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Yang Y, Xu S, He H, Zhu X, Liu Y, Hu M, Jiang B, Li Y, Ai X, Fu G, Zhang H. Yersinia ruckeri Infection and Enteric Redmouth Disease among Endangered Chinese Sturgeons, China, 2022. Emerg Infect Dis 2024; 30:1125-1132. [PMID: 38781928 PMCID: PMC11138986 DOI: 10.3201/eid3006.231354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024] Open
Abstract
During October 2022, enteric redmouth disease (ERM) affected Chinese sturgeons at a farm in Hubei, China, causing mass mortality. Affected fish exhibited characteristic red mouth and intestinal inflammation. Investigation led to isolation of a prominent bacterial strain, zhx1, from the internal organs and intestines of affected fish. Artificial infection experiments confirmed the role of zhx1 as the pathogen responsible for the deaths. The primary pathologic manifestations consisted of degeneration, necrosis, and inflammatory reactions, resulting in multiple organ dysfunction and death. Whole-genome sequencing of the bacteria identified zhx1 as Yersinia ruckeri, which possesses 135 drug-resistance genes and 443 virulence factor-related genes. Drug-susceptibility testing of zhx1 demonstrated high sensitivity to chloramphenicol and florfenicol but varying degrees of resistance to 18 other antimicrobial drugs. Identifying the pathogenic bacteria associated with ERM in Chinese sturgeons establishes a theoretical foundation for the effective prevention and control of this disease.
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Chen S, Loch TP, Walker ED. Draft genome sequence of the emerging fish pathogen Flavobacterium tructae strain S12. Microbiol Resour Announc 2023; 12:e0048823. [PMID: 37921484 PMCID: PMC10720513 DOI: 10.1128/mra.00488-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 10/14/2023] [Indexed: 11/04/2023] Open
Abstract
The draft genome of Flavobacterium tructae strain S12, isolated from hatchery-reared Chinook salmon (Oncorhynchus tshawytscha) fingerlings, consisted of 5,695,942 bp, a G + C content of 35.6%, 4,775 predicted open reading frames, a putative type IX secretion system, collagenase, and hemolysin. F. tructae strains can be used as models for emerging Flavobacterium pathogens.
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Affiliation(s)
- Shicheng Chen
- Medical Laboratory Sciences Program, College of Health and Human Sciences, Northern Illinois University, DeKalb, Illinois, USA
| | - Thomas P. Loch
- Department of Fisheries and Wildlife, College of Agriculture and Natural Resources, Michigan State University, East Lansing, Michigan, USA
| | - Edward D. Walker
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
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3
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Ye C, Liu D, Huang K, Li D, Ma X, Jin Y, Xiong H. Isolation of starch and protein degrading strain Bacillus subtilis FYZ1-3 from tobacco waste and genomic analysis of its tolerance to nicotine and inhibition of fungal growth. Front Microbiol 2023; 14:1260149. [PMID: 38033584 PMCID: PMC10687635 DOI: 10.3389/fmicb.2023.1260149] [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: 07/17/2023] [Accepted: 10/24/2023] [Indexed: 12/02/2023] Open
Abstract
Aerobic fermentation is an effective technique for the large-scale processing of tobacco waste. However, the specificity of the structure and composition of tobacco-derived organic matter and the toxic alkaloids in the material make it currently difficult to directly use microbial agents. In this study, a functional strain FYZ1-3 was isolated and screened from thermophilic phase samples of tobacco waste composting. This strain could withstand temperatures as high as 80°C and grow normally at 0.6% nicotine content. Furthermore, it had a strong decomposition capacity of tobacco-derived starch and protein, with amylase activity of 122.3 U/mL and protease activity and 52.3 U/mL, respectively. To further understand the mechanism of the metabolic transformation of the target, whole genome sequencing was used and the secondary metabolite gene cluster was predicted. The inhibitory effect of the strain on common tobacco fungi was verified using the plate confrontation and agar column methods. The results showed that the strain FYZ1-3 was Bacillus subtilis, with a genome size of 4.17 Mb and GC content of 43.68%; 4,338 coding genes were predicted. The genome was annotated and analyzed using multiple databases to determine its ability to efficiently degrade starch proteins at the molecular level. Moreover, 14 functional genes related to nicotine metabolism were identified, primarily located on the distinct genomic island of FYZ1-3, giving a speculation for its nicotine tolerance capability on the molecular mechanism. By mining the secondary metabolite gene cluster prediction, we found potential synthetic bacteriocin, antimicrobial peptide, and other gene clusters on its chromosome, which may have certain antibacterial properties. Further experiments confirmed that the FYZ1-3 strain was a potent growth inhibitor of Penicillium chrysogenum, Aspergillus sydowii, A. fumigatus, and Talaromyces funiculosus. The creation and industrial use of the functional strains obtained in this study provide a theoretical basis for its industrial use, where it would be of great significance to improve the utilization rate of tobacco waste.
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Affiliation(s)
- Changwen Ye
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
- China Tobacco Standardization Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China
| | - Dandan Liu
- China Tobacco Standardization Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China
| | - Kuo Huang
- China Tobacco Standardization Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China
| | - Dong Li
- China Tobacco Standardization Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China
| | - Xinxin Ma
- School of Environment, Tsinghua University, Beijing, China
| | - Yiying Jin
- School of Environment, Tsinghua University, Beijing, China
| | - Hanguo Xiong
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
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4
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Cantillo Villa Y, Triga A, Katharios P. Polyinfection in Fish Aeromoniasis: A Study of Co-Isolated Aeromonas Species in Aeromonas veronii Outbreaks. Pathogens 2023; 12:1337. [PMID: 38003801 PMCID: PMC10674900 DOI: 10.3390/pathogens12111337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/08/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
We studied the phenotypic and genomic characteristics related to the virulence and antibiotic resistance of two Aeromonas strains, which were co-isolated before an outbreak of Aeromonas veronii among diseased seabass on Agathonisi Island, Greece, in April 2015. The first strain, AG2.13.2, is a potentially pathogenic mesophilic variant of Aeromonas salmonicida, and the second, AG2.13.5, corresponds to an Aeromonas rivipollensis related to A. rivipollensis KN-Mc-11N1 with an ANI value of 97.32%. AG2.13.2 lacks the type III secretion system just like other mesophilic strains of A. salmonicida. This characteristic has been associated with lower virulence. However, the genome of AG2.13.2 contains other important virulence factors such as type II and type VI secretion systems, and toxins such as rtxA, aerolysin aer/act, and different types of hemolysins. The strain also carries several genes associated with antibiotic resistance such as the tetE efflux pump, and exhibits resistance to tetracycline, ampicillin, and oxolinic acid. In an in vivo challenge test with gilthead seabream larvae, the A. veronii bv sobria strain AG5.28.6 exhibited the highest virulence among all tested strains. Conversely, both A. salmonicida and A. rivipollensis showed minimal virulence when administered alone. Interestingly, when A. veronii bv sobria AG5.28.6 was co-administered with A. rivipollensis, the larvae survival probability increased compared to those exposed to A. veronii bv sobria AG5.28.6 alone. This finding indicates an antagonistic interaction between A. veronii bv sobria AG5.28.6 and A. rivipollensis AG2.13.5. The co-administration of A. veronii bv sobria AG5.28.6 with Aeromonas salmonicida did not yield distinct survival probabilities. Our results validate that the primary pathogen responsible for European seabass aeromoniasis is Aeromonas veronii bv sobria.
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Affiliation(s)
- Yanelys Cantillo Villa
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), 71500 Gournes, Greece; (Y.C.V.); (A.T.)
- Department of Biology, University of Crete, 71110 Heraklion, Greece
| | - Adriana Triga
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), 71500 Gournes, Greece; (Y.C.V.); (A.T.)
- Department of Biology, University of Crete, 71110 Heraklion, Greece
| | - Pantelis Katharios
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), 71500 Gournes, Greece; (Y.C.V.); (A.T.)
- Aquatic Biologicals, Thalassocosmos, 71500 Gournes, Greece
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Carrau A, Tano J, Moyano L, Ripa MB, Petrocelli S, Piskulic L, Moreira LM, Patané JSL, Setubal JC, Orellano EG. A novel BLUF photoreceptor modulates the Xanthomonas citri subsp. citri-host plant interaction. Photochem Photobiol Sci 2023; 22:1901-1918. [PMID: 37209300 DOI: 10.1007/s43630-023-00420-6] [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: 01/02/2023] [Accepted: 04/05/2023] [Indexed: 05/22/2023]
Abstract
Plant-pathogen interaction is influenced by multiple environmental factors, including temperature and light. Recent works have shown that light modulates not only the defense response of plants but also the pathogens virulence. Xanthomonas citri subsp. citri (Xcc) is the bacterium responsible for citrus canker, an important plant disease worldwide. The Xcc genome presents four genes encoding putative photoreceptors: one bacteriophytochrome and three blue light photoreceptors, one LOV and two BLUFs (bluf1: XAC2120 and bluf2: XAC3278). The presence of two BLUFs proteins is an outstanding feature of Xcc. In this work we show that the bluf2 gene is functional. The mutant strain, XccΔbluf2, was constructed demonstrating that BLUF2 regulates swimming-type motility, adhesion to leaves, exopolysaccharide production and biofilm formation, features involved in the Xcc virulence processes. An important aspect during the plant-pathogen interaction is the oxidative response of the host and the consequent reaction of the pathogen. We observed that ROS detoxification is regulated by Xcc bluf2 gene. The phenotypes of disease in orange plants produced by WT and XccΔbluf2 strains were evaluated, observing different phenotypes. Altogether, these results show that BLUF2 negatively regulates virulence during citrus canker. This work constitutes the first report on BLUF-like receptors in plant pathogenic bacteria.
