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Arehart CH, Sterrett JD, Garris RL, Quispe-Pilco RE, Gignoux CR, Evans LM, Stanislawski MA. Poly-omic risk scores predict inflammatory bowel disease diagnosis. mSystems 2024; 9:e0067723. [PMID: 38095449 PMCID: PMC10805030 DOI: 10.1128/msystems.00677-23] [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: 07/26/2023] [Accepted: 11/02/2023] [Indexed: 01/11/2024] Open
Abstract
Inflammatory bowel disease (IBD) is characterized by complex etiology and a disrupted colonic ecosystem. We provide a framework for the analysis of multi-omic data, which we apply to study the gut ecosystem in IBD. Specifically, we train and validate models using data on the metagenome, metatranscriptome, virome, and metabolome from the Human Microbiome Project 2 IBD multi-omic database, with 1,785 repeated samples from 130 individuals (103 cases and 27 controls). After splitting the participants into training and testing groups, we used mixed-effects least absolute shrinkage and selection operator regression to select features for each omic. These features, with demographic covariates, were used to generate separate single-omic prediction scores. All four single-omic scores were then combined into a final regression to assess the relative importance of the individual omics and the predictive benefits when considered together. We identified several species, pathways, and metabolites known to be associated with IBD risk, and we explored the connections between data sets. Individually, metabolomic and viromic scores were more predictive than metagenomics or metatranscriptomics, and when all four scores were combined, we predicted disease diagnosis with a Nagelkerke's R2 of 0.46 and an area under the curve of 0.80 (95% confidence interval: 0.63, 0.98). Our work supports that some single-omic models for complex traits are more predictive than others, that incorporating multiple omic data sets may improve prediction, and that each omic data type provides a combination of unique and redundant information. This modeling framework can be extended to other complex traits and multi-omic data sets.IMPORTANCEComplex traits are characterized by many biological and environmental factors, such that multi-omic data sets are well-positioned to help us understand their underlying etiologies. We applied a prediction framework across multiple omics (metagenomics, metatranscriptomics, metabolomics, and viromics) from the gut ecosystem to predict inflammatory bowel disease (IBD) diagnosis. The predicted scores from our models highlighted key features and allowed us to compare the relative utility of each omic data set in single-omic versus multi-omic models. Our results emphasized the importance of metabolomics and viromics over metagenomics and metatranscriptomics for predicting IBD status. The greater predictive capability of metabolomics and viromics is likely because these omics serve as markers of lifestyle factors such as diet. This study provides a modeling framework for multi-omic data, and our results show the utility of combining multiple omic data types to disentangle complex disease etiologies and biological signatures.
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Affiliation(s)
- Christopher H. Arehart
- Interdisciplinary Quantitative Biology PhD Program, University of Colorado, Boulder, Colorado, USA
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
- Institute for Behavioral Genetics, University of Colorado, Boulder, Colorado, USA
| | - John D. Sterrett
- Interdisciplinary Quantitative Biology PhD Program, University of Colorado, Boulder, Colorado, USA
- Department of Integrative Physiology, University of Colorado, Boulder, Colorado, USA
| | - Rosanna L. Garris
- Interdisciplinary Quantitative Biology PhD Program, University of Colorado, Boulder, Colorado, USA
- Department of Biochemistry, University of Colorado, Boulder, Colorado, USA
| | - Ruth E. Quispe-Pilco
- Interdisciplinary Quantitative Biology PhD Program, University of Colorado, Boulder, Colorado, USA
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Christopher R. Gignoux
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Luke M. Evans
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
- Institute for Behavioral Genetics, University of Colorado, Boulder, Colorado, USA
| | - Maggie A. Stanislawski
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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2
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Pathogenicity of fish pathogen Pseudomonas plecoglossicida and preparation of its inactivated vaccine. Microb Pathog 2022; 166:105488. [PMID: 35367573 DOI: 10.1016/j.micpath.2022.105488] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 03/13/2022] [Accepted: 03/14/2022] [Indexed: 01/20/2023]
Abstract
Many fishes infected with Pseudomonas plecoglossicida generally suffer from "visceral white spot disease" or even die. In this study, a dominant pathogen strain was isolated from the intestinal tract of diseased crucian carp in the Wangcheng Lake area, Changsha, and it was identified as P. plecoglossicida. The selected strain was a new strain named as P. plecoglossicida LQJ06.Strain LQJ06 basically colonized the intestine and poisoned zebrafish as show by fluorescent labelling.Pathological structural analysis of tissue sections indicated that the intestinal tract was seriously damaged, epithelial cells in the intestinal tissue were necrotic, intestinal villi were sloughed, liver cells were vacuolated, nuclei were pyknotic and shifted, and lymphocytes were proliferated in the spleen. P. plecoglossicida LQJ06 strain could invade and proliferate in the grass carp liver cell line L8824, which led to a stress response, including apoptosis.Cell morphology was