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Kwan SY, Sabotta CM, Cruz LR, Wong MC, Ajami NJ, McCormick JB, Fisher-Hoch SP, Beretta L. Gut phageome in Mexican Americans: a population at high risk for metabolic dysfunction-associated steatotic liver disease and diabetes. mSystems 2024:e0043424. [PMID: 39166873 DOI: 10.1128/msystems.00434-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 07/19/2024] [Indexed: 08/23/2024] Open
Abstract
Mexican Americans are disproportionally affected by metabolic dysfunction-associated steatotic liver disease (MASLD), which often co-occurs with diabetes. Despite extensive evidence on the causative role of the gut microbiome in MASLD, studies determining the involvement of the gut phageome are scarce. In this cross-sectional study, we characterized the gut phageome in Mexican Americans of South Texas by stool shotgun metagenomic sequencing of 340 subjects, concurrently screened for liver steatosis by transient elastography. Inter-individual variations in the phageome were associated with gender, country of birth, diabetes, and liver steatosis. The phage signatures for diabetes and liver steatosis were subsequently determined. Enrichment of Inoviridae was associated with both diabetes and liver steatosis. Diabetes was further associated with the enrichment of predominantly temperate Escherichia phages, some of which possessed virulence factors. Liver steatosis was associated with the depletion of Lactococcus phages r1t and BK5-T, and enrichment of the globally prevalent Crassvirales phages, including members of genus cluster IX (Burzaovirus coli, Burzaovirus faecalis) and VI (Kahnovirus oralis). The Lactococcus phages showed strong correlations and co-occurrence with Lactococcus lactis, while the Crassvirales phages, B. coli, B. faecalis, and UAG-readthrough crAss clade correlated and co-occurred with Prevotella copri. In conclusion, we identified the gut phageome signatures for two closely linked metabolic diseases with significant global burden. These phage signatures may have utility in risk modeling and disease prevention in this high-risk population, and identification of potential bacterial targets for phage therapy.IMPORTANCEPhages influence human health and disease by shaping the gut bacterial community. Using stool samples from a high-risk Mexican American population, we provide insights into the gut phageome changes associated with diabetes and liver steatosis, two closely linked metabolic diseases with significant global burden. Common to both diseases was an enrichment of Inoviridae, a group of phages that infect bacterial hosts chronically without lysis, allowing them to significantly influence bacterial growth, virulence, motility, biofilm formation, and horizontal gene transfer. Diabetes was additionally associated with the enrichment of Escherichia coli-infecting phages, some of which contained virulence factors. Liver steatosis was additionally associated with the depletion of Lactococcus lactis-infecting phages, and enrichment of Crassvirales phages, a group of virulent phages with high global prevalence and persistence across generations. These phageome signatures may have utility in risk modeling, as well as identify potential bacterial targets for phage therapy.