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Affiliation(s)
- Analía Carrau
- Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK, Rosario, Argentina
| | - Josefina Tano
- Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK, Rosario, Argentina
| | - Laura Moyano
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Biodiversidad y Biología Experimental, Buenos Aires, Argentina
- Instituto de Biodiversidad y Biología Experimental y Aplicada, Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad de Buenos Aires (IBBEA, CONICET-UBA), Buenos Aires, Argentina
| | - María Belén Ripa
- Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK, Rosario, Argentina
| | - Silvana Petrocelli
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK, Rosario, Argentina
| | - Laura Piskulic
- Área Estadística y Procesamiento de Datos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Leandro Marcio Moreira
- Programa de Pós-Graduação em Biotecnologia, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
- Departamento de Ciências Biológicas, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
| | | | | | - Elena Graciela Orellano
- Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK, Rosario, Argentina.
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McCarlie SJ, Boucher CE, Bragg RR. Genomic Islands Identified in Highly Resistant Serratia sp. HRI: A Pathway to Discover New Disinfectant Resistance Elements. Microorganisms 2023; 11:microorganisms11020515. [PMID: 36838480 PMCID: PMC9964261 DOI: 10.3390/microorganisms11020515] [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: 01/13/2023] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
Molecular insights into the mechanisms of resistance to disinfectants are severely limited, together with the roles of various mobile genetic elements. Genomic islands are a well-characterised molecular resistance element in antibiotic resistance, but it is unknown whether genomic islands play a role in disinfectant resistance. Through whole-genome sequencing and the bioinformatic analysis of Serratia sp. HRI, an isolate with high disinfectant resistance capabilities, nine resistance islands were predicted and annotated within the genome. Resistance genes active against several antimicrobials were annotated in these islands, most of which are multidrug efflux pumps belonging to the MFS, ABC and DMT efflux families. Antibiotic resistance islands containing genes encoding for multidrug resistance proteins ErmB (macrolide and erythromycin resistance) and biclomycin were also found. A metal fitness island harbouring 13 resistance and response genes to copper, silver, lead, cadmium, zinc, and mercury was identified. In the search for disinfectant resistance islands, two genomic islands were identified to harbour smr genes, notorious for conferring disinfectant resistance. This suggests that genomic islands are capable of conferring disinfectant resistance, a phenomenon that has not yet been observed in the study of biocide resistance and tolerance.
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Laamarti M, Chemao-Elfihri MW, Essabbar A, Manni A, Kartti S, Alouane T, Temsamani L, Eljamali JE, Sbabou L, Ouadghiri M, Filali-Maltouf A, Belyamani L, Ibrahimi A. Genomic analysis of two Bacillus safensis isolated from Merzouga desert reveals desert adaptive and potential plant growth-promoting traits. Funct Integr Genomics 2022; 22:1173-1187. [PMID: 36175602 DOI: 10.1007/s10142-022-00905-0] [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: 08/15/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 11/04/2022]
Abstract
Deserts represent extreme environments for microorganisms, and conditions such as high soil salinity, nutrient deficiency, and increased levels of UV radiation make desert soil communities of high biotechnological potential. In this study, we isolated, sequenced, and assembled the genomes of Bacillus safensis strains BcP62 and Bcs93, to which we performed comparative genome analyses. Using the DDH and ANI of both strains with the available B. safensis genomes, we identified three potential subspecies within this group. Intra-species core genome phylogenetic analysis did not result in clustering genomes by niche type, with some exceptions. This study also revealed that the genomes of the analyzed strains possessed plant growth-promoting characteristics, most of which were conserved in all B. safensis strains. Furthermore, we highlight the genetic features of B. safensis BcP62 and Bcs93 related to survival in the Merzouga desert in Morocco. These strains could be potentially used in agriculture as PGPB in extreme environments, given their high tolerability to unfavorable conditions.
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Affiliation(s)
- Meriem Laamarti
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Mohammed Walid Chemao-Elfihri
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Abdelmounim Essabbar
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Amina Manni
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Souad Kartti
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Tarek Alouane
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Loubna Temsamani
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Jamal-Eddine Eljamali
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Laila Sbabou
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco.,Université Mohamned VI des Sciences de la Santé (UM6SS), Casablanca, Morocco
| | - Mouna Ouadghiri
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Abdelkarim Filali-Maltouf
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Lahcen Belyamani
- Université Mohamned VI des Sciences de la Santé (UM6SS), Casablanca, Morocco.,Emergency Department, Military Hospital Mohammed V, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Azeddine Ibrahimi
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, Morocco. .,Université Mohamned VI des Sciences de la Santé (UM6SS), Casablanca, Morocco.
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8
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Liu L, Peng S, Song W, Zhao H, Li H, Wang H. Genomic Analysis of an Excellent Wine-Making Strain Oenococcus oeni SD-2a. Pol J Microbiol 2022; 71:279-292. [PMID: 35716166 PMCID: PMC9252139 DOI: 10.33073/pjm-2022-026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/14/2022] [Indexed: 12/27/2022] Open
Abstract
Oenococcus oeni is an important microorganism in wine-making-related engineering, and it improves wine quality and stability through malolactic fermentation. Although the genomes of more than 200 O. oeni strains have been sequenced, only a few include completed genome maps. Here, the genome sequence of O. oeni SD-2a, isolated from Shandong, China, has been determined. It is a fully assembled genome sequence of this strain. The complete genome is 1,989,703 bp with a G+C content of 37.8% without a plasmid. The genome includes almost all the essential genes involved in central metabolic pathways and the stress genes reported in other O. oeni strains. Some natural competence-related genes, like comEA, comEC, comFA, comG operon, and comFC, suggest that O. oeni SD-2a may have natural transformation potential. A comparative genomics analysis revealed 730 gene clusters in O. oeni SD-2a homologous to those in four other lactic acid bacteria species (O. oeni PSU-1, O. oeni CRBO-11381, Lactiplantibacillus plantarum UNQLp11, and Pediococcus pentosaceus KCCM40703). A collinearity analysis showed poor collinearity between O. oeni SD-2a and O. oeni PSU-1, indicating great differences in their evolutionary histories. The results provide general knowledge of O. oeni SD-2a and lay the foundation for specific gene function analyses. ![]()
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Affiliation(s)
- Longxiang Liu
- Shandong Provincial Engineering and Technology Research Center for Wild Plant Resources Development and Application of Yellow River Delta, College of Biological and Environmental Engineering, Binzhou University, Binzhou, China
| | - Shuai Peng
- College of food science and engineering, Gansu Agricultural University, Lanzhou, China
| | - Weiyu Song
- Shandong Provincial Engineering and Technology Research Center for Wild Plant Resources Development and Application of Yellow River Delta, College of Biological and Environmental Engineering, Binzhou University, Binzhou, China
| | - Hongyu Zhao
- College of Enology, Northwest A&F University, Yangling, China.,Shaanxi Engineering Research Center for Viti-Viniculture, Yangling, China
| | - Hua Li
- College of Enology, Northwest A&F University, Yangling, China.,Shaanxi Engineering Research Center for Viti-Viniculture, Yangling, China
| | - Hua Wang
- College of Enology, Northwest A&F University, Yangling, China.,Shaanxi Engineering Research Center for Viti-Viniculture, Yangling, China
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9
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Alsheikh-Hussain AS, Ben Zakour NL, Forde BM, Silayeva O, Barnes AC, Beatson SA. A high-quality reference genome for the fish pathogen Streptococcus iniae. Microb Genom 2022; 8:000777. [PMID: 35229712 PMCID: PMC9176272 DOI: 10.1099/mgen.0.000777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fish mortality caused by Streptococcus iniae is a major economic problem in aquaculture in warm and temperate regions globally. There is also risk of zoonotic infection by S. iniae through handling of contaminated fish. In this study, we present the complete genome sequence of S. iniae strain QMA0248, isolated from farmed barramundi in South Australia. The 2.12 Mb genome of S. iniae QMA0248 carries a 32 kb prophage, a 12 kb genomic island and 92 discrete insertion sequence (IS) elements. These include nine novel IS types that belong mostly to the IS3 family. Comparative and phylogenetic analysis between S. iniae QMA0248 and publicly available complete S. iniae genomes revealed discrepancies that are probably due to misassembly in the genomes of isolates ISET0901 and ISNO. Long-range PCR confirmed five rRNA loci in the PacBio assembly of QMA0248, and, unlike S. iniae 89353, no tandemly repeated rRNA loci in the consensus genome. However, we found sequence read evidence that the tandem rRNA repeat existed within a subpopulation of the original QMA0248 culture. Subsequent nanopore sequencing revealed that the tandem rRNA repeat was the most prevalent genotype, suggesting that there is selective pressure to maintain fewer rRNA copies under uncertain laboratory conditions. Our study not only highlights assembly problems in existing genomes, but provides a high-quality reference genome for S. iniae QMA0248, including manually curated mobile genetic elements, that will assist future S. iniae comparative genomic and evolutionary studies.