changed owing to the toxicity of the culture supernatant of the LQJ06 strain, which mainly manifested as aggregation between cells, pyknosisd and slow growth or even death.An inactivated vaccine derived from P. plecoglossicida LQJ06 prepared in this study was safe and nontoxic to grass carp liver cells. Compared with those after oral administration, most of the cellular immune factors were expressed earlier and at a higher level after injection immunization. The intestinal tract and liver from zebrafish mainly expressed the IFN-γ2 and IL-1β genes, respectively, after immunization. The upregulation of these immune-related genes proved that the vaccine could strengthen the immunity of zebrafish, induce inflammation and promote resistance to pathogenic infection. The results of these preliminary tests provide a scientific basis for further research on the prevention and control of P. plecoglossicida, and an essential preliminary basis for the development of an inactivated vaccine against P. plecoglossicida.
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3
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Holtappels D, Fortuna KJ, Moons L, Broeckaert N, Bäcker LE, Venneman S, Rombouts S, Lippens L, Baeyen S, Pollet S, Noben JP, Oechslin F, Vallino M, Aertsen A, Maes M, Van Vaerenbergh J, Lavigne R, Wagemans J. The potential of bacteriophages to control Xanthomonas campestris pv. campestris at different stages of disease development. Microb Biotechnol 2022; 15:1762-1782. [PMID: 35084112 PMCID: PMC9151335 DOI: 10.1111/1751-7915.14004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 12/23/2022] Open
Abstract
Xanthomonas campestris pv. campestris (Xcc) is a vascular pathogen that invades the xylem of Brassica crops. Current chemical and antibiotics‐based control measures for this bacterium are unsustainable and inefficient. After establishing a representative collection of Xcc strains, we isolated and characterized bacteriophages from two clades of phages to assess their potential in phage‐based biocontrol. The most promising phages, FoX2 and FoX6, specifically recognize (lipo) polysaccharides, associated with the wxc gene cluster, on the surface of the bacterial cell wall. Next, we determined and optimized the applicability of FoX2 and FoX6 in an array of complementary bioassays, ranging from seed decontamination to irrigation‐ and spray‐based applications. Here, an irrigation‐based application showed promising results. In a final proof‐of‐concept, a CaCl2‐formulated phage cocktail was shown to control the outbreak of Xcc in the open field. This comprehensive approach illustrates the potential of phage biocontrol of black rot disease in Brassica and serves as a reference for the broader implementation of phage biocontrol in integrated pest management strategies.
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Affiliation(s)
| | | | - Lauren Moons
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | | | - Léon E Bäcker
- Laboratory of Food Microbiology, KU Leuven, Leuven, Belgium
| | - Sofie Venneman
- Proefstation voor de groenteteelt, Sint-Katelijne-Waver, Belgium
| | - Sofie Rombouts
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium.,Flanders Research Institute for Agriculture, Fisheries and Food, Ghent, Belgium
| | - Louis Lippens
- Provinciaal Proefcentrum voor de Groenteteelt Oost-Vlaanderen, Kruishoutem, Belgium
| | - Steve Baeyen
- Flanders Research Institute for Agriculture, Fisheries and Food, Ghent, Belgium
| | | | - Jean-Paul Noben
- Biomedical Research Institute and Transnational University Limburg, Hasselt University, Hasselt, Belgium
| | - Frank Oechslin
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Marta Vallino
- Institute for Sustainable Plant Protection, National Research Counsil of Italy, Turin, Italy
| | - Abram Aertsen
- Laboratory of Food Microbiology, KU Leuven, Leuven, Belgium
| | | | | | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
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4
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Ramos-Vivas J, Superio J, Galindo-Villegas J, Acosta F. Phage Therapy as a Focused Management Strategy in Aquaculture. Int J Mol Sci 2021; 22:10436. [PMID: 34638776 PMCID: PMC8508683 DOI: 10.3390/ijms221910436] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 12/12/2022] Open
Abstract
Therapeutic bacteriophages, commonly called as phages, are a promising potential alternative to antibiotics in the management of bacterial infections of a wide range of organisms including cultured fish. Their natural immunogenicity often induces the modulation of a variated collection of immune responses within several types of immunocytes while promoting specific mechanisms of bacterial clearance. However, to achieve standardized treatments at the practical level and avoid possible side effects in cultivated fish, several improvements in the understanding of their biology and the associated genomes are required. Interestingly, a particular feature with therapeutic potential among all phages is the production of lytic enzymes. The use of such enzymes against human and livestock pathogens has already provided in vitro and in vivo promissory results. So far, the best-understood phages utilized to fight against either Gram-negative or Gram-positive bacterial species in fish culture are mainly restricted to the Myoviridae and Podoviridae, and the Siphoviridae, respectively. However, the current functional use of phages against bacterial pathogens of cultured fish is still in its infancy. Based on the available data, in this review, we summarize the current knowledge about phage, identify gaps, and provide insights into the possible bacterial control strategies they might represent for managing aquaculture-related bacterial diseases.
