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Kallies R, Hu D, Abdulkadir N, Schloter M, Rocha U. Identification of Huge Phages from Wastewater Metagenomes. Viruses 2023; 15:2330. [PMID: 38140571 PMCID: PMC10747093 DOI: 10.3390/v15122330] [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: 10/29/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023] Open
Abstract
Huge phages have genomes larger than 200 kilobases, which are particularly interesting for their genetic inventory and evolution. We screened 165 wastewater metagenomes for the presence of viral sequences. After identifying over 600 potential huge phage genomes, we reduced the dataset using manual curation by excluding viral contigs that did not contain viral protein-coding genes or consisted of concatemers of several small phage genomes. This dataset showed seven fully annotated huge phage genomes. The phages grouped into distinct phylogenetic clades, likely forming new genera and families. A phylogenomic analysis between our huge phages and phages with smaller genomes, i.e., less than 200 kb, supported the hypothesis that huge phages have undergone convergent evolution. The genomes contained typical phage protein-coding genes, sequential gene cassettes for metabolic pathways, and complete inventories of tRNA genes covering all standard and rare amino acids. Our study showed a pipeline for huge phage analyses that may lead to new enzymes for therapeutic or biotechnological applications.
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Affiliation(s)
- René Kallies
- Department for Environmental Microbiology, Helmholtz Centre for Environmental Research, Permoserstr. 15, D-04318 Leipzig, Germany; (D.H.); (N.A.)
| | - Die Hu
- Department for Environmental Microbiology, Helmholtz Centre for Environmental Research, Permoserstr. 15, D-04318 Leipzig, Germany; (D.H.); (N.A.)
| | - Nafi’u Abdulkadir
- Department for Environmental Microbiology, Helmholtz Centre for Environmental Research, Permoserstr. 15, D-04318 Leipzig, Germany; (D.H.); (N.A.)
| | - Michael Schloter
- Department of Environmental Health, Helmholtz Munich, Ingolstaedter Landstr. 1, D-85758 Neuherberg, Germany;
| | - Ulisses Rocha
- Department for Environmental Microbiology, Helmholtz Centre for Environmental Research, Permoserstr. 15, D-04318 Leipzig, Germany; (D.H.); (N.A.)
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Sousa C, Ferreira R, Santos SB, Azevedo NF, Melo LDR. Advances on diagnosis of Helicobacter pylori infections. Crit Rev Microbiol 2023; 49:671-692. [PMID: 36264672 DOI: 10.1080/1040841x.2022.2125287] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 09/12/2022] [Indexed: 11/09/2022]
Abstract
The association of Helicobacter pylori to several gastric diseases, such as chronic gastritis, peptic ulcer disease, and gastric cancer, and its high prevalence worldwide, raised the necessity to use methods for a proper and fast diagnosis and monitoring the pathogen eradication. Available diagnostic methods can be classified as invasive or non-invasive, and the selection of the best relies on the clinical condition of the patient, as well as on the sensitivity, specificity, and accessibility of the diagnostic test. This review summarises all diagnostic methods currently available, including the invasive methods: endoscopy, histology, culture, and molecular methods, and the rapid urease test (RUT), as well as the non-invasive methods urea breath test (UBT), serological assays, biosensors, and microfluidic devices and the stool antigen test (SAT). Moreover, it lists the diagnostic advantages and limitations, as well as the main advances for each methodology. In the end, research on the development of new diagnostic methods, such as bacteriophage-based H. pylori diagnostic tools, is also discussed.