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Affiliation(s)
- Areej S. Alsheikh-Hussain
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Nouri L. Ben Zakour
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
- The Westmead Institute for Medical Research and the University of Sydney, Sydney, New South Wales, Australia
| | - Brian M. Forde
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Oleksandra Silayeva
- School of Biological Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Andrew C. Barnes
- School of Biological Science, The University of Queensland, Brisbane, Queensland, Australia
- *Correspondence: Andrew C. Barnes,
| | - Scott A. Beatson
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
- *Correspondence: Scott A. Beatson,
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10
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Jiang A, Zou C, Xu X, Ke Z, Hou J, Jiang G, Fan C, Gong J, Wei J. Complete genome sequence of biocontrol strain Paenibacillus peoriae HJ-2 and further analysis of its biocontrol mechanism. BMC Genomics 2022; 23:161. [PMID: 35209846 PMCID: PMC8876185 DOI: 10.1186/s12864-022-08330-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 01/19/2022] [Indexed: 01/25/2023] Open
Abstract
Background Paris polyphylla is a herb widely used in traditional Chinese medicine to treat various diseases. Stem rot diseases seriously affected the yield of P. polyphylla in subtropical areas of China. Therefore, cost-effective, chemical-free, eco-friendly strategies to control stem rot on P. polyphylla are valuable and urgently needed. Results In this paper, we reported the biocontrol efficiency of Paenibacillus peoriae HJ-2 and its complete genome sequence. Strain HJ-2 could serve as a potential biocontrol agent against stem rot on P. polyphylla in the greenhouse and field. The genome of HJ-2 consists of a single 6,001,192 bp chromosome with an average GC content of 45% and 5,237 predicted protein coding genes, 39 rRNAs and 108 tRNAs. The phylogenetic tree indicated that HJ-2 is most closely related to P. peoriae IBSD35. Functional analysis of genome revealed numerous genes/gene clusters involved in plant colonization, biofilm formation, plant growth promotion, antibiotic and resistance inducers synthesis. Moreover, metabolic pathways that potentially contribute to biocontrol mechanisms were identified. Conclusions This study revealed that P. peoriae HJ-2 could serve as a potential BCA against stem rot on P. polyphylla. Based on genome analysis, the genome of HJ-2 contains more than 70 genes and 12 putative gene clusters related to secondary metabolites, which have previously been described as being involved in chemotaxis motility, biofilm formation, growth promotion, antifungal activity and resistance inducers biosynthesis. Compared with other strains, variation in the genes/gene clusters may lead to different antimicrobial spectra and biocontrol efficacies. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08330-0.
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Affiliation(s)
- Aiming Jiang
- College of Agriculture, Guangxi University, Nanning, 530004, China.,College of Chemistry and Environmental Engineering, Hanjiang Normal University, Shiyan, 442000, China
| | - Chengwu Zou
- College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Xiang Xu
- Institute of Basic Medical Sciences, Hubei University of Medicine, Shiyan, 442000, China
| | - Zunwei Ke
- College of Chemistry and Environmental Engineering, Hanjiang Normal University, Shiyan, 442000, China
| | - Jiangan Hou
- College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Guihe Jiang
- College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Chunli Fan
- College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Jianhua Gong
- College of Chemistry and Environmental Engineering, Hanjiang Normal University, Shiyan, 442000, China
| | - Jiguang Wei
- College of Agriculture, Guangxi University, Nanning, 530004, China.
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11
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Lobb B, Tremblay BJM, Moreno-Hagelsieb G, Doxey AC. PathFams: statistical detection of pathogen-associated protein domains. BMC Genomics 2021; 22:663. [PMID: 34521345 PMCID: PMC8442362 DOI: 10.1186/s12864-021-07982-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 09/01/2021] [Indexed: 11/10/2022] Open
Abstract
Background A substantial fraction of genes identified within bacterial genomes encode proteins of unknown function. Identifying which of these proteins represent potential virulence factors, and mapping their key virulence determinants, is a challenging but important goal. Results To facilitate virulence factor discovery, we performed a comprehensive analysis of 17,929 protein domain families within the Pfam database, and scored them based on their overrepresentation in pathogenic versus non-pathogenic species, taxonomic distribution, relative abundance in metagenomic datasets, and other factors. Conclusions We identify pathogen-associated domain families, candidate virulence factors in the human gut, and eukaryotic-like mimicry domains with likely roles in virulence. Furthermore, we provide an interactive database called PathFams to allow users to explore pathogen-associated domains as well as identify pathogen-associated domains and domain architectures in user-uploaded sequences of interest. PathFams is freely available at https://pathfams.uwaterloo.ca. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07982-8.
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Affiliation(s)
- Briallen Lobb
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | | | | | - Andrew C Doxey
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada.
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12
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Espinosa-Camacho LF, Delgado G, Cravioto A, Morales-Espinosa R. Diversity in the composition of the accessory genome of Mexican Pseudomonas aeruginosa strains. Genes Genomics 2021; 44:53-77. [PMID: 34410625 DOI: 10.1007/s13258-021-01155-3] [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: 03/05/2021] [Accepted: 08/13/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Pseudomonas aeruginosa is an important opportunistic pathogen especially in nosocomial infections due to its easy adaptation to different environments; this characteristic is due to the great genetic diversity that presents its genome. In addition, it is considered a pathogen of critical priority due to the high antimicrobial resistance. OBJECTIVES The aim of this study was to characterize the mobile genetic elements present in the chromosome of six Mexican P. aeruginosa strains isolated from adults with pneumonia and children with bacteremia. METHODS The genomic DNA of six P. aeruginosa strains were isolated and sequenced using PacBio RS-II platform. They were annotated using Prokaryotic Genome Annotation Pipeline and manually curated and analyzed for the presence of mobile genetic elements, antibiotic resistances genes, efflux pumps and virulence factors using several bioinformatics programs and databases. RESULTS The global analysis of the strains chromosomes showed a novel chromosomal rearrangement in two strains, possibly mediated by subsequent recombination and inversion events. They have a high content of mobile genetic elements: 21 genomic islands, four new islets, four different integrative conjugative elements, 28 different prophages, one CRISPR-Cas arrangements, and one class 1 integron. The acquisition of antimicrobials resistance genes into these elements are in concordance with their phenotype of multi-drug resistance. CONCLUSION The accessory genome increased the ability of the strains to adapt or survive to the hospital environment, promote genomic plasticity and chromosomal rearrangements, which may affect the expression or functionality of the gene and might influence the clinical outcome, having an impact on the treatment.
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Affiliation(s)
- Luis F Espinosa-Camacho
- Laboratorio de Genómica Bacteriana, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Colonia Ciudad Universitaria, Coyoacán, C.P. 04510, Mexico City, Mexico
| | - Gabriela Delgado
- Laboratorio de Genómica Bacteriana, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Colonia Ciudad Universitaria, Coyoacán, C.P. 04510, Mexico City, Mexico
| | - Alejandro Cravioto
- Laboratorio de Genómica Bacteriana, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Colonia Ciudad Universitaria, Coyoacán, C.P. 04510, Mexico City, Mexico
| | - Rosario Morales-Espinosa
- Laboratorio de Genómica Bacteriana, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Colonia Ciudad Universitaria, Coyoacán, C.P. 04510, Mexico City, Mexico.
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13
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Riedel T, Neumann-Schaal M, Wittmann J, Schober I, Hofmann JD, Lu CW, Dannheim A, Zimmermann O, Lochner M, Groß U, Overmann J. Characterization of Clostridioides difficile DSM 101085 with A-B-CDT+ Phenotype from a Late Recurrent Colonization. Genome Biol Evol 2021; 12:566-577. [PMID: 32302381 PMCID: PMC7250501 DOI: 10.1093/gbe/evaa072] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/10/2020] [Indexed: 12/29/2022] Open
Abstract
During the last decades, hypervirulent strains of Clostridioides difficile with frequent disease recurrence and increased mortality appeared. Clostridioides difficile DSM 101085 was isolated from a patient who suffered from several recurrent infections and colonizations, likely contributing to a fatal outcome. Analysis of the toxin repertoire revealed the presence of a complete binary toxin locus and an atypical pathogenicity locus consisting of only a tcdA pseudogene and a disrupted tcdC gene sequence. The pathogenicity locus shows upstream a transposon and has been subject to homologous recombination or lateral gene transfer events. Matching the results of the genome analysis, neither TcdA nor TcdB production but the expression of cdtA and cdtB was detected. This highlights a potential role of the binary toxin C. difficile toxin in this recurrent colonization and possibly further in a host-dependent virulence. Compared with the C. difficile metabolic model strains DSM 28645 (630Δerm) and DSM 27147 (R20291), strain DSM 101085 showed a specific metabolic profile, featuring changes in the threonine degradation pathways and alterations in the central carbon metabolism. Moreover, products originating from Stickland pathways processing leucine, aromatic amino acids, and methionine were more abundant in strain DSM 101085, indicating a more efficient use of these substrates. The particular characteristics of strain C. difficile DSM 101085 may represent an adaptation to a low-protein diet in a patient with recurrent infections.