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Affiliation(s)
- Suet-Ying Kwan
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Caroline M Sabotta
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Lorenzo R Cruz
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Matthew C Wong
- The Platform for Innovative Microbiome and Translational Research (PRIME-TR), Moon Shots Program, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Nadim J Ajami
- The Platform for Innovative Microbiome and Translational Research (PRIME-TR), Moon Shots Program, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Joseph B McCormick
- School of Public Health, University of Texas Health Science Center at Houston, Brownsville Regional Campus, Brownsville, Texas, USA
| | - Susan P Fisher-Hoch
- School of Public Health, University of Texas Health Science Center at Houston, Brownsville Regional Campus, Brownsville, Texas, USA
| | - Laura Beretta
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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Zeng X, Liang S, Dong J, Gao G, Hu Y, Sun Y. The trade-off of Vibrio parahaemolyticus between bacteriophage resistance and growth competitiveness. Front Microbiol 2024; 15:1346251. [PMID: 38919495 PMCID: PMC11196418 DOI: 10.3389/fmicb.2024.1346251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 04/10/2024] [Indexed: 06/27/2024] Open
Abstract
Vibrio parahaemolyticus is a food-borne pathogen, which is often isolated from various seafood products. In this study, two kinds of bacteriophages was isolated from the offshore sediments samples. The anti-phage mutant strain were obtained after seventeen rounds of co-culture of Vibrio parahaemolyticus and mixed bacteriophage, multigroup sequencing was carried out on spontaneous the anti-phage mutant strain and the wild-type strain. We used the Sanger sequencing to verify the accuracy of the mutation sites. Biolog GEN III MicroPlates were used to evaluate the metabolic capacity of wild-type strains and the anti-phage mutant strain. In this study, we found that with flaG gene (slight homology to N terminus of multiple flagellins) mutated, making the bacteriophage unable to absorb to the cell surface of the host. And, the growth competitiveness of the anti-phage mutant strain is lower than the wild-type strain. These results indicated that the fitness cost, including loss of the growth competitiveness, constitutes a barrier to the prevalence of these defense mechanisms. And the selection pressure on different anti-phage strategies depends on the trade-off between mortality imposed by bacteriophages and fitness cost of the defense strategy under the given environmental conditions. In conclusion, this study provides valuable insights into the phage-host interaction and phage resistance in Vibrio parahaemolyticus. Our study provided knowledge for the evolutionary adaption of bacteria against the bacteriophage, which could add more information to understand the phage resistance mechanism before applying in the industry.
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Affiliation(s)
- Xiuxiu Zeng
- Guoke Ningbo Life Science and Health Industry Research Institute, Ningbo, Zhejiang, China
| | | | - Jiayi Dong
- Guoke Ningbo Life Science and Health Industry Research Institute, Ningbo, Zhejiang, China
| | | | - Yaoren Hu
- Ningbo Hospital, Ningbo, Zhejiang, China
| | - Yuechao Sun
- Guoke Ningbo Life Science and Health Industry Research Institute, Ningbo, Zhejiang, China
- Ningbo Hospital, Ningbo, Zhejiang, China
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3
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Ligeti B, Szepesi-Nagy I, Bodnár B, Ligeti-Nagy N, Juhász J. ProkBERT family: genomic language models for microbiome applications. Front Microbiol 2024; 14:1331233. [PMID: 38282738 PMCID: PMC10810988 DOI: 10.3389/fmicb.2023.1331233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/11/2023] [Indexed: 01/30/2024] Open
Abstract
Background In the evolving landscape of microbiology and microbiome analysis, the integration of machine learning is crucial for understanding complex microbial interactions, and predicting and recognizing novel functionalities within extensive datasets. However, the effectiveness of these methods in microbiology faces challenges due to the complex and heterogeneous nature of microbial data, further complicated by low signal-to-noise ratios, context-dependency, and a significant shortage of appropriately labeled datasets. This study introduces the ProkBERT model family, a collection of large language models, designed for genomic tasks. It provides a generalizable sequence representation for nucleotide sequences, learned from unlabeled genome data. This approach helps overcome the above-mentioned limitations in the field, thereby improving our understanding of microbial ecosystems and their impact on health and disease. Methods ProkBERT models are based on transfer learning and self-supervised methodologies, enabling them to use the abundant yet complex microbial data effectively. The introduction of the novel Local Context-Aware (LCA) tokenization technique marks a significant advancement, allowing ProkBERT to overcome the contextual limitations of traditional transformer models. This methodology not only retains rich local context but also demonstrates remarkable adaptability across various bioinformatics tasks. Results In practical applications such as promoter prediction and phage identification, the ProkBERT models show superior performance. For promoter prediction tasks, the top-performing model achieved a Matthews Correlation Coefficient (MCC) of 0.74 for E. coli and 0.62 in mixed-species contexts. In phage identification, ProkBERT models consistently outperformed established tools like VirSorter2 and DeepVirFinder, achieving an MCC of 0.85. These results underscore the models' exceptional accuracy and generalizability in both supervised and unsupervised tasks. Conclusions The ProkBERT model family is a compact yet powerful tool in the field of microbiology and bioinformatics. Its capacity for rapid, accurate analyses and its adaptability across a spectrum of tasks marks a significant advancement in machine learning applications in microbiology. The models are available on GitHub (https://github.com/nbrg-ppcu/prokbert) and HuggingFace (https://huggingface.co/nerualbioinfo) providing an accessible tool for the community.