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Affiliation(s)
- Cláudia Sousa
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Rute Ferreira
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
- i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
| | - Sílvio B Santos
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Nuno F Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Luís D R Melo
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
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do Socorro Fôro Ramos E, Bahia SL, de Oliveira Ribeiro G, Villanova F, de Pádua Milagres FA, Brustulin R, Pandey RP, Deng X, Delwart E, da Costa AC, Leal É. Characterization of Phietavirus Henu 2 in the virome of individuals with acute gastroenteritis. Virus Genes 2023; 59:464-472. [PMID: 37004601 DOI: 10.1007/s11262-023-01990-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 03/15/2023] [Indexed: 04/04/2023]
Abstract
There is a growing interest in phages as potential biotechnological tools in human health owing to the antibacterial activity of these viruses. In this study, we characterized a new member (named PhiV_005_BRA/2016) of the recently identified phage species Phietavirus Henu 2. PhiV_005_BRA/2016 was detected through metagenomic analysis of stool samples of individuals with acute gastroenteritis. PhiV_005_BRA/2016 contains double-stranded linear DNA (dsDNA), it has a genome of 43,513 base pairs (bp), with a high identity score (99%) with phage of the genus Phietavirus, species of Phietavirus Henu 2. Life style prediction indicated that PhiV_005_BRA/2016 is a lysogenic phage whose the main host is methicillin-resistant Staphylococcus aureus (MRSA). Indeed, we found PhiV_005_BRA/2016 partially integrated in the genome of distinct MRSA strains. Our findings highlights the importance of large-scale screening of bacteriophages to better understand the emergence of multi-drug resistant bacterial.
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Affiliation(s)
- Endrya do Socorro Fôro Ramos
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicais, Universidade Federal do Pará, Belém, Pará, 66075-000, Brazil
| | - Santana Lobato Bahia
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicais, Universidade Federal do Pará, Belém, Pará, 66075-000, Brazil
| | - Geovani de Oliveira Ribeiro
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicais, Universidade Federal do Pará, Belém, Pará, 66075-000, Brazil
| | - Fabiola Villanova
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicais, Universidade Federal do Pará, Belém, Pará, 66075-000, Brazil
| | - Flávio Augusto de Pádua Milagres
- Secretaria de Saúde do Tocantins, Palmas, Tocantins, 77453-000, Brazil
- Laboratório Central de Saúde Pública do Tocantins (LACEN/TO), Palmas, Tocantins, 77016-330, Brazil
| | - Rafael Brustulin
- Secretaria de Saúde do Tocantins, Palmas, Tocantins, 77453-000, Brazil
- Laboratório Central de Saúde Pública do Tocantins (LACEN/TO), Palmas, Tocantins, 77016-330, Brazil
| | - Ramendra Pati Pandey
- Centre for Drug Design Discovery and Development (C4D), SRM University Delhi-NCR, Rajiv Gandhi Education City, Sonepat, Haryana, 131029, India
| | - Xutao Deng
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA, 94118-4417, USA
- Department Laboratory Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Eric Delwart
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA, 94118-4417, USA
- Department Laboratory Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
| | | | - Élcio Leal
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicais, Universidade Federal do Pará, Belém, Pará, 66075-000, Brazil.
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Rahimi A, Soudi S, Vakilian S, Jamshidi-Adegani F, Sadeghizadeh M, Al-Hashmi S. BACTERIOPHAGE M13 MODULATES THE SEPSIS-RELATED INFLAMMATORY RESPONSES AND ORGAN DAMAGE IN A CLP MODEL. Shock 2023; 59:493-504. [PMID: 36576361 DOI: 10.1097/shk.0000000000002076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
ABSTRACT Background: Sepsis is a life-threatening disorder that leads to the induction of inflammatory responses and organ failure. Phage therapy is a new approach to controlling infections resistant to common treatments, including sepsis. Several studies have shown the effect of lytic bacteriophages on infection control by reducing the bacterial load. The present study deals with lysogenic bacteriophage M13 on the inflammatory responses caused by cecal ligation and puncture (CLP)-induced sepsis in a mouse model. Methods Bacteriophage M13 harvested from ER2738, titrated, and confirmed by transmission electron microscopy analysis. In vitro toxicity and immunomodulatory effect of bacteriophage M13 were assessed on splenocytes by measurement of cell viability and the production level of cytokines, nitric oxide, and reactive oxygen species. For in vivo experiments, 8-weeks-old male C57BL/6 mice were randomly divided into the following three groups: CLP + NS (treated with normal saline), CLP + M13 (treated with an intraperitoneal injection of 10 9 PFU/mL of bacteriophage M13), and sham + NS (induced surgery but without ligation and puncture, treated with NS). The mice were killed at different time points after surgery (6, 24, 48, and 72, n = 10 for each time point of each group). The kidney, liver, and lungs were harvested for histopathological analysis, and blood was obtained for cytokine and liver enzyme assay. The spleen was used to assess the bacterial load using colony-forming unit assay. The rectal temperature and survival were evaluated during the study. Results According to the in vitro results, 10 9 PFU/mL of bacteriophage M13 was not toxic and did not affect the level of cytokine, nitric oxide, and reactive oxygen species production by splenocytes, but it reduced the inflammatory response of splenocytes in responses to LPS. In vivo studies indicated that the amount of proinflammatory cytokines, liver enzymes, bacterial load, and organ failure were decreased in the CLP + M13 group compared with CLP + NS, whereas the survival rate was increased. Conclusions These experiments demonstrated that bacteriophage M13 could lessen the consequences related to sepsis in CLP mice and can be considered a therapeutic approach in sepsis.