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Affiliation(s)
- Thomas Riedel
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Meina Neumann-Schaal
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,Department of Bioinformatics and Biochemistry and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Germany
| | - Johannes Wittmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Isabel Schober
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Julia Danielle Hofmann
- Department of Bioinformatics and Biochemistry and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Germany
| | - Chia-Wen Lu
- Institute of Infection Immunology, TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture between the Medical School Hannover (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
| | - Antonia Dannheim
- Department of Bioinformatics and Biochemistry and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Germany
| | - Ortrud Zimmermann
- Institute of Medical Microbiology, University Medical Center Göttingen, Germany
| | - Matthias Lochner
- Institute of Infection Immunology, TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture between the Medical School Hannover (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
| | - Uwe Groß
- Institute of Medical Microbiology, University Medical Center Göttingen, Germany.,Göttingen International Health Network, Göttingen, Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany.,Institute of Microbiology, Technical University of Braunschweig, Germany
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14
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Bose D, Mukhopadhyay S. The hunt for a yet unknown: Common molecular signature in some genetically monomorphic enterobacteria. J Basic Microbiol 2021; 61:524-546. [PMID: 33991346 DOI: 10.1002/jobm.202000630] [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: 11/24/2020] [Revised: 04/04/2021] [Accepted: 04/22/2021] [Indexed: 11/09/2022]
Abstract
Mark Achtman introduced the term "genetically monomorphic bacteria" (GM bacteria) for some human and plant pathogens. They displayed a great uniformity in terms of their "genetic" properties. This "uniformity" poses a challenge to microbiologists. To address these problems, we used CodonW and IslandViewer 3 as analytical tools and took Escherichia coli, Salmonella, and Shigella strains as a model organisms. We hypothesized that GM bacterium contains a common molecular signature among them. We have found a significant correlation regarding the number of protein-coding genes, predicted highly expressed genes, and the highest length of gene in this regard. On the other hand, the correspondence analysis of pathogenicity-related genes identified by IslandViewer 3 displayed a somewhat unique pattern in GM bacteria. The probable pathogenic genes are clustered into two separate groups, which is a hallmark of some pattern. Similar genes of non-monomorphic pathogenic strain clustered almost similarly, but the clusters are joined together, they are not completely separated. These features, in our considered view, may be considered as codon usages signatures of these bacteria, and E. coli in particular.
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Affiliation(s)
- Debadin Bose
- Department of Botany, Kabi Nazrul College, Murarai, West Bengal, India
| | - Subhasis Mukhopadhyay
- Distributed Information Centre for Bioinformatics, Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Calcutta, West Bengal, India
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15
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Shaligram S, Narwade NP, Kumbhare SV, Bordoloi M, Tamuli KJ, Nath S, Parimelazhagan T, Patil VS, Kapley A, Pawar SP, Dhotre DP, Muddeshwar MG, Purohit HJ, Shouche YS. Integrated Genomic and Functional Characterization of the Anti-diabetic Potential of Arthrobacter sp. SW1. Curr Microbiol 2021; 78:2577-2588. [PMID: 33983483 DOI: 10.1007/s00284-021-02523-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 04/28/2021] [Indexed: 11/29/2022]
Abstract
For decades, bacterial natural products have served as valuable resources for developing novel drugs to treat several human diseases. Recent advancements in the integrative approach of using genomic and functional tools have proved beneficial in obtaining a comprehensive understanding of these biomolecules. This study presents an in-depth characterization of the anti-diabetic activity exhibited by a bacterial isolate SW1, isolated from an effluent treatment plant. As a primary screening, we assessed the isolate for its potential to inhibit alpha-amylase and alpha-glucosidase enzymes. Upon confirmation, we further utilized LC-MS, ESI-MS/MS, and NMR spectroscopy to identify and characterize the biomolecule. These efforts were coupled with the genomic assessment of the biosynthetic gene cluster involved in the anti-diabetic compound production. Our investigation discovered that the isolate SW1 inhibited both α-amylase and α-glucosidase activity. The chemical analysis suggested the production of acarbose, an anti-diabetic biomolecule, which was further confirmed by the presence of biosynthetic gene cluster "acb" in the genome. Our in-depth chemical characterization and genome mining approach revealed the potential of bacteria from an unconventional niche, an effluent treatment plant. To the best of our knowledge, it is one of the first few reports of acarbose production from the genus Arthrobacter.
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Affiliation(s)
- Shraddha Shaligram
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Central Tower, Sai Trinity Complex, Pashan, Pune, 411021, India.
| | - Nitin P Narwade
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Central Tower, Sai Trinity Complex, Pashan, Pune, 411021, India
| | - Shreyas V Kumbhare
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Central Tower, Sai Trinity Complex, Pashan, Pune, 411021, India
| | - Manobjyoti Bordoloi
- Chemical Sciences and Technology Division, CSIR North East Institute of Science & Technology, Jorhat, Assam, 785006, India.
| | - Kashyap J Tamuli
- Chemical Sciences and Technology Division, CSIR North East Institute of Science & Technology, Jorhat, Assam, 785006, India
| | - Shyamalendu Nath
- Chemical Sciences and Technology Division, CSIR North East Institute of Science & Technology, Jorhat, Assam, 785006, India
| | - T Parimelazhagan
- Department of Botany, Bioprospecting Laboratory, Bharathiar University, Coimbatore, Tamil Nadu, India
| | - Vikas S Patil
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Central Tower, Sai Trinity Complex, Pashan, Pune, 411021, India
| | - Atya Kapley
- Environmental Biotechnology and Genomics Division, National Environmental Engineering Research Institute, CSIR-NEERI, Nehru Marg, Nagpur, 440020, India
| | - Shrikant P Pawar
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Central Tower, Sai Trinity Complex, Pashan, Pune, 411021, India
| | - Dhiraj P Dhotre
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Central Tower, Sai Trinity Complex, Pashan, Pune, 411021, India
| | - M G Muddeshwar
- Department of Biochemistry, Government Medical College, Nagpur, Maharashtra, 440009, India
| | - Hemant J Purohit
- Environmental Biotechnology and Genomics Division, National Environmental Engineering Research Institute, CSIR-NEERI, Nehru Marg, Nagpur, 440020, India
| | - Yogesh S Shouche
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Central Tower, Sai Trinity Complex, Pashan, Pune, 411021, India
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16
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Functional Analysis of Phenazine Biosynthesis Genes in Burkholderia spp. Appl Environ Microbiol 2021; 87:AEM.02348-20. [PMID: 33741619 DOI: 10.1128/aem.02348-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 03/09/2021] [Indexed: 01/15/2023] Open
Abstract
Burkholderia encompasses a group of ubiquitous Gram-negative bacteria that includes numerous saprophytes as well as species that cause infections in animals, immunocompromised patients, and plants. Some species of Burkholderia produce colored, redox-active secondary metabolites called phenazines. Phenazines contribute to competitiveness, biofilm formation, and virulence in the opportunistic pathogen Pseudomonas aeruginosa, but knowledge of their diversity, biosynthesis, and biological functions in Burkholderia is lacking. In this study, we screened publicly accessible genome sequence databases and identified phenazine biosynthesis genes in multiple strains of the Burkholderia cepacia complex, some isolates of the B. pseudomallei clade, and the plant pathogen B. glumae We then focused on B. lata ATCC 17760 to reveal the organization and function of genes involved in the production of dimethyl 4,9-dihydroxy-1,6-phenazinedicarboxylate. Using a combination of isogenic mutants and plasmids carrying different segments of the phz locus, we characterized three novel genes involved in the modification of the phenazine tricycle. Our functional studies revealed a connection between the presence and amount of phenazines and the dynamics of biofilm growth in flow cell and static experimental systems but at the same time failed to link the production of phenazines with the capacity of Burkholderia to kill fruit flies and rot onions.IMPORTANCE Although the production of phenazines in Burkholderia was first reported almost 70 years ago, the role these metabolites play in the biology of these economically important microorganisms remains poorly understood. Our results revealed that the phenazine biosynthetic pathway in Burkholderia has a complex evolutionary history, which likely involved horizontal gene transfers among several distantly related groups of organisms. The contribution of phenazines to the formation of biofilms suggests that Burkholderia, like fluorescent pseudomonads, may benefit from the unique redox-cycling properties of these versatile secondary metabolites.
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17
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Hooykaas MJG, Hooykaas PJJ. The genome sequence of hairy root Rhizobium rhizogenes strain LBA9402: Bioinformatics analysis suggests the presence of a new opine system in the agropine Ri plasmid. Microbiologyopen 2021; 10:e1180. [PMID: 33970547 PMCID: PMC8087989 DOI: 10.1002/mbo3.1180] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 12/17/2022] Open
Abstract
We report here the complete genome sequence of the Rhizobium rhizogenes (formerly Agrobacterium rhizogenes) strain LBA9402 (NCPPB1855rifR), a pathogenic strain causing hairy root disease. To assemble a complete genome, we obtained short reads from Illumina sequencing and long reads from Oxford Nanopore Technology sequencing. The genome consists of a 3,958,212 bp chromosome, a 2,005,144 bp chromid (secondary chromosome) and a 252,168 bp Ri plasmid (pRi1855), respectively. The primary chromosome was very similar to that of the avirulent biocontrol strain K84, but the chromid showed a 724 kbp deletion accompanied by a large 1.8 Mbp inversion revealing the dynamic nature of these secondary chromosomes. The sequence of the agropine Ri plasmid was compared to other types of Ri and Ti plasmids. Thus, we identified the genes responsible for agropine catabolism, but also a unique segment adjacent to the TL region that has the signature of a new opine catabolic gene cluster including the three genes that encode the three subunits of an opine dehydrogenase. Our sequence analysis also revealed a novel gene at the very right end of the TL-DNA, which is unique for the agropine Ri plasmid. The protein encoded by this gene was most related to the succinamopine synthases of chrysopine and agropine Ti plasmids and thus may be involved in the synthesis of the unknown opine that can be degraded by the adjacent catabolic cluster. The available sequence will facilitate the use of R. rhizogenes and especially LBA9402 in both the laboratory and for biotechnological purposes.