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Affiliation(s)
- José Ramos-Vivas
- Grupo de Investigación en Acuicultura, Universidad de Las Palmas de Gran Canaria, 35214 Las Palmas de Gran Canaria, Spain; (J.R.-V.); (F.A.)
- Research Group on Foods, Nutritional Biochemistry and Health, Universidad Europea del Atlántico, 39011 Santander, Spain
- Department of Project Management, Universidad Internacional Iberoamericana, Campeche 24560, Mexico
| | - Joshua Superio
- Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway;
| | | | - Félix Acosta
- Grupo de Investigación en Acuicultura, Universidad de Las Palmas de Gran Canaria, 35214 Las Palmas de Gran Canaria, Spain; (J.R.-V.); (F.A.)
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5
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Vázquez R, Blanco-Gañán S, Ruiz S, García P. Mining of Gram-Negative Surface-Active Enzybiotic Candidates by Sequence-Based Calculation of Physicochemical Properties. Front Microbiol 2021; 12:660403. [PMID: 34113327 PMCID: PMC8185167 DOI: 10.3389/fmicb.2021.660403] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/07/2021] [Indexed: 01/21/2023] Open
Abstract
Phage (endo)lysins are nowadays one of the most promising ways out of the current antibiotic resistance crisis. Either as sole therapeutics or as a complement to common antibiotic chemotherapy, lysins are already entering late clinical phases to get regulatory agencies’ authorization. Even the old paradigm of the inability of lysins to attack Gram-negative bacteria from without has already been overcome in a variety of ways: either by engineering approaches or investigating the natural mechanisms by which some wild-type lysins are able to interact with the bacterial surface. Such inherent ability of some lysins has been linked to antimicrobial peptide (AMP)-like regions, which are, on their own, a significant source for novel antimicrobials. Currently, though, many of the efforts for searching novel lysin-based antimicrobial candidates rely on experimental screenings. In this work, we have bioinformatically analyzed the C-terminal end of a collection of lysins from phages infecting the Gram-negative genus Pseudomonas. Through the computation of physicochemical properties, the probability of such regions to be an AMP was estimated by means of a predictive k-nearest neighbors (kNN) model. This way, a subset of putatively membrane-interacting lysins was obtained from the original database. Two of such candidates (named Pae87 and Ppl65) were prospectively tested in terms of muralytic, bacteriolytic, and bactericidal activity. Both of them were found to possess an activity against Pseudomonas aeruginosa and other Gram-negative bacterial pathogens, implying that the prediction of AMP-like regions could be a useful approach toward the mining of phage lysins to design and develop antimicrobials or antimicrobial parts for further engineering.