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Affiliation(s)
- Arezou Rahimi
- Department of Immunology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Sara Soudi
- Department of Immunology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Saeid Vakilian
- Laboratory for Stem Cell and Regenerative Medicine, Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Fatemeh Jamshidi-Adegani
- Laboratory for Stem Cell and Regenerative Medicine, Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Majid Sadeghizadeh
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Sulaiman Al-Hashmi
- Laboratory for Stem Cell and Regenerative Medicine, Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
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Elois MA, da Silva R, Pilati GVT, Rodríguez-Lázaro D, Fongaro G. Bacteriophages as Biotechnological Tools. Viruses 2023; 15:v15020349. [PMID: 36851563 PMCID: PMC9963553 DOI: 10.3390/v15020349] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/14/2023] [Accepted: 01/18/2023] [Indexed: 01/28/2023] Open
Abstract
Bacteriophages are ubiquitous organisms that can be specific to one or multiple strains of hosts, in addition to being the most abundant entities on the planet. It is estimated that they exceed ten times the total number of bacteria. They are classified as temperate, which means that phages can integrate their genome into the host genome, originating a prophage that replicates with the host cell and may confer immunity against infection by the same type of phage; and lytics, those with greater biotechnological interest and are viruses that lyse the host cell at the end of its reproductive cycle. When lysogenic, they are capable of disseminating bacterial antibiotic resistance genes through horizontal gene transfer. When professionally lytic-that is, obligately lytic and not recently descended from a temperate ancestor-they become allies in bacterial control in ecological imbalance scenarios; these viruses have a biofilm-reducing capacity. Phage therapy has also been advocated by the scientific community, given the uniqueness of issues related to the control of microorganisms and biofilm production when compared to other commonly used techniques. The advantages of using bacteriophages appear as a viable and promising alternative. This review will provide updates on the landscape of phage applications for the biocontrol of pathogens in industrial settings and healthcare.
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Affiliation(s)
- Mariana Alves Elois
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
| | - Raphael da Silva
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
| | - Giulia Von Tönnemann Pilati
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
| | - David Rodríguez-Lázaro
- Microbiology Division, Faculty of Sciences, University of Burgos, 09001 Burgos, Spain
- Research Centre for Emerging Pathogens and Global Health, University of Burgos, 09001 Burgos, Spain
| | - Gislaine Fongaro
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
- Correspondence:
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Alsaadi A, Imam M, Alghamdi AA, Alghoribi MF. Towards promising antimicrobial alternatives: The future of bacteriophage research and development in Saudi Arabia. J Infect Public Health 2022; 15:1355-1362. [DOI: 10.1016/j.jiph.2022.10.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/04/2022] [Accepted: 10/24/2022] [Indexed: 11/11/2022] Open
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Abril AG, Carrera M, Notario V, Sánchez-Pérez Á, Villa TG. The Use of Bacteriophages in Biotechnology and Recent Insights into Proteomics. Antibiotics (Basel) 2022; 11:653. [PMID: 35625297 PMCID: PMC9137636 DOI: 10.3390/antibiotics11050653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/11/2022] [Accepted: 05/12/2022] [Indexed: 12/10/2022] Open
Abstract
Phages have certain features, such as their ability to form protein-protein interactions, that make them good candidates for use in a variety of beneficial applications, such as in human or animal health, industry, food science, food safety, and agriculture. It is essential to identify and characterize the proteins produced by particular phages in order to use these viruses in a variety of functional processes, such as bacterial detection, as vehicles for drug delivery, in vaccine development, and to combat multidrug resistant bacterial infections. Furthermore, phages can also play a major role in the design of a variety of cheap and stable sensors as well as in diagnostic assays that can either specifically identify specific compounds or detect bacteria. This article reviews recently developed phage-based techniques, such as the use of recombinant tempered phages, phage display and phage amplification-based detection. It also encompasses the application of phages as capture elements, biosensors and bioreceptors, with a special emphasis on novel bacteriophage-based mass spectrometry (MS) applications.