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Schnaars V, Wöhlbrand L, Scheve S, Hinrichs C, Reinhardt R, Rabus R. Proteogenomic Insights into the Physiology of Marine, Sulfate-Reducing, Filamentous Desulfonema limicola and Desulfonema magnum. Microb Physiol 2021; 31:1-20. [PMID: 33611323 PMCID: PMC8315694 DOI: 10.1159/000513383] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 11/19/2020] [Indexed: 11/19/2022]
Abstract
The genus Desulfonema belongs to the deltaproteobacterial family Desulfobacteraceae and comprises marine, sulfate-reducing bacteria that form filaments and move by gliding. This study reports on the complete, manually annotated genomes of Dn. limicola 5ac10T (6.91 Mbp; 6,207 CDS) and Dn. magnum 4be13T (8.03 Mbp; 9,970 CDS), integrated with substrate-specific proteome profiles (8 vs. 11). The richness in mobile genetic elements is shared with other Desulfobacteraceae members, corroborating horizontal gene transfer as major driver in shaping the genomes of this family. The catabolic networks of Dn. limicola and Dn. magnum have the following general characteristics: 98 versus 145 genes assigned (having genomic shares of 1.7 vs. 2.2%), 92.5 versus 89.7% proteomic coverage, and scattered gene clusters for substrate degradation and energy metabolism. The Dn. magnum typifying capacity for aromatic compound degradation (e.g., p-cresol, 3-phenylpropionate) requires 48 genes organized in operon-like structures (87.7% proteomic coverage; no homologs in Dn. limicola). The protein complements for aliphatic compound degradation, central pathways, and energy metabolism are highly similar between both genomes and were identified to a large extent (69-96%). The differential protein profiles revealed a high degree of substrate-specificity for peripheral reaction sequences (forming central intermediates), agreeing with the high number of sensory/regulatory proteins predicted for both strains. By contrast, central pathways and modules of the energy metabolism were constitutively formed under the tested substrate conditions. In accord with their natural habitats that are subject to fluctuating changes of physicochemical parameters, both Desulfonema strains are well equipped to cope with various stress conditions. Next to superoxide dismutase and catalase also desulfoferredoxin and rubredoxin oxidoreductase are formed to counter exposure to molecular oxygen. A variety of proteases and chaperones were detected that function in maintaining cellular homeostasis upon heat or cold shock. Furthermore, glycine betaine/proline betaine transport systems can respond to hyperosmotic stress. Gliding movement probably relies on twitching motility via type-IV pili or adventurous motility. Taken together, this proteogenomic study demonstrates the adaptability of Dn. limicola and Dn. magnum to its dynamic habitats by means of flexible catabolism and extensive stress response capacities.
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Affiliation(s)
- Vanessa Schnaars
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Lars Wöhlbrand
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Sabine Scheve
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Christina Hinrichs
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Richard Reinhardt
- Max-Planck-Genome-Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Ralf Rabus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany,
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Kubicek-Sutherland JZ, Xie G, Shakya M, Dighe PK, Jacobs LL, Daligault H, Davenport K, Stromberg LR, Stromberg ZR, Cheng Q, Kempaiah P, Ong’echa JM, Otieno V, Raballah E, Anyona S, Ouma C, Chain PSG, Perkins DJ, Mukundan H, McMahon BH, Doggett NA. Comparative genomic and phenotypic characterization of invasive non-typhoidal Salmonella isolates from Siaya, Kenya. PLoS Negl Trop Dis 2021; 15:e0008991. [PMID: 33524010 PMCID: PMC7877762 DOI: 10.1371/journal.pntd.0008991] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 02/11/2021] [Accepted: 11/17/2020] [Indexed: 02/07/2023] Open
Abstract
Non-typhoidal Salmonella (NTS) is a major global health concern that often causes bloodstream infections in areas of the world affected by malnutrition and comorbidities such as HIV and malaria. Developing a strategy to control the emergence and spread of highly invasive and antimicrobial resistant NTS isolates requires a comprehensive analysis of epidemiological factors and molecular pathogenesis. Here, we characterize 11 NTS isolates that caused bloodstream infections in pediatric patients in Siaya, Kenya from 2003-2010. Nine isolates were identified as S. Typhimurium sequence type 313 while the other two were S. Enteritidis. Comprehensive genotypic and phenotypic analyses were performed to compare these isolates to those previously identified in sub-Saharan Africa. We identified a S. Typhimurium isolate referred to as UGA14 that displayed novel plasmid, pseudogene and resistance features as compared to other isolates reported from Africa. Notably, UGA14 is able to ferment both lactose and sucrose due to the acquisition of insertion elements on the pKST313 plasmid. These findings show for the first time the co-evolution of plasmid-mediated lactose and sucrose metabolism along with cephalosporin resistance in NTS further elucidating the evolutionary mechanisms of invasive NTS phenotypes. These results further support the use of combined genomic and phenotypic approaches to detect and characterize atypical NTS isolates in order to advance biosurveillance efforts that inform countermeasures aimed at controlling invasive and antimicrobial resistant NTS.
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Affiliation(s)
| | - Gary Xie
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States
| | - Migun Shakya
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States
| | - Priya K. Dighe
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States
| | - Lindsey L. Jacobs
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States
| | | | - Karen Davenport
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States
| | | | | | - Qiuying Cheng
- Center for Global Health, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Prakasha Kempaiah
- Center for Global Health, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - John Michael Ong’echa
- University of New Mexico/KEMRI Laboratories of Parasitic and Viral Diseases, Kenya Medical Research Institute, Kisumu, Kenya
| | - Vincent Otieno
- University of New Mexico/KEMRI Laboratories of Parasitic and Viral Diseases, Kenya Medical Research Institute, Kisumu, Kenya
| | - Evans Raballah
- University of New Mexico/KEMRI Laboratories of Parasitic and Viral Diseases, Kenya Medical Research Institute, Kisumu, Kenya
- Department of Medical Laboratory Science, School of Public Health, Biomedical Sciences and Technology, Masinde Muliro University of Science and Technology, Kakamega, Kenya
| | - Samuel Anyona
- University of New Mexico/KEMRI Laboratories of Parasitic and Viral Diseases, Kenya Medical Research Institute, Kisumu, Kenya
- Department of Medical Biochemistry, School of Medicine, Maseno University, Maseno, Kenya
| | - Collins Ouma
- University of New Mexico/KEMRI Laboratories of Parasitic and Viral Diseases, Kenya Medical Research Institute, Kisumu, Kenya
- Department of Biomedical Sciences and Technology, School of Public Health and Community Development, Maseno University, Maseno, Kenya
| | | | - Douglas J. Perkins
- Center for Global Health, University of New Mexico, Albuquerque, New Mexico, United States of America
- University of New Mexico/KEMRI Laboratories of Parasitic and Viral Diseases, Kenya Medical Research Institute, Kisumu, Kenya
| | - Harshini Mukundan
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States
- * E-mail:
| | | | - Norman A. Doggett
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States
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20
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Weiten A, Kalvelage K, Becker P, Reinhardt R, Hurek T, Reinhold-Hurek B, Rabus R. Complete Genomes of the Anaerobic Degradation Specialists Aromatoleum petrolei ToN1T and Aromatoleum bremense PbN1T. Microb Physiol 2021; 31:16-35. [PMID: 33477134 DOI: 10.1159/000513167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 11/17/2020] [Indexed: 11/19/2022]
Abstract
The betaproteobacterial genus Aromatoleum comprises facultative denitrifiers specialized in the anaerobic degradation of recalcitrant organic compounds (aromatic and terpenoid). This study reports on the complete and manually annotated genomes of Ar. petrolei ToN1T (5.41 Mbp) and Ar. bremense PbN1T (4.38 Mbp), which cover the phylogenetic breadth of the genus Aromatoleum together with previously genome sequenced Ar. aromaticum EbN1T [Rabus et al., Arch Microbiol. 2005 Jan;183(1):27-36]. The gene clusters for the anaerobic degradation of aromatic and terpenoid (strain ToN1T only) compounds are scattered across the genomes of strains ToN1T and PbN1T. The richness in mobile genetic elements is shared with other Aromatoleum spp., substantiating that horizontal gene transfer should have been a major driver in shaping the genomes of this genus. The composite catabolic network of strains ToN1T and PbN1T comprises 88 proteins, the coding genes of which occupy 86.1 and 76.4 kbp (1.59 and 1.75%) of the respective genome. The strain-specific gene clusters for anaerobic degradation of ethyl-/propylbenzene (strain PbN1T) and toluene/monoterpenes (strain ToN1T) share high similarity with their counterparts in Ar. aromaticum strains EbN1T and pCyN1, respectively. Glucose is degraded via the ED-pathway in strain ToN1T, while gluconeogenesis proceeds via the reverse EMP-pathway in strains ToN1T, PbN1T, and EbN1T. The diazotrophic, endophytic lifestyle of closest related genus Azoarcus is known to be associated with nitrogenase and type-6 secretion system (T6SS). By contrast, strains ToN1T, PbN1T, and EbN1T lack nif genes for nitrogenase (including cofactor synthesis and enzyme maturation). Moreover, strains PbN1T and EbN1T do not possess tss genes for T6SS, while strain ToN1T does and facultative endophytic "Aromatoleum" sp. CIB is known to even have both. These findings underpin the functional heterogeneity among Aromatoleum members, correlating with the high plasticity of their genomes.
