; Hanover NH 03755 USA
| | | | - Julien Farasin
- Université de Bretagne Occidentale (UBO, UEB); Institut Universitaire Européen de la Mer (IUEM) - UMR 6197; Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); rue Dumont d'Urville; F-29280 Plouzané France
- CNRS; IUEM - UMR 6197; Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); rue Dumont d'Urville; F-29280 Plouzané France
- Ifremer; UMR 6197; Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); Technopôle Pointe du diablea; F-29280 Plouzané France
| | - Nadège Bienvenu
- Université de Bretagne Occidentale (UBO, UEB); Institut Universitaire Européen de la Mer (IUEM) - UMR 6197; Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); rue Dumont d'Urville; F-29280 Plouzané France
- CNRS; IUEM - UMR 6197; Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); rue Dumont d'Urville; F-29280 Plouzané France
- Ifremer; UMR 6197; Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); Technopôle Pointe du diablea; F-29280 Plouzané France
| | - Anne-Claire Baudoux
- Sorbonne Universités; UPMC Univ Paris 06; Paris 75005 France
- UMR 7144; Equipe DIPO; Station Biologique de Roscoff; Roscoff 29680 France
- CNRS; UMR 7144; Adaptation et Diversité en Milieu Marin; Station Biologique de Roscoff; Roscoff 29680 France
| | - Grégoire Michoud
- Université de Bretagne Occidentale (UBO, UEB); Institut Universitaire Européen de la Mer (IUEM) - UMR 6197; Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); rue Dumont d'Urville; F-29280 Plouzané France
- CNRS; IUEM - UMR 6197; Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); rue Dumont d'Urville; F-29280 Plouzané France
- Ifremer; UMR 6197; Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); Technopôle Pointe du diablea; F-29280 Plouzané France
| | - Mohamed Jebbar
- Université de Bretagne Occidentale (UBO, UEB); Institut Universitaire Européen de la Mer (IUEM) - UMR 6197; Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); rue Dumont d'Urville; F-29280 Plouzané France
- CNRS; IUEM - UMR 6197; Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); rue Dumont d'Urville; F-29280 Plouzané France
- Ifremer; UMR 6197; Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); Technopôle Pointe du diablea; F-29280 Plouzané France
| | - Claire Geslin
- Université de Bretagne Occidentale (UBO, UEB); Institut Universitaire Européen de la Mer (IUEM) - UMR 6197; Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); rue Dumont d'Urville; F-29280 Plouzané France
- CNRS; IUEM - UMR 6197; Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); rue Dumont d'Urville; F-29280 Plouzané France
- Ifremer; UMR 6197; Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); Technopôle Pointe du diablea; F-29280 Plouzané France
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19
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Liu Z, Zhao C, Deng Y, Huang Y, Liu B. Characterization of a thermostable recombinant β-galactosidase from a thermophilic anaerobic bacterial consortium YTY-70. BIOTECHNOL BIOTEC EQ 2015. [DOI: 10.1080/13102818.2015.1015244] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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20
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Liu Z, Zhang Z, Yan H, Li J, Shi L. Isolation and molecular characterization of multidrug-resistant Enterobacteriaceae strains from pork and environmental samples in Xiamen, China. J Food Prot 2015; 78:78-88. [PMID: 25581181 DOI: 10.4315/0362-028x.jfp-14-172] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
This study was conducted to investigate the prevalence and molecular characterization of multidrug-resistant (MDR) Enterobacteriaceae isolated from swine meat and the breeding environment. A total of 102 MDR Enterobacteriaceae strains belonging to five genera were obtained from 210 samples collected from a large-scale swine farm from March 2012 to June 2013 in Xiamen, People's Republic of China. Among these MDR isolates, Escherichia coli strains were found most frequently in both meat and environmental samples, followed by Citrobacter spp., Klebsiella spp., and Shigella spp. The neighbor-joining phylogenetic tree indicated that 70.3 % of Escherichia and 50 % of Citrobacter isolates from meat samples shared 100 % homology with relevant isolates from environmental samples. Resistance was most frequently observed to sulfonamide, trimethoprim, aminoglycoside, chloramphenicol, β-lactam, and tetracycline. Close correlation was noted between antibiotic resistance phenotype and the genes responsible for resistance to sulfonamide (sulI), trimethoprim (dhfrI), aminoglycoside (aadA, aac(3)-I, aphA-1, and aac(3)-IV), chloramphenicol (catI and cmlA), β-lactam (blaSHV, blaOXA, and blaTEM), florfenicol (floR), and tetracycline (tet(A) and tet(B)), which were widely distributed with prevalences of 72.5, 6.9, 62.7, 14.7, 78.4, 11.8, 25.5, 42.2, 12.7, 14.7, 39.2, 87.2, 68.6, and 34.3 % , respectively. Class 1 integrons carrying aadA22, dfrA17-aadA5, or dfrA12-aadA2 cassette arrays were commonly found in isolates from all samples. The gene cassette aac(6')-Ib-cr-arr-3-dfrA27-aadA16 was first found in an Enterobacter amnigenus isolate. Conjugation experiments revealed the plasmid-mediated transfer of class 1 integrons. Our results indicate that swine meat and the farming environment can be sources of antibiotic-resistant bacteria, which could be potentially transmitted to humans via the meat products industry chain.