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Affiliation(s)
- Roberto Vázquez
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Sofía Blanco-Gañán
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), Madrid, Spain
| | - Susana Ruiz
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Pedro García
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
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6
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Forcone K, Coutinho FH, Cavalcanti GS, Silveira CB. Prophage Genomics and Ecology in the Family Rhodobacteraceae. Microorganisms 2021; 9:microorganisms9061115. [PMID: 34064105 PMCID: PMC8224337 DOI: 10.3390/microorganisms9061115] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/12/2021] [Accepted: 05/17/2021] [Indexed: 12/20/2022] Open
Abstract
Roseobacters are globally abundant bacteria with critical roles in carbon and sulfur biogeochemical cycling. Here, we identified 173 new putative prophages in 79 genomes of Rhodobacteraceae. These prophages represented 1.3 ± 0.15% of the bacterial genomes and had no to low homology with reference and metagenome-assembled viral genomes from aquatic and terrestrial ecosystems. Among the newly identified putative prophages, 35% encoded auxiliary metabolic genes (AMGs), mostly involved in secondary metabolism, amino acid metabolism, and cofactor and vitamin production. The analysis of integration sites and gene homology showed that 22 of the putative prophages were actually gene transfer agents (GTAs) similar to a GTA of Rhodobacter capsulatus. Twenty-three percent of the predicted prophages were observed in the TARA Oceans viromes generated from free viral particles, suggesting that they represent active prophages capable of induction. The distribution of these prophages was significantly associated with latitude and temperature. The prophages most abundant at high latitudes encoded acpP, an auxiliary metabolic gene involved in lipid synthesis and membrane fluidity at low temperatures. Our results show that prophages and gene transfer agents are significant sources of genomic diversity in roseobacter, with potential roles in the ecology of this globally distributed bacterial group.
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Affiliation(s)
- Kathryn Forcone
- Department of Biology, University of Miami, 1301 Memorial Dr., Coral Gables, Miami, FL 33146, USA; (K.F.); (G.S.C.)
| | - Felipe H. Coutinho
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández de Elche, Aptdo. 18, Ctra. Alicante-Valencia, s/n, 03550 San Juan de Alicante, Spain;
| | - Giselle S. Cavalcanti
- Department of Biology, University of Miami, 1301 Memorial Dr., Coral Gables, Miami, FL 33146, USA; (K.F.); (G.S.C.)
| | - Cynthia B. Silveira
- Department of Biology, University of Miami, 1301 Memorial Dr., Coral Gables, Miami, FL 33146, USA; (K.F.); (G.S.C.)
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149, USA
- Correspondence:
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7
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Wang JB, Yu MS, Tseng TT, Lin LC. Molecular Characterization of Ahp2, a Lytic Bacteriophage of Aeromonas hydrophila. Viruses 2021; 13:v13030477. [PMID: 33799428 PMCID: PMC8001559 DOI: 10.3390/v13030477] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/07/2021] [Accepted: 03/11/2021] [Indexed: 12/11/2022] Open
Abstract
Aeromonas hydrophila is an opportunistic pathogen that infects fish, amphibians, mammals, and humans. This study isolated a myophage, vB_AhyM_Ahp2 (Ahp2), that lytically infects A. hydrophila. We observed that 96% of the Ahp2 particles adsorbed to A. hydrophila within 18 min. Ahp2 also showed a latent period of 15 min with a burst size of 142 PFU/cell. This phage has a linear double-stranded DNA genome of 47,331 bp with a GC content of 57%. At least 20 Ahp2 proteins were detected by SDS-polyacrylamide gel electrophoresis; among them, a 40-kDa protein was predicted as the major capsid protein. Sequence analysis showed that Ahp2 has a genome organization closely related to a group of Aeromonas phages (13AhydR10RR, 14AhydR10RR, 85AhydR10RR, phage 3, 32 Asp37, 59.1), which infect Aeromonas hydrophila and Aeromonas salmonicida. The tail module encompassing ORF27-29 in the Ahp2 genome was present in all Aeromonas phages analyzed in this study and likely determines the host range of the virus. This study found that Ahp2 completely lyses A. hydrophila AH300206 in 3.5 h at a MOI of 0.0001 and does not lysogenize its host. Altogether, these findings show that Ahp2 is a lytic Aeromonas phage and could be a candidate for therapeutic phage cocktails.