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Affiliation(s)
- Arne Weiten
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Kristin Kalvelage
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Patrick Becker
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Richard Reinhardt
- Max-Planck-Genome-Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Thomas Hurek
- Department of Microbe-Plant Interactions, Faculty of Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Barbara Reinhold-Hurek
- Department of Microbe-Plant Interactions, Faculty of Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Ralf Rabus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany,
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21
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Maus I, Tubbesing T, Wibberg D, Heyer R, Hassa J, Tomazetto G, Huang L, Bunk B, Spröer C, Benndorf D, Zverlov V, Pühler A, Klocke M, Sczyrba A, Schlüter A. The Role of Petrimonas mucosa ING2-E5A T in Mesophilic Biogas Reactor Systems as Deduced from Multiomics Analyses. Microorganisms 2020; 8:E2024. [PMID: 33348776 PMCID: PMC7768429 DOI: 10.3390/microorganisms8122024] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 12/17/2022] Open
Abstract
Members of the genera Proteiniphilum and Petrimonas were speculated to represent indicators reflecting process instability within anaerobic digestion (AD) microbiomes. Therefore, Petrimonas mucosa ING2-E5AT was isolated from a biogas reactor sample and sequenced on the PacBio RSII and Illumina MiSeq sequencers. Phylogenetic classification positioned the strain ING2-E5AT in close proximity to Fermentimonas and Proteiniphilum species (family Dysgonomonadaceae). ING2-E5AT encodes a number of genes for glycosyl-hydrolyses (GH) which are organized in Polysaccharide Utilization Loci (PUL) comprising tandem susCD-like genes for a TonB-dependent outer-membrane transporter and a cell surface glycan-binding protein. Different GHs encoded in PUL are involved in pectin degradation, reflecting a pronounced specialization of the ING2-E5AT PUL systems regarding the decomposition of this polysaccharide. Genes encoding enzymes participating in amino acids fermentation were also identified. Fragment recruitments with the ING2-E5AT genome as a template and publicly available metagenomes of AD microbiomes revealed that Petrimonas species are present in 146 out of 257 datasets supporting their importance in AD microbiomes. Metatranscriptome analyses of AD microbiomes uncovered active sugar and amino acid fermentation pathways for Petrimonas species. Likewise, screening of metaproteome datasets demonstrated expression of the Petrimonas PUL-specific component SusC providing further evidence that PUL play a central role for the lifestyle of Petrimonas species.
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Affiliation(s)
- Irena Maus
- Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany; (I.M.); (D.W.); (J.H.); (A.P.)
| | - Tom Tubbesing
- Faculty of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany; (T.T.); (L.H.); (A.S.)
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany; (I.M.); (D.W.); (J.H.); (A.P.)
| | - Robert Heyer
- Bioprocess Engineering, Otto von Guericke University Magdeburg, Universitätspl. 2, 39106 Magdeburg, Germany; (R.H.); (D.B.)
- Database and Software Engineering Group, Department of Computer Science, Institute for Technical and Business Information Systems, Otto von Guericke University Magdeburg, Universitätspl. 2, 39106 Magdeburg, Germany
| | - Julia Hassa
- Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany; (I.M.); (D.W.); (J.H.); (A.P.)
- Department of Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy, Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Geizecler Tomazetto
- Biological and Chemical Engineering Section (BCE), Department of Engineering, Aarhus University, 8000 Aarhus, Denmark;
| | - Liren Huang
- Faculty of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany; (T.T.); (L.H.); (A.S.)
| | - Boyke Bunk
- Department Bioinformatics and Databases, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstraße 7B, 38124 Braunschweig, Germany; (B.B.); (C.S.)
| | - Cathrin Spröer
- Department Bioinformatics and Databases, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstraße 7B, 38124 Braunschweig, Germany; (B.B.); (C.S.)
| | - Dirk Benndorf
- Bioprocess Engineering, Otto von Guericke University Magdeburg, Universitätspl. 2, 39106 Magdeburg, Germany; (R.H.); (D.B.)
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, 39106 Magdeburg, Germany
- Microbiology, Anhalt University of Applied Sciences, Bernburger Straße 55, 06354 Köthen, Germany
| | - Vladimir Zverlov
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany;
- Institute of Molecular Genetics, National Research Centre «Kurchatov Institute», Kurchatov Sq. 2, 123128 Moscow, Russia
| | - Alfred Pühler
- Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany; (I.M.); (D.W.); (J.H.); (A.P.)
| | - Michael Klocke
- Institute of Agricultural and Urban Ecological Projects Affiliated to Berlin Humboldt University (IASP), Philippstraße 13, 10115 Berlin, Germany;
| | - Alexander Sczyrba
- Faculty of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany; (T.T.); (L.H.); (A.S.)
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany; (I.M.); (D.W.); (J.H.); (A.P.)
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22
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Maguire F, Jia B, Gray KL, Lau WYV, Beiko RG, Brinkman FSL. Metagenome-assembled genome binning methods with short reads disproportionately fail for plasmids and genomic Islands. Microb Genom 2020; 6:mgen000436. [PMID: 33001022 PMCID: PMC7660262 DOI: 10.1099/mgen.0.000436] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 09/04/2020] [Indexed: 12/12/2022] Open
Abstract
Metagenomic methods enable the simultaneous characterization of microbial communities without time-consuming and bias-inducing culturing. Metagenome-assembled genome (MAG) binning methods aim to reassemble individual genomes from this data. However, the recovery of mobile genetic elements (MGEs), such as plasmids and genomic islands (GIs), by binning has not been well characterized. Given the association of antimicrobial resistance (AMR) genes and virulence factor (VF) genes with MGEs, studying their transmission is a public-health priority. The variable copy number and sequence composition of MGEs makes them potentially problematic for MAG binning methods. To systematically investigate this issue, we simulated a low-complexity metagenome comprising 30 GI-rich and plasmid-containing bacterial genomes. MAGs were then recovered using 12 current prediction pipelines and evaluated. While 82-94 % of chromosomes could be correctly recovered and binned, only 38-44 % of GIs and 1-29 % of plasmid sequences were found. Strikingly, no plasmid-borne VF nor AMR genes were recovered, and only 0-45 % of AMR or VF genes within GIs. We conclude that short-read MAG approaches, without further optimization, are largely ineffective for the analysis of mobile genes, including those of public-health importance, such as AMR and VF genes. We propose that researchers should explore developing methods that optimize for this issue and consider also using unassembled short reads and/or long-read approaches to more fully characterize metagenomic data.
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Affiliation(s)
- Finlay Maguire
- Faculty of Computer Science, Dalhousie University, 6050 University Avenue, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Baofeng Jia
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Kristen L. Gray
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Wing Yin Venus Lau
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Robert G. Beiko
- Faculty of Computer Science, Dalhousie University, 6050 University Avenue, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Fiona S. L. Brinkman
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
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23
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Bertelli C, Tilley KE, Brinkman FSL. Microbial genomic island discovery, visualization and analysis. Brief Bioinform 2020; 20:1685-1698. [PMID: 29868902 PMCID: PMC6917214 DOI: 10.1093/bib/bby042] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/30/2018] [Indexed: 12/27/2022] Open
Abstract
Horizontal gene transfer (also called lateral gene transfer) is a major mechanism for microbial genome evolution, enabling rapid adaptation and survival in specific niches. Genomic islands (GIs), commonly defined as clusters of bacterial or archaeal genes of probable horizontal origin, are of particular medical, environmental and/or industrial interest, as they disproportionately encode virulence factors and some antimicrobial resistance genes and may harbor entire metabolic pathways that confer a specific adaptation (solvent resistance, symbiosis properties, etc). As large-scale analyses of microbial genomes increases, such as for genomic epidemiology investigations of infectious disease outbreaks in public health, there is increased appreciation of the need to accurately predict and track GIs. Over the past decade, numerous computational tools have been developed to tackle the challenges inherent in accurate GI prediction. We review here the main types of GI prediction methods and discuss their advantages and limitations for a routine analysis of microbial genomes in this era of rapid whole-genome sequencing. An assessment is provided of 20 GI prediction software methods that use sequence-composition bias to identify the GIs, using a reference GI data set from 104 genomes obtained using an independent comparative genomics approach. Finally, we present guidelines to assist researchers in effectively identifying these key genomic regions.