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Affiliation(s)
- Ana G. Abril
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15898 Santiago de Compostela, Spain;
- Department of Food Technology, Spanish National Research Council (CSIC), Marine Research Institute (IIM), 36208 Vigo, Spain;
| | - Mónica Carrera
- Department of Food Technology, Spanish National Research Council (CSIC), Marine Research Institute (IIM), 36208 Vigo, Spain;
| | - Vicente Notario
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA;
| | - Ángeles Sánchez-Pérez
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, NSW 2006, Australia;
| | - Tomás G. Villa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15898 Santiago de Compostela, Spain;
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Kim SG, Roh E, Park J, Giri SS, Kwon J, Kim SW, Kang JW, Lee SB, Jung WJ, Lee YM, Cho K, Park SC. The Bacteriophage pEp_SNUABM_08 Is a Novel Singleton Siphovirus with High Host Specificity for Erwinia pyrifoliae. Viruses 2021; 13:1231. [PMID: 34202208 PMCID: PMC8310351 DOI: 10.3390/v13071231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/18/2021] [Accepted: 06/24/2021] [Indexed: 01/16/2023] Open
Abstract
Species belonging to the genus Erwinia are predominantly plant pathogens. A number of bacteriophages capable of infecting Erwinia have been used for the control of plant diseases such as fire blight. Public repositories provide the complete genome information for such phages, which includes genomes ranging from 30 kb to 350 kb in size. However, limited information is available regarding bacteriophages belonging to the family Siphoviridae. A novel lytic siphophage, pEp_SNUABM_08, which specifically infects Erwinia pyrifoliae, was isolated from the soil of an affected apple orchard in South Korea. A comprehensive genome analysis was performed using the Erwinia-infecting siphophage. The whole genome of pEp_SNUABM_08 comprised 62,784 bp (GC content, 57.24%) with 79 open reading frames. The genomic characteristics confirmed that pEp_SNUABM_08 is a singleton lytic bacteriophage belonging to the family Siphoviridae, and no closely related phages have been reported thus far. Our study not only characterized a unique phage, but also provides insight into the genetic diversity of Erwinia bacteriophages.
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Affiliation(s)
- Sang Guen Kim
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.S.G.); (J.K.); (S.W.K.); (J.W.K.); (S.B.L.); (W.J.J.); (Y.M.L.); (K.C.)
| | - Eunjung Roh
- Crop Protection Division, National Institute of Agriculture Sciences, Rural Development Administration, Wanju 55365, Korea; (E.R.); (J.P.)
| | - Jungkum Park
- Crop Protection Division, National Institute of Agriculture Sciences, Rural Development Administration, Wanju 55365, Korea; (E.R.); (J.P.)
| | - Sib Sankar Giri
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.S.G.); (J.K.); (S.W.K.); (J.W.K.); (S.B.L.); (W.J.J.); (Y.M.L.); (K.C.)
| | - Jun Kwon
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.S.G.); (J.K.); (S.W.K.); (J.W.K.); (S.B.L.); (W.J.J.); (Y.M.L.); (K.C.)
| | - Sang Wha Kim
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.S.G.); (J.K.); (S.W.K.); (J.W.K.); (S.B.L.); (W.J.J.); (Y.M.L.); (K.C.)
| | - Jeong Woo Kang
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.S.G.); (J.K.); (S.W.K.); (J.W.K.); (S.B.L.); (W.J.J.); (Y.M.L.); (K.C.)
| | - Sung Bin Lee
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.S.G.); (J.K.); (S.W.K.); (J.W.K.); (S.B.L.); (W.J.J.); (Y.M.L.); (K.C.)
| | - Won Joon Jung
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.S.G.); (J.K.); (S.W.K.); (J.W.K.); (S.B.L.); (W.J.J.); (Y.M.L.); (K.C.)
| | - Young Min Lee
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.S.G.); (J.K.); (S.W.K.); (J.W.K.); (S.B.L.); (W.J.J.); (Y.M.L.); (K.C.)
| | - Kevin Cho
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.S.G.); (J.K.); (S.W.K.); (J.W.K.); (S.B.L.); (W.J.J.); (Y.M.L.); (K.C.)
| | - Se Chang Park
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.S.G.); (J.K.); (S.W.K.); (J.W.K.); (S.B.L.); (W.J.J.); (Y.M.L.); (K.C.)