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Affiliation(s)
- Jian-Bin Wang
- Laboratory of Microbial Genetics, Institute of Medical Sciences, Tzu Chi University, No. 701, Sec. 3, Zhongyang Rd., Hualien 97004, Taiwan;
| | - Mei-Shiuan Yu
- Department of Microbiology, School of Medicine, Tzu Chi University, No. 701, Sec. 3, Zhongyang Rd., Hualien 97004, Taiwan;
- Master Program in Microbiology and Immunology, School of Medicine, Tzu Chi University, No. 701, Sec. 3, Zhongyang Rd., Hualien 97004, Taiwan
| | - Tsai-Tien Tseng
- Department of Molecular and Cellular Biology, Kennesaw State University, 1000 Chastain Road, Kennesaw, GA 30144, USA;
| | - Ling-Chun Lin
- Department of Microbiology, School of Medicine, Tzu Chi University, No. 701, Sec. 3, Zhongyang Rd., Hualien 97004, Taiwan;
- Master Program in Microbiology and Immunology, School of Medicine, Tzu Chi University, No. 701, Sec. 3, Zhongyang Rd., Hualien 97004, Taiwan
- Correspondence: e-mail: ; Tel.: +886-3-8565301
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8
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Sun Y, Zhu Z, Weng S, He J, Dong C. Characterization of a highly lethal barramundi (Lates calcarifer) model of Pseudomonas plecoglossicida infection. Microb Pathog 2020; 149:104516. [PMID: 32971158 DOI: 10.1016/j.micpath.2020.104516] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 08/17/2020] [Accepted: 08/18/2020] [Indexed: 11/15/2022]
Abstract
Pseudomonas plecoglossicida is a highly lethal causative agent associated with severe economic losses in aquaculture industry. P. plecoglossicida has been documented as a highly alarming pathogen in a wide variety of freshwater cultured fish including ayu (Plecoglossus altivelis), rainbow trout (Oncorhynchus mykiss) and pejerrey (Odontesthes bonariensis), and marine cultured fish such as large yellow croaker (Larimichthys crocea) and orange-spotted grouper (Epinephelus coioides) etc. Fish infected with P. plecoglossicida usually exhibited various symptoms, including lethargy, inappetence, disorientation, abdominal swelling with severe ascites and numerous white spots covered on the surface of spleen tissue. In present study, barramundi, zebrafish, spotted seabass and mandarinfish were investigated as potential hosts of P. plecoglossicida. Among them, barramundi was confirmed the most sensitive host fish species for P. plecoglossicida infection. Dynamic histopathology revealed that P. plecoglossicida caused various histopathological effects to barramundi: a) spleen: granulomas appeared at 2 days post infection (dpi) and matured at 4 dpi; b) liver: steatosis at 1 dpi and fat necrosis over time, and damaged the most compared to spleens and metanephros; c) metanephros: Bowman capsule space became larger and glomerulus shrank were even collapsed at 1 dpi; d) ascites: either bacterium or melanin were wrapped in cells from ascites. All these results indicated that P. plecoglossicida could cause systemic diseases with typical clinical sighs to barramundi and would be an alarming pathogen to barramundi industry.
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Affiliation(s)
- Yujia Sun
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, PR China; Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, Guangdong, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Zhiming Zhu
- Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, Guangdong, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, 510275, PR China; School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, Guangdong, PR China
| | - Shaoping Weng
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, PR China; Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, Guangdong, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Jianguo He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, PR China; Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, Guangdong, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, 510275, PR China; School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, Guangdong, PR China
| | - Chuanfu Dong
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, PR China; Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, Guangdong, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, 510275, PR China.
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9
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Kawato Y, Istiqomah I, Gaafar AY, Hanaoka M, Ishimaru K, Yasuike M, Nishiki I, Nakamura Y, Fujiwara A, Nakai T. A novel jumbo Tenacibaculum maritimum lytic phage with head-fiber-like appendages. Arch Virol 2019; 165:303-311. [PMID: 31786689 DOI: 10.1007/s00705-019-04485-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 10/26/2019] [Indexed: 01/21/2023]
Abstract
A novel jumbo bacteriophage (myovirus) is described. The lytic phage of Tenacibaculum maritimum, which is the etiological agent of tenacibaculosis in a variety of farmed marine fish worldwide, was plaque-isolated from seawater around a fish aquaculture field in Japan. The phage had an isometric head 110-120 nm in diameter, from which several 50- to 100-nm-long flexible fiber-like appendages emanate, and a 150-nm-long rigid contractile tail. The full genomes of the two representative phages (PTm1 and PTm5) were 224,680 and 226,876 bp long, respectively, both with 29.7% GC content, and the number of predicted open reading frames (ORFs) was 308 and 306, respectively. The average nucleotide sequence identity between PTm1 and PTm5 was 99.95%, indicating they are quite similar to each other. A genetic relationship was found in 15.0-16.6% of the predicted ORFs among the T. maritimum phages PTm1 and PTm5, the Tenacibaculum spp. phage pT24, and the Sphingomonas paucimobilis phage PAU. Phylogenetic analysis based on the terminase large subunit genes revealed that these four phages (PTm1, PTm5, pT24 and PAU) are more closely related than the other 10 jumbo myoviruses that have similar genome sizes. Transmission electron microscopy observations suggest that the head fibers of the T. maritimum phage function as tentacles to search and recognize the host cell surface to facilitate infection.