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Affiliation(s)
- Balázs Ligeti
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
| | - István Szepesi-Nagy
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
| | - Babett Bodnár
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
| | - Noémi Ligeti-Nagy
- Language Technology Research Group, HUN-REN Hungarian Research Centre for Linguistics, Budapest, Hungary
| | - János Juhász
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
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Wang RH, Yang S, Liu Z, Zhang Y, Wang X, Xu Z, Wang J, Li SC. PhageScope: a well-annotated bacteriophage database with automatic analyses and visualizations. Nucleic Acids Res 2024; 52:D756-D761. [PMID: 37904614 PMCID: PMC10767790 DOI: 10.1093/nar/gkad979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 11/01/2023] Open
Abstract
Bacteriophages are viruses that infect bacteria or archaea. Understanding the diverse and intricate genomic architectures of phages is essential to study microbial ecosystems and develop phage therapy strategies. However, the existing phage databases are short of meticulous annotations. To this end, we propose PhageScope (https://phagescope.deepomics.org), an online phage database with comprehensive annotations. PhageScope harbors a collection of 873 718 phage sequences from various sources. Applying fifteen state-of-the-art tools to perform systematic annotations and analyses, PhageScope provides annotations on genome completeness, host range, lifestyle information, taxonomy classification, nine types of structural and functional genetic elements, and three types of comparative genomic studies for curated phages. Additionally, PhageScope incorporates automatic analyses and visualizations for curated and customized phages, serving as an efficient platform for phage study.
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Affiliation(s)
- Ruo Han Wang
- Department of Computer Science, City University of Hong Kong, Hong Kong
| | - Shuo Yang
- Department of Computer Science, City University of Hong Kong, Hong Kong
| | - Zhixuan Liu
- Department of Computer Science, City University of Hong Kong, Hong Kong
| | - Yuanzheng Zhang
- Department of Computer Science, City University of Hong Kong, Hong Kong
| | - Xueying Wang
- Department of Computer Science, City University of Hong Kong, Hong Kong
- City University of Hong Kong (Dongguan), Dongguan, China
| | - Zixin Xu
- Department of Computer Science, City University of Hong Kong, Hong Kong
| | - Jianping Wang
- Department of Computer Science, City University of Hong Kong, Hong Kong
| | - Shuai Cheng Li
- Department of Computer Science, City University of Hong Kong, Hong Kong
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Zheng K, Liang Y, Paez-Espino D, Zou X, Gao C, Shao H, Sung YY, Mok WJ, Wong LL, Zhang YZ, Tian J, Chen F, Jiao N, Suttle CA, He J, McMinn A, Wang M. Identification of hidden N4-like viruses and their interactions with hosts. mSystems 2023; 8:e0019723. [PMID: 37702511 PMCID: PMC10654107 DOI: 10.1128/msystems.00197-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 07/19/2023] [Indexed: 09/14/2023] Open
Abstract
IMPORTANCE The findings of this study are significant, as N4-like viruses represent a unique viral lineage with a distinct replication mechanism and a conserved core genome. This work has resulted in a comprehensive global map of the entire N4-like viral lineage, including information on their distribution in different biomes, evolutionary divergence, genomic diversity, and the potential for viral-mediated host metabolic reprogramming. As such, this work significantly contributes to our understanding of the ecological function and viral-host interactions of bacteriophages.