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Affiliation(s)
- Claire Bertelli
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Keith E Tilley
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Fiona S L Brinkman
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
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24
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Ma L, Zhang W, Liu Z, Huang Y, Zhang Q, Tian X, Zhang C, Zhu Y. Complete genome sequence of Streptomyces sp. SCSIO 03032 isolated from Indian Ocean sediment, producing diverse bioactive natural products. Mar Genomics 2020; 55:100803. [PMID: 33517980 DOI: 10.1016/j.margen.2020.100803] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 06/19/2020] [Accepted: 06/25/2020] [Indexed: 12/13/2022]
Abstract
Streptomyces sp. SCSIO 03032, isolated from a deep-sea sediment sample (-3412 m) from the Indian Ocean, produces several classes of bioactive compounds including α-pyridone antibiotics (piericidins), polycyclic macrolactams (heronamides) and bisindole alkaloids (spiroindimicins, indimicins and lynamicins). Here we report the complete genome sequence of Streptomyces sp. SCSIO 03032, which consists of a 6,287,975 bp linear chromosome. The genome analysis reveals the presence of 29 putative biosynthetic gene clusters for secondary metabolites, including those for piericidins, heronamides and spiroindimicins/indimicins/lynamicins. The genome sequence suggests that Streptomyces sp. SCSIO 03032 could be a producer for novel bioactive natural products with potential applications in drug discovery.
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Affiliation(s)
- Liang Ma
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Wenjun Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Zhiwen Liu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Yanbing Huang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China; Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning 530007, China
| | - Qingbo Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Xinpeng Tian
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Changsheng Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Yiguang Zhu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China.
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25
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The Basis for Natural Multiresistance to Phage in Pseudomonas aeruginosa. Antibiotics (Basel) 2020; 9:antibiotics9060339. [PMID: 32570896 PMCID: PMC7344871 DOI: 10.3390/antibiotics9060339] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/01/2020] [Accepted: 06/16/2020] [Indexed: 01/21/2023] Open
Abstract
Pseudomonas aeruginosa is responsible for long-term infections and is particularly resistant to treatments when hiding inside the extracellular matrix or biofilms. Phage therapy might represent an alternative to antibiotic treatment, but up to 10% of clinical strains appear to resist multiple phages. We investigated the characteristics of P. aeruginosa clinical strains naturally resistant to phages and compared them to highly susceptible strains. The phage-resistant strains were defective in lipopolysaccharide (LPS) biosynthesis, were nonmotile and displayed an important degree of autolysis, releasing phages and pyocins. Complete genome sequencing of three resistant strains showed the existence of a large accessory genome made of multiple insertion elements, genomic islands, pyocins and prophages, including two phages performing lateral transduction. Mutations were found in genes responsible for the synthesis of LPS and/or type IV pilus, the major receptors for most phages. CRISPR-Cas systems appeared to be absent or inactive in phage-resistant strains, confirming that they do not play a role in the resistance to lytic phages but control the insertion of exogenous sequences. We show that, despite their apparent weakness, the multiphage-resistant strains described in this study displayed selective advantages through the possession of various functions, including weapons to eliminate other strains of the same or closely related species.
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26
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Shao S, van Heusden GPH, Hooykaas PJJ. Complete Sequence of Succinamopine Ti-Plasmid pTiEU6 Reveals Its Evolutionary Relatedness with Nopaline-Type Ti-Plasmids. Genome Biol Evol 2020; 11:2480-2491. [PMID: 31386108 PMCID: PMC6733357 DOI: 10.1093/gbe/evz173] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/05/2019] [Indexed: 01/14/2023] Open
Abstract
Agrobacterium tumefaciens is the etiological agent of plant crown gall disease, which is induced by the delivery of a set of oncogenic genes into plant cells from its tumor-inducing (Ti) plasmid. Here we present the first complete sequence of a succinamopine-type Ti-plasmid. Plasmid pTiEU6 is comprised of 176,375 bp with an overall GC content of 56.1% and 195 putative protein-coding sequences could be identified. This Ti-plasmid is most closely related to nopaline-type Ti-plasmids. It contains a single T-region which is somewhat smaller than that of the nopaline-type Ti-plasmids and in which the gene for nopaline synthesis is replaced by a gene (sus) for succinamopine synthesis. Also in pTiEU6 the nopaline catabolic genes are replaced by genes for succinamopine catabolism. In order to trace the evolutionary origin of pTiEU6, we sequenced six nopaline Ti-plasmids to enlarge the scope for comparison to this class of plasmids. Average nucleotide identity analysis revealed that pTiEU6 was most closely related to nopaline Ti-plasmids pTiT37 and pTiSAKURA. In line with this traces of several transposable elements were present in all the nopaline Ti plasmids and in pTiEU6, but one specific transposable element insertion, that of a copy of IS1182, was present at the same site only in pTiEU6, pTiT37, and pTiSAKURA, but not in the other Ti plasmids. This suggests that pTiEU6 evolved after diversification of nopaline Ti-plasmids by DNA recombination between a pTiT37-like nopaline Ti-plasmid and another plasmid, thus introducing amongst others new catabolic genes matching a new opine synthase gene for succinamopine synthesis.
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Affiliation(s)
- Shuai Shao
- Molecular and Developmental Genetics, Institute of Biology, Leiden University, The Netherlands
| | - G Paul H van Heusden
- Molecular and Developmental Genetics, Institute of Biology, Leiden University, The Netherlands
| | - Paul J J Hooykaas
- Molecular and Developmental Genetics, Institute of Biology, Leiden University, The Netherlands
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27
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Nascimento FX, Hernández AG, Glick BR, Rossi MJ. Plant growth-promoting activities and genomic analysis of the stress-resistant Bacillus megaterium STB1, a bacterium of agricultural and biotechnological interest. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2020; 25:e00406. [PMID: 31886139 PMCID: PMC6920507 DOI: 10.1016/j.btre.2019.e00406] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/05/2019] [Accepted: 12/01/2019] [Indexed: 12/14/2022]
Abstract
In this work, the stress-resistant Bacillus megaterium STB1 is characterized and its ability to promote plant growth under normal and stress conditions is demonstrated. The genomic sequence of this bacterium, and a detailed analysis of the genes involved in facilitating its stress resistance and plant growth-promoting activities is also reported. The B. megaterium STB1 genome is rich in genetic elements involved in multiple stress resistance, xenobiotic degradation, pathogen antagonistic activities, and other traits related to soil and rhizosphere colonization. Moreover, genes participating in the biosynthesis of auxins and cytokinins, the modulation of polyamines, GABA, brassinosteroids and ethylene levels were also found. Ultimately, this study brings new insights into the role of B. megaterium as a plant growth-promoting bacterium and opens new opportunities for the development of novel strategies for agriculture and biotechnology.
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Affiliation(s)
- Francisco X. Nascimento
- IBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, 2780-157, Portugal
- Laboratório de Microbiologia e Bioprocessos, MIP-CCB, Universidade Federal de Santa Catarina, Florianópolis, SC, 88040-900, Brazil
| | - Anabel G. Hernández
- Laboratório de Microbiologia e Bioprocessos, MIP-CCB, Universidade Federal de Santa Catarina, Florianópolis, SC, 88040-900, Brazil
| | - Bernard R. Glick
- Department of Biology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Márcio J. Rossi
- Laboratório de Microbiologia e Bioprocessos, MIP-CCB, Universidade Federal de Santa Catarina, Florianópolis, SC, 88040-900, Brazil
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28
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Puri A, Bajaj A, Verma H, Kumar R, Singh Y, Lal R. Complete genome sequence of Paracoccus sp. strain AK26: Insights into multipartite genome architecture and methylotropy. Genomics 2020; 112:2572-2582. [PMID: 32057914 DOI: 10.1016/j.ygeno.2020.02.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 01/01/2020] [Accepted: 02/10/2020] [Indexed: 11/26/2022]
Abstract
The present study reports the functional annotation of complete genome of methylotrophic bacterium Paracoccus sp. strain AK26. The 3.6 Mb genome with average GC content of 65.7% was distributed across five replicons; including chromosome (2.7 Mb) and four extrachromosomal replicons pAK1 (471Kb), pAK2 (189Kb), pAK3 (129Kb) and pAK4 (84 Kb). Interestingly, nearly 23% of the Cluster of Orthologous Group (COG) of proteins were annotated on extrachromosomal replicons and 185Kb genome content was attributed to segregated 19 genomic island regions. Among the four replicons, pAK4 was identified as essential and integral part of the genome, as supported by codon usage, GC content (66%) and synteny analysis. Comparative genome analysis for methylotrophy showed mechanistic variations in oxidation and assimilation of C1 compounds among closely related Paracoccus spp. Collectively, present study reports the functional characterization and genomic architecture of strain AK26 and provides genetic basis for quinone and isoprenoid based secondary metabolites synthesis using strain AK26.
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Affiliation(s)
- Akshita Puri
- Department of Zoology, University of Delhi, Delhi, India
| | - Abhay Bajaj
- Department of Zoology, University of Delhi, Delhi, India; National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Helianthous Verma
- Department of Zoology, University of Delhi, Delhi, India; Ramjas college, University of Delhi, India
| | - Roshan Kumar
- Department of Zoology, University of Delhi, Delhi, India; P.G. Department of Zoology, Magadh University, Bodh-Gaya, 824234, Bihar, India
| | - Yogendra Singh
- Department of Zoology, University of Delhi, Delhi, India.
| | - Rup Lal
- Department of Zoology, University of Delhi, Delhi, India; NASI Senior Scientist Platinum Jubilee Fellow, The Energy and Resources Institute Darbari Seth Block, IHC Complex, Lodhi Road, New Delhi 110003, India.