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Affiliation(s)
- Yasuhiko Kawato
- Nansei Main Station, National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Watarai, Mie, Japan
| | - Indah Istiqomah
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Japan.,Department of Fisheries, Faculty of Agriculture, Gadjah Mada University, Yogyakarta, Indonesia
| | - Alkhateib Y Gaafar
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Japan.,Veterinary Research Division, National Research Centre, Cairo, Egypt
| | - Makoto Hanaoka
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Japan
| | - Katsuya Ishimaru
- Aquaculture Research Institute, Kindai University, Wakayama, Japan
| | - Motoshige Yasuike
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Japan
| | - Issei Nishiki
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Japan
| | - Yoji Nakamura
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Japan
| | - Atushi Fujiwara
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Japan
| | - Toshihiro Nakai
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Japan.
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10
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Chen J, Zhu Y, Yin M, Xu Y, Liang X, Huang Y. Characterization of maltocin S16, a phage tail‐like bacteriocin with antibacterial activity againstStenotrophomonas maltophiliaandEscherichia coli. J Appl Microbiol 2019; 127:78-87. [DOI: 10.1111/jam.14294] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 12/19/2018] [Accepted: 04/23/2019] [Indexed: 01/05/2023]
Affiliation(s)
- J. Chen
- Department of Microbiology College of Life Sciences Wuhan University Wuhan China
| | - Y. Zhu
- Department of Microbiology College of Life Sciences Wuhan University Wuhan China
| | - M. Yin
- Department of Microbiology College of Life Sciences Wuhan University Wuhan China
| | - Y. Xu
- Department of Microbiology College of Life Sciences Wuhan University Wuhan China
| | - X. Liang
- Department of Microbiology College of Life Sciences Wuhan University Wuhan China
| | - Y.‐P. Huang
- Department of Microbiology College of Life Sciences Wuhan University Wuhan China
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11
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Chen Y, Yang L, Sun E, Song J, Wu B. Characterisation of a newly detected bacteriophage infecting Bordetella bronchiseptica in swine. Arch Virol 2018; 164:33-40. [PMID: 30229303 PMCID: PMC7087125 DOI: 10.1007/s00705-018-4034-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 08/16/2018] [Indexed: 12/20/2022]
Abstract
A novel virulent bacteriophage, vB_BbrM_PHB04, infecting Bordetella bronchiseptica was isolated from wastewater collected at a swine farm in China. Phage vB_BbrM_PHB04 exhibited growth over a wide range of temperature and pH conditions and showed different efficiency of plating values and lytic spectra within the same strains at 25 °C and 37 °C. High-throughput sequencing revealed that vB_BbrM_PHB04 has a linear double-stranded DNA genome with 124 putative open reading frames. Overall, the genome of vB_BbrM_PHB04 showed very low similarity (the highest nucleotide identity 82%, 1% coverage) to other phage sequences in the GenBank database. Phylogenetic analysis indicated that vB_BbrM_PHB04 is a new member of the family Myoviridae. In addition, polymerase chain reaction-based detection of phage genes in phage-resistant B. bronchiseptica variants revealed no evidence of lysogenic activity of phage vB_BbrM_PHB04.