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Affiliation(s)
- Kaiyang Zheng
- Key Laboratory of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
| | - Yantao Liang
- Key Laboratory of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
| | - David Paez-Espino
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Mammoth Biosciences Inc., South San Francisco, California, USA
| | - Xiao Zou
- Qingdao Central Hospital, Qingdao, China
| | - Chen Gao
- Key Laboratory of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
| | - Hongbing Shao
- Key Laboratory of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
| | - Yeong Yik Sung
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu (UMT), Kuala Terengganu, Malaysia
| | - Wen Jye Mok
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu (UMT), Kuala Terengganu, Malaysia
| | - Li Lian Wong
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu (UMT), Kuala Terengganu, Malaysia
| | - Yu-Zhong Zhang
- Key Laboratory of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Jiwei Tian
- Key Laboratory of Physical Oceanography, Ministry of Education, Ocean University of China, Qingdao, China
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, USA
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Curtis A. Suttle
- Department of Earth, Ocean and Atmospheric Sciences, Institute for the Oceans and Fisheries, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Microbiology and Immunology, Institute for the Oceans and Fisheries, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Botany, Institute for the Oceans and Fisheries, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Jianfeng He
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai, China
| | - Andrew McMinn
- Key Laboratory of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Min Wang
- Key Laboratory of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- The Affiliated Hospital of Qingdao University, Qingdao, China
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Sun S, Zhang X. Genetic characteristics and integration specificity of Salmonella enterica temperate phages. Front Microbiol 2023; 14:1199843. [PMID: 37593543 PMCID: PMC10428622 DOI: 10.3389/fmicb.2023.1199843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 07/12/2023] [Indexed: 08/19/2023] Open
Abstract
Introduction Temperate phages can engage in the horizontal transfer of functional genes to their bacterial hosts. Thus, their genetic material becomes an intimate part of bacterial genomes and plays essential roles in bacterial mutation and evolution. Specifically, temperate phages can naturally transmit genes by integrating their genomes into the bacterial host genomes via integrases. Our previous study showed that Salmonella enterica contains the largest number of temperate phages among all publicly available bacterial species. S. enterica is an important pathogen that can cause serious systemic infections and even fatalities. Methods Initially, we extracted all S. enterica temperate phages from the extensively developed temperate phage database established in our previous study. Subsequently, we conducted an in-depth analysis of the genetic characteristics and integration specificity exhibited by these S. enterica temperate phages. Results Here we identified 8,777 S. enterica temperate phages, all of which have integrases in their genomes. We found 491 non-redundant S. enterica temperate phage integrases (integrase entries). S. enterica temperate phage integrases were classified into three types: intA, intS, and phiRv2. Correlation analysis showed that the sequence lengths of S. enterica integrase and core regions of attB and attP were strongly correlated. Further phylogenetic analysis and taxonomic classification indicated that both the S. enterica temperate phage genomes and the integrase gene sequences were of high diversities. Discussion Our work provides insight into the essential integration specificity and genetic diversity of S. enterica temperate phages. This study paves the way for a better understanding of the interactions between phages and S. enterica. By analyzing a large number of S. enterica temperate phages and their integrases, we provide valuable insights into the genetic diversity and prevalence of these elements. This knowledge has important implications for developing targeted therapeutic interventions, such as phage therapy, to combat S. enterica infections. By harnessing the lytic capabilities of temperate phages, they can be engineered or utilized in phage cocktails to specifically target and eradicate S. enterica strains, offering an alternative or complementary approach to traditional antibiotic treatments. Our study has implications for public health and holds potential significance in combating clinical infections caused by S. enterica.