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Affiliation(s)
- Zongbao Liu
- College of Light Industry and Food Technology, South China University of Technology, Guangzhou 510640, People's Republic of China; State Key Laboratory of Food Safety Technology for Meat Products and Synergetic Innovation Center of Food Safety and Nutrition, Xiamen Yinxiang Group Co., Ltd., Xiamen 361100, People's Republic of China
| | - Zhigang Zhang
- State Key Laboratory of Food Safety Technology for Meat Products and Synergetic Innovation Center of Food Safety and Nutrition, Xiamen Yinxiang Group Co., Ltd., Xiamen 361100, People's Republic of China
| | - He Yan
- College of Light Industry and Food Technology, South China University of Technology, Guangzhou 510640, People's Republic of China
| | - Jianrong Li
- Food Safety Key Lab of Liaoning Province, Bohai University, Jinzhou 121013, People's Republic of China.
| | - Lei Shi
- College of Light Industry and Food Technology, South China University of Technology, Guangzhou 510640, People's Republic of China; State Key Laboratory of Food Safety Technology for Meat Products and Synergetic Innovation Center of Food Safety and Nutrition, Xiamen Yinxiang Group Co., Ltd., Xiamen 361100, People's Republic of China.
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21
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Isolation and characterization of thermophilic bacterial strains from Soldhar (Tapovan) hot spring in Central Himalayan Region, India. ANN MICROBIOL 2014. [DOI: 10.1007/s13213-014-0984-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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22
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Chauhan K, Seale RB, Deeth HC, Turner MS. Hypervariable pili and flagella genes provide suitable new targets for DNA high-resolution melt-based genotyping of dairy Geobacillus spp. J Food Prot 2014; 77:1715-22. [PMID: 25285488 DOI: 10.4315/0362-028x.jfp-14-115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Although nonpathogenic in nature, spores of Geobacillus are able to attach to surfaces, germinate, and form biofilms, allowing rapid multiplication and persistence within milk powder processing plants, causing final product contamination, and eventually leading to a loss of revenue in terms of downgraded product quality. As a result, Geobacillus spp. have been found to be common contaminants of milk powder worldwide. Genotyping methods can help in gaining insight into the ecology and transmission of these thermophilic bacteria within and between dairy processing plants. The objective of this study was to use the assembled draft genomes of two Geobacillus spp. to identify and test new hypervariable genotyping targets for differentiating closely related dairy Geobacillus isolates. The two Geobacillus spp. strains obtained from high spore count powders were obtained in 2010 (isolate 7E) and in 1995 (isolate 126) and were previously shown to be of same genotype based on a variable number tandem repeat genotyping method. Significant nucleotide sequence variation was found in genes encoding pili and flagella, which were further investigated as suitable loci for a new high-resolution melt analysis (HRMA)-based genotyping method. Three genes encoding pulG (containing prepilin-type N-terminal cleavage domain), pilT (pili retraction protein), and fliW (flagellar assembly protein) were selected as targets for the new pili/flagella gene (PilFla) HRMA genotyping method. The three-gene-based PilFla-HRMA genotyping method differentiated 35 milk powder Geobacillus spp. isolates into 19 different genotype groups (D = 0.93), which compared favorably to the previous method (which used four variable number tandem repeat loci) that generated 16 different genotype groups (D = 0.90). In conclusion, through comparative genomics of two closely related dairy Geobacillus strains, we have identified new hypervariable regions that prove to be useful targets for highly discriminatory genotyping.