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Affiliation(s)
- Yibao Chen
- State Key laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Lan Yang
- State Key laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Erchao Sun
- State Key laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Jiaoyang Song
- State Key laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Bin Wu
- State Key laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, China. .,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
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12
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Guo Z, Huang J, Yan G, Lei L, Wang S, Yu L, Zhou L, Gao A, Feng X, Han W, Gu J, Yang J. Identification and Characterization of Dpo42, a Novel Depolymerase Derived from the Escherichia coli Phage vB_EcoM_ECOO78. Front Microbiol 2017; 8:1460. [PMID: 28824588 PMCID: PMC5539073 DOI: 10.3389/fmicb.2017.01460] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 07/20/2017] [Indexed: 11/13/2022] Open
Abstract
Biofilm formation, one of the most important virulence factors of pathogenic bacteria, protects bacteria against desiccation, antibiotics, phages and host immune responses. However, phage-derived depolymerases show antibiofilm activity and demonstrate great potential to treat infections caused by biofilm-forming bacteria. In this study, the Escherichia coli phage vB_EcoM_ECOO78 was isolated and characterised, and we observed its ability to lyse five out of 34 tested E. coli clinical isolates. The highest phage titre was observed at a multiplicity of infection of 10-5 and a burst size of approximately 74 plaque forming units (PFU)/infection. Electron micrographs indicated that vB_EcoM_ECOO78 belongs to the family Myoviridae. The presence of increasing halos surrounding the lysis plaques formed by vB_EcoM_ECOO78 indicated that this phage may encode a depolymerase. Based on a sequencing analysis, the complete genome of vB_EcoM_ECOO78 was found to be 41,289 bp in size, with a GC content of 53.07%. Additionally, vB_EcoM_ECOO78 has 56 predicted open reading frames, 51 (91.07%) of which are assumed to be functional. A BLAST analysis indicated that ORF42 of vB_EcoM_ECOO78 (Dpo42) has low identity with other reported phage-associated depolymerases. Dpo42 was expressed and purified as a soluble protein using E. coli BL21. The biofilm formation ability of E. coli isolates and the antibiofilm activity of Dpo42 were tested by performing spot assays and using a 96-well micro-titre plate method. Dpo42 degraded the capsular polysaccharides surrounding E. coli and exhibited dose-dependent biofilm-formation prevention activity. Based on these results, Dpo42 appears to be a novel phage-derived depolymerase that represents a new potential strategy for preventing E. coli biofilm formation.
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Affiliation(s)
- Zhimin Guo
- Department of Respiratory Medicine, The Second Hospital of Jilin UniversityChangchun, China.,Department of Clinical Laboratory, The First Hospital of Jilin UniversityChangchun, China
| | - Jing Huang
- Department of Clinical Laboratory, The First Hospital of Jilin UniversityChangchun, China
| | - Guangmou Yan
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin UniversityChangchun, China
| | - Liancheng Lei
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin UniversityChangchun, China
| | - Shuang Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin UniversityChangchun, China
| | - Ling Yu
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin UniversityChangchun, China
| | - Liang Zhou
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin UniversityChangchun, China
| | - Anchong Gao
- Agricultural Experiment Base, Jilin UniversityChangchun, China
| | - Xin Feng
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin UniversityChangchun, China
| | - Wenyu Han
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin UniversityChangchun, China
| | - Jingmin Gu
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin UniversityChangchun, China
| | - Junling Yang
- Department of Respiratory Medicine, The Second Hospital of Jilin UniversityChangchun, China
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13
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Lal TM, Sano M, Ransangan J. Genome characterization of a novel vibriophage VpKK5 (Siphoviridae) specific to fish pathogenic strain of Vibrio parahaemolyticus. J Basic Microbiol 2016; 56:872-88. [PMID: 26960780 DOI: 10.1002/jobm.201500611] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 02/19/2016] [Indexed: 12/25/2022]
Abstract
Vibrio parahaemolyticus has long been known pathogenic to shrimp but only recently it is also reported pathogenic to tropical cultured marine finfish. Traditionally, bacterial diseases in aquaculture are often treated using synthetic antibiotics but concern due to side effects of these chemicals is elevating hence, new control strategies which are both environmental and consumer friendly, are urgently needed. One promising control strategy is the bacteriophage therapy. In this study, we report the isolation and characterization of a novel vibriophage (VpKK5), belonging to the family Siphoviridae that was specific and capable of complete lysing the fish pathogenic strain of V. parahaemolyticus. The VpKK5 exhibited short eclipse and latent periods of 24 and 36 min, respectively, but with a large burst size of 180 pfu/cell. The genome analysis revealed that the VpKK5 is a novel bacteriophage with the estimated genome size of 56,637 bp and has 53.1% G + C content. The vibriophage has about 80 predicted open reading frames consisted of 37 complete coding sequences which did not match to any protein databases. The analysis also found no lysogeny and virulence genes in the genome of VpKK5. With such genome features, we suspected the vibriophage is novel and could be explored for phage therapy against fish pathogenic strains of V. parahaemolyticus in the near future.