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Affiliation(s)
- Siqi Sun
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- Department of Life Sciences and Technology, Beijing University of Chemical Technology, Chaoyang, Beijing, China
| | - Xianglilan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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Jarocki P, Komoń-Janczara E, Młodzińska A, Sadurski J, Kołodzińska K, Łaczmański Ł, Panek J, Frąc M. Occurrence and genetic diversity of prophage sequences identified in the genomes of L. casei group bacteria. Sci Rep 2023; 13:8603. [PMID: 37237003 DOI: 10.1038/s41598-023-35823-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 05/24/2023] [Indexed: 05/28/2023] Open
Abstract
It is widely believed that microorganisms belonging to L. casei group can have positive effects on the human body. Therefore, these bacteria are used in many industrial processes, including the production of dietary supplements and probiotic preparations. When using live microorganisms in technological processes, it is important to use those without phage sequences within their genomes that can ultimately lead to lysis of the bacteria. It has been shown that many prophages have a benign nature, meaning that they don't directly lead to lysis or inhibit microbial growth. Moreover, the presence of phage sequences in the genomes of these bacteria increases their genetic diversity, which may contribute to easier colonization of new ecological niches. In the 439 analyzed genomes of the L. casei group, 1509 sequences of prophage origin were detected. The average length of intact prophage sequences analyzed was just under 36 kb. GC content of tested sequences was similar for all analyzed species (44.6 ± 0.9%). Analyzing the protein coding sequences collectively, it was found that there was an average of 44 putative ORFs per genome, while the ORF density of all phage genomes varied from 0.5 to 2.1. The average nucleotide identity calculated on sequence alignments for analyzed sequences was 32.7%. Of the 56 L. casei strains used in the next part of the study, 32 did not show culture growth above the OD600 value of 0.5, even at a mitomycin C concentration of 0.25 μg/ml. Primers used for this study allowed for the detection of prophage sequences for over 90% of tested bacterial strains. Finally, prophages of selected strains were induced using mitomycin C, phage particles were isolated and then genomes of viruses obtained were sequenced and analyzed.
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Affiliation(s)
- Piotr Jarocki
- Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, 8 Skromna St., 20-704, Lublin, Poland.
| | - Elwira Komoń-Janczara
- Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, 8 Skromna St., 20-704, Lublin, Poland
| | | | - Jan Sadurski
- Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, 8 Skromna St., 20-704, Lublin, Poland
| | - Kinga Kołodzińska
- Laboratory of Genomics and Bioinformatics, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Łukasz Łaczmański
- Laboratory of Genomics and Bioinformatics, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Jacek Panek
- Department of Soil and Plant System, Laboratory of Molecular and Environmental Microbiology, Institute of Agrophysics, Polish Academy of Sciences, Lublin, Poland
| | - Magdalena Frąc
- Department of Soil and Plant System, Laboratory of Molecular and Environmental Microbiology, Institute of Agrophysics, Polish Academy of Sciences, Lublin, Poland
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Characterization of the novel temperate Staphylococcus haemolyticus phage IME1365_01. Arch Virol 2023; 168:41. [PMID: 36609576 DOI: 10.1007/s00705-022-05650-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 10/03/2022] [Indexed: 01/09/2023]
Abstract
The presence of a novel functional prophage, IME1365_01, was predicted from bacterial high-throughput sequencing data and then successfully induced from Staphylococcus haemolyticus by mitomycin C treatment. Transmission electron microscopy showed that phage IME1365_01 has an icosahedral head (43 nm in diameter) and a long tail (172 nm long). This phage possesses a double-stranded DNA genome of 44,875 bp with a G+C content of 35.35%. A total of 63 putative open reading frames (ORFs) were identified in its genome. BLASTn analysis revealed that IME1365_01 is similar to Staphylococcus phage vB_SepS_E72, but with a genome homology coverage of only 26%. The phage genome does not have fixed termini. In ORF24 of phage IME1365_01, a conserved Toll-interleukin-1 receptor domain of the TIR_2 superfamily (accession no. c123749) is located at its N-terminus, and this might serve as a component of an anti-bacterial system. In conclusion, we developed a platform to obtain active temperate phage from prediction, identification, and induction from its bacterial host. After mass screening using this platform, numerous temperate phages and their innate anti-bacterial elements can provide extensive opportunities for therapy against bacterial (especially drug-resistant bacterial) infections.
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