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Viruses with U-DNA: New Avenues for Biotechnology. Viruses 2021; 13:v13050875. [PMID: 34068736 PMCID: PMC8150378 DOI: 10.3390/v13050875] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/05/2021] [Accepted: 05/06/2021] [Indexed: 02/07/2023] Open
Abstract
Deoxyuridine in DNA has recently been in the focus of research due to its intriguing roles in several physiological and pathophysiological situations. Although not an orthodox DNA base, uracil may appear in DNA via either cytosine deamination or thymine-replacing incorporations. Since these alterations may induce mutation or may perturb DNA–protein interactions, free living organisms from bacteria to human contain several pathways to counteract uracilation. These efficient and highly specific repair routes uracil-directed excision repair initiated by representative of uracil-DNA glycosylase families. Interestingly, some bacteriophages exist with thymine-lacking uracil-DNA genome. A detailed understanding of the strategy by which such phages can replicate in bacteria where an efficient repair pathway functions for uracil-excision from DNA is expected to reveal novel inhibitors that can also be used for biotechnological applications. Here, we also review the several potential biotechnological applications already implemented based on inhibitors of uracil-excision repair, such as Crispr-base-editing and detection of nascent uracil distribution pattern in complex genomes.
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Zeng H, Li C, Luo D, Zhang J, Ding Y, Chen M, Yang X, Lei T, Wu S, Ye Q, Pang R, Gu Q, Wu Q. Novel phage vB_CtuP_B1 for controlling Cronobacter malonaticus and Cronobacter turicensis in ready-to-eat lettuce and powered infant formula. Food Res Int 2021; 143:110255. [PMID: 33992361 DOI: 10.1016/j.foodres.2021.110255] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/25/2021] [Accepted: 02/17/2021] [Indexed: 01/27/2023]
Abstract
Cronobacter spp. are important foodborne pathogens that are a threat to people of all ages, but especially neonates and infants. Bacteriophages are biological agents that are potentially useful for the control of foodborne pathogens. However, there has been little research on the control of C. malonaticus and C. turicensis using bacteriophages. In the present study, a novel lytic phage vB_CtuP_B1 (hereafter referred to as B1)-which can simultaneously lyse C. malonaticus and C. turicensis- was isolated from river water in Guangzhou, China, and was used in the control of Cronobacter contaminated food. The phage has a short tail, and has been identified as a new species of Kayfunavirus based on genomic and phylogenetic analyses. One-step growth and stability assays revealed that phage B1 has a very short latent period (<5 min) and a large burst size (4006 pfu/cell), and is highly stable between 25 and 60 °C and between pH 5 and 11. Its genome encodes two lytic proteins, but does not contain any genes responsible for antibiotic resistance and virulence factors. In broth, the phage B1 completely inhibited the growth of C. malonaticus cro2475W and C. turicensis cro1541A1-1 for up to 6 h. On lettuce, phage B1 reduced the viable count of C. turicensis cro1541A1-1 to below the detection limit for bacteria on lettuce (<10 cfu/mL) after 6 h at 4 °C and 2 h at 25 °C, and also significantly reduced the viable count of C. malonaticus cro2475W at those temperatures. In powdered infant formula, the viable counts of both the phage-treated bacterial hosts were significantly reduced after 2 h of storage at 4 °C or 37 °C. Furthermore, phage B1 reduced the viable count of C. turicensis cro1541A1-1 to below the detection limit (<10 cfu/mL) from 4 h to 24 h at 37 °C. It significantly inhibited the growth of C. turicensis cro1541A1-1 than that of C. malonaticus cro2475W (P < 0.05). In conclusion, phage B1 with high stability and strong lytic ability is potentially useful for controlling C. malonaticus and C. turicensis.
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Affiliation(s)
- Haiyan Zeng
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Chengsi Li
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Dandan Luo
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Jumei Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Yu Ding
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Moutong Chen
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Xiaojuan Yang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Tao Lei
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Shi Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Qinghua Ye
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Rui Pang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Qihui Gu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
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