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Affiliation(s)
- Tamrin M Lal
- Microbiology and Fish Disease Laboratory, Borneo Marine Research Institute, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu, Sabah, Malaysia
| | - Motohiko Sano
- Laboratory of Fish Pathology, Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Minato-ku, Tokyo, Japan
| | - Julian Ransangan
- Microbiology and Fish Disease Laboratory, Borneo Marine Research Institute, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu, Sabah, Malaysia
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14
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Ghequire MGK, Dillen Y, Lambrichts I, Proost P, Wattiez R, De Mot R. Different Ancestries of R Tailocins in Rhizospheric Pseudomonas Isolates. Genome Biol Evol 2015; 7:2810-28. [PMID: 26412856 PMCID: PMC4684702 DOI: 10.1093/gbe/evv184] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Bacterial genomes accommodate a variety of mobile genetic elements, including bacteriophage-related clusters that encode phage tail-like protein complexes playing a role in interactions with eukaryotic or prokaryotic cells. Such tailocins are unable to replicate inside target cells due to the lack of a phage head with associated DNA. A subset of tailocins mediate antagonistic activities with bacteriocin-like specificity. Functional characterization of bactericidal tailocins of two Pseudomonas putida rhizosphere isolates revealed not only extensive similarity with the tail assembly module of the Pseudomonas aeruginosa R-type pyocins but also differences in genomic integration site, regulatory genes, and lytic release modules. Conversely, these three features are quite similar between strains of the P. putida and Pseudomonas fluorescens clades, although phylogenetic analysis of tail genes suggests them to have evolved separately. Unlike P. aeruginosa R pyocin elements, the tailocin gene clusters of other pseudomonads frequently carry cargo genes, including bacteriocins. Compared with P. aeruginosa, the tailocin tail fiber sequences that act as specificity determinants have diverged much more extensively among the other pseudomonad species, mostly isolates from soil and plant environments. Activity of the P. putida antibacterial particles requires a functional lipopolysaccharide layer on target cells, but contrary to R pyocins from P. aeruginosa, strain susceptibilities surpass species boundaries.
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Affiliation(s)
- Maarten G K Ghequire
- Centre of Microbial and Plant Genetics (CMPG), University of Leuven, Heverlee, Belgium
| | - Yörg Dillen
- Group of Morphology, Biomedical Research Institute (BIOMED), Hasselt University, Diepenbeek, Leuven, Belgium
| | - Ivo Lambrichts
- Group of Morphology, Biomedical Research Institute (BIOMED), Hasselt University, Diepenbeek, Leuven, Belgium
| | - Paul Proost
- Laboratory of Molecular Immunology, Department of Microbiology and Immunology, Rega Institute, University of Leuven, Belgium
| | - Ruddy Wattiez
- Proteomics and Microbiology Laboratory, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - René De Mot
- Centre of Microbial and Plant Genetics (CMPG), University of Leuven, Heverlee, Belgium
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15
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Full-genome sequence of a novel myovirus, GF-2, infecting Edwardsiella tarda: comparison with other Edwardsiella myoviral genomes. Arch Virol 2015; 160:2129-33. [PMID: 26049743 DOI: 10.1007/s00705-015-2472-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 05/27/2015] [Indexed: 01/23/2023]
Abstract
Edwardsiellosis, which is caused by Edwardsiella tarda, a Gram-negative bacterium, is one of the most serious infectious diseases in both marine and freshwater fish farms worldwide. Previously, we reported the complete genome sequences of three E. tarda-lytic bacteriophages (two podoviruses and a myovirus), which were isolated from fish tissues and fish-rearing seawater. Further genomic information regarding E. tarda phages is important for understanding phage-host interactions as well as for applications of the phages for the control of disease. Here, we report the complete genome sequence of a novel E. tarda phage (GF-2) of myovirus morphology (family Myoviridae), isolated from tissue homogenates of a cultured Japanese flounder (Paralichthys olivaceus) that succumbed to edwardsiellosis in Japan. The size of the entire genome was 43,129 bp, with a GC content of 51.3 % and containing 82 open reading frames (ORFs). The GF-2 genome possesses lysogeny-related genes that have not been found in the reported Edwardsiella phage genomes. Comparative genomics of Edwardsiella myophages suggest that the C-terminal domains of the tail fiber proteins have relevance to their host specificity. Thus, GF-2 genome information provides a novel resource for our understanding of the molecular mechanisms involved in their host specificity and for detection of E. tarda in aquaculture environments.
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