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Affiliation(s)
- Kanika Chauhan
- School of Agriculture and Food Sciences, The University of Queensland, St. Lucia Campus, Brisbane, Queensland 4072, Australia
| | - R Brent Seale
- School of Agriculture and Food Sciences, Auckland University of Technology, City Campus, Auckland 1010, New Zealand
| | - Hilton C Deeth
- School of Agriculture and Food Sciences, The University of Queensland, St. Lucia Campus, Brisbane, Queensland 4072, Australia
| | - Mark S Turner
- School of Agriculture and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia Campus, Brisbane, Queensland 4072, Australia.
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23
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Draft Genome Sequence of Geobacillus kaustophilus GBlys, a Lysogenic Strain with Bacteriophage OH2. GENOME ANNOUNCEMENTS 2013; 1:1/4/e00634-13. [PMID: 23950135 PMCID: PMC3744691 DOI: 10.1128/genomea.00634-13] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Geobacillus kaustophilus strain GBlys was isolated along with the bacteriophage ϕOH2, which infects G. kaustophilus NBRC 102445T. Here we present a draft sequence of this strain’s genome, which consists of 216 contigs for a total of 3,541,481 bp, 3,679 predicted coding sequences, and a G+C content of 52.1%.
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24
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Archaeal viruses, not archaeal phages: an archaeological dig. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2013; 2013:251245. [PMID: 23653528 PMCID: PMC3638648 DOI: 10.1155/2013/251245] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 02/19/2013] [Accepted: 02/22/2013] [Indexed: 11/17/2022]
Abstract
Viruses infect members of domains Bacteria, Eukarya, and Archaea. While those infecting domain Eukarya are nearly universally described as "Viruses", those of domain Bacteria, to a substantial extent, instead are called "Bacteriophages," or "Phages." Should the viruses of domain Archaea therefore be dubbed "Archaeal phages," "Archaeal viruses," or some other construct? Here we provide documentation of published, general descriptors of the viruses of domain Archaea. Though at first the term "Phage" or equivalent was used almost exclusively in the archaeal virus literature, there has been a nearly 30-year trend away from this usage, with some persistence of "Phage" to describe "Head-and-tail" archaeal viruses, "Halophage" to describe viruses of halophilic Archaea, use of "Prophage" rather than "Provirus," and so forth. We speculate on the root of the early 1980's transition from "Phage" to "Virus" to describe these infectious agents, consider the timing of introduction of "Archaeal virus" (which can be viewed as analogous to "Bacterial virus"), identify numerous proposed alternatives to "Archaeal virus," and also provide discussion of the general merits of the term, "Phage." Altogether we identify in excess of one dozen variations on how the viruses of domain Archaea are described, and document the timing of both their introduction and use.
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25
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Mazaheri Nezhad Fard R, Barton MD, Heuzenroeder MW. Novel Bacteriophages in Enterococcus spp. Curr Microbiol 2009; 60:400-6. [PMID: 19967374 DOI: 10.1007/s00284-009-9555-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2009] [Accepted: 11/13/2009] [Indexed: 02/06/2023]
Abstract
Most of the bacteriophages (phages) currently reported in Enterococcus spp. belong to tailed families of bacteriophages Podoviridae, Siphoviridae, and Myoviridae. There is a little information on non-tailed bacteriophages isolated from enterococci. Samples of sewage and piggery effluents were tested on pig and chicken isolates of Enterococcus faecalis, E. faecium and E. gallinarum for lytic phages. In addition, isolates were exposed to mitomycin C to induce lysogenic phages. Bacteriophages that were detected were visualized by electron microscopy. Ten bacteriophages were of isometric shape with long flexible or non-flexible tails, while one had a long head with a long flexible tail; all contained double-stranded DNA molecules. Seven Polyhedral, filamentous, and pleomorphic-shaped phages containing DNA or RNA were also observed. The pleomorphic phages were droplet- or lemon-shaped in morphology. This study is the first report on polyhedral phages in Enterococcus spp. of animal origin and also the first report of filamentous and pleomorphic phages in enterococci.
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