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29
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Zhang Y, Wang Y, Qin Y, Li P. Complete genome sequence of Bacillus velezensis LPL-K103, an antifungal cyclic lipopeptide bacillomycin L producer from the surface of lemon. 3 Biotech 2020; 10:8. [PMID: 31844600 PMCID: PMC6889109 DOI: 10.1007/s13205-019-1995-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 11/18/2019] [Indexed: 11/28/2022] Open
Abstract
Bacillus velezensis LPL-K103, which shows strong antifungal function, was isolated from the surface of lemon in Beijing, China. The complete genome of B. velezensis LPL-K103 contains a circular chromosome of 3,933,292 bp (46.61% G+C content). According to genomic analysis, 4080 protein-coding genes, 113 RNAs (27 rRNAs + 86 tRNAs), and a non-ribosomal peptide synthase gene cluster involved in antifungal cyclic lipopeptide bacillomycin L biosynthesis were identified. Here, we propose that the biosynthesis pathway of bacillomycin L in LPL-K103 depends on its genome information.
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Affiliation(s)
- Ying Zhang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Key Laboratory of Functional Dairy, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083 China
| | - Yao Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Key Laboratory of Functional Dairy, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083 China
| | - Yuxuan Qin
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Key Laboratory of Functional Dairy, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083 China
| | - Pinglan Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Key Laboratory of Functional Dairy, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083 China
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30
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Wang X, Yu M, Wang L, Lin H, Li B, Xue CX, Sun H, Zhang XH. Comparative genomic and metabolic analysis of manganese-oxidizing mechanisms in Celeribacter manganoxidans DY25 T: Its adaptation to the environment of polymetallic nodules. Genomics 2019; 112:2080-2091. [PMID: 31809796 DOI: 10.1016/j.ygeno.2019.12.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 11/23/2019] [Accepted: 12/02/2019] [Indexed: 11/28/2022]
Abstract
Manganese (Mn) nodule is one of the ubiquitous polymetallic concretions and mainly consists of Mn - Fe oxi-hydroxide precipitations. A primary oxidation of Mn(II) to MnO2, in which microorganisms may play important roles, is followed by agglomeration of MnO2 into nodules. Celeribater manganoxidans DY25T, belonging to family Rhodobacteraceae, has ability to catalyze the formation of MnO2 [1]. The concentration of MnO2 formed by harvested cells reached 7.08 μM after suspended in 10 mM HEPES (pH 7.5). Genomic and physiological characteristics of strain DY25T provided a better understanding of its Mn-oxidizing mechanism. Fifteen genes (including four multicopper oxidases) may be involved in Mn(II)-oxidation, whereas only three of them can promote this process. Sulfur-oxidizing activity was detected, which may be associated with manganese oxidation. Genes involved in import and export of primary elemental ingredients (C, N, P and S) and metallic elements (e.g. Mn) were discovered, demonstrating its potential roles in the biogeochemical cycle.
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Affiliation(s)
- Xiaolei Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Min Yu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Long Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Heyu Lin
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Bei Li
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Chun-Xu Xue
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Hao Sun
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Xiao-Hua Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
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31
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Smyrli M, Triga A, Dourala N, Varvarigos P, Pavlidis M, Quoc VH, Katharios P. Comparative Study on A Novel Pathogen of European Seabass. Diversity of Aeromonas veronii in the Aegean Sea. Microorganisms 2019; 7:microorganisms7110504. [PMID: 31671797 PMCID: PMC6921072 DOI: 10.3390/microorganisms7110504] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/16/2019] [Accepted: 10/25/2019] [Indexed: 01/01/2023] Open
Abstract
Aeromonas veronii is an emerging pathogen causing severe pathology and mortalities in European seabass aquaculture in the Aegean Sea, Mediterranean. More than 50 strains of the pathogen were characterized biochemically and genetically in order to study the epidemiology of the disease, as well as the phylogeny and virulence of the bacterium. Based on the phenotypic characteristics, the isolates form three groups consisting of: (a) the West Aegean Sea, non-motile, non-pigment-producing strains, (b) the West Aegean Sea, motile, and pigment-producing strains and (c) the East Aegean Sea motile strains that produce minute amounts of pigment. All strains were highly similar at the genomic level; however, the pattern of West/East geographic origin was reflected in biochemical properties, in general genomic level comparison and in the putative virulent factors studied. Type VI secretion system was not detected in the western strains. The outer membrane protein (OMP) profile which contains proteins that are putative antigenic factors, was very similar between strains from the different areas. Although most of the OMPs were detected in all strains with great sequence similarity, diversification according to geographic origin was evident in known antigenic factors such as the maltoporin LamB. A systematic comparative analysis of the strains is presented and discussed in view of the emergence of A. veronii as a significant pathogen for the Mediterranean aquaculture.
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Affiliation(s)
- Maria Smyrli
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, 71500 Crete, Greece.
- Department of Biology, University of Crete, Heraklion, 70013 Crete, Greece.
| | - Adriana Triga
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, 71500 Crete, Greece.
- Department of Biology, University of Crete, Heraklion, 70013 Crete, Greece.
| | - Nancy Dourala
- Fish Pathology Department, Selonda Aquaculture, 15125 Athens, Greece.
| | | | - Michael Pavlidis
- Department of Biology, University of Crete, Heraklion, 70013 Crete, Greece.
| | - Viet Ha Quoc
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, 71500 Crete, Greece.
| | - Pantelis Katharios
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, 71500 Crete, Greece.
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32
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Freschi L, Bertelli C, Jeukens J, Moore MP, Kukavica-Ibrulj I, Emond-Rheault JG, Hamel J, Fothergill JL, Tucker NP, McClean S, Klockgether J, de Soyza A, Brinkman FSL, Levesque RC, Winstanley C. Genomic characterisation of an international Pseudomonas aeruginosa reference panel indicates that the two major groups draw upon distinct mobile gene pools. FEMS Microbiol Lett 2019; 365:5035990. [PMID: 29897457 DOI: 10.1093/femsle/fny120] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 05/14/2018] [Indexed: 12/25/2022] Open
Abstract
Pseudomonas aeruginosa is an important opportunistic pathogen, especially in the context of infections of cystic fibrosis (CF). In order to facilitate coordinated study of this pathogen, an international reference panel of P. aeruginosa isolates was assembled. Here we report the genome sequencing and analysis of 33 of these isolates and 7 reference genomes to further characterise this panel. Core genome single nucleotide variant phylogeny demonstrated that the panel strains are widely distributed amongst the P. aeruginosa population. Common loss-of-function mutations reported as adaptive during CF (such as in mucA and mexA) were identified amongst isolates from chronic respiratory infections. From the 40 strains analysed, 37 unique resistomes were predicted, based on the Resistance Gene Identifier method using the Comprehensive Antibiotic Resistance Database. Notably, hierarchical clustering and phylogenetic reconstructions based on the presence/absence of genomic islands (GIs), prophages and other regions of genome plasticity (RGPs) supported the subdivision of P. aeruginosa into two main groups. This is the largest, most diverse analysis of GIs and associated RGPs to date, and the results suggest that, at least at the largest clade grouping level (group 1 vs group 2), each group may be drawing upon distinct mobile gene pools.
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Affiliation(s)
- Luca Freschi
- Institute for Integrative and Systems Biology (IBIS), University Laval, Québec City, QC G1V 0A6, Canada
| | - Claire Bertelli
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.,Institute of Microbiology, University Hospital Center and University of Lausanne, CH-1011 Lausanne, Switzerland
| | - Julie Jeukens
- Institute for Integrative and Systems Biology (IBIS), University Laval, Québec City, QC G1V 0A6, Canada
| | - Matthew P Moore
- Institute of Infection and Global Health, University of Liverpool, Liverpool L69 7BE, UK
| | - Irena Kukavica-Ibrulj
- Institute for Integrative and Systems Biology (IBIS), University Laval, Québec City, QC G1V 0A6, Canada
| | | | - Jérémie Hamel
- Institute for Integrative and Systems Biology (IBIS), University Laval, Québec City, QC G1V 0A6, Canada
| | - Joanne L Fothergill
- Institute of Microbiology, University Hospital Center and University of Lausanne, CH-1011 Lausanne, Switzerland
| | - Nicholas P Tucker
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK
| | - Siobhán McClean
- Centre of Microbial Host Interactions, Institute of Technology Tallaght, Tallaght, Dublin D24 FKT9, Ireland
| | - Jens Klockgether
- Clinic for Paediatric Pneumology, Allergology, and Neonatology, Hannover Medical School, D-30625, Hannover, Germany
| | - Anthony de Soyza
- Institute for Cellular Medicine, Newcastle University, Newcastle-upon-Tyne NE2 4HH, UK
| | - Fiona S L Brinkman
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Roger C Levesque
- Institute for Integrative and Systems Biology (IBIS), University Laval, Québec City, QC G1V 0A6, Canada
| | - Craig Winstanley
- Institute of Infection and Global Health, University of Liverpool, Liverpool L69 7BE, UK
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Vrbovská V, Kovařovic V, Mašlaňová I, Indráková A, Petráš P, Šedo O, Švec P, Fišarová L, Šiborová M, Mikulášek K, Sedláček I, Doškař J, Pantůček R. Staphylococcus petrasii diagnostics and its pathogenic potential enhanced by mobile genetic elements. Int J Med Microbiol 2019; 309:151355. [PMID: 31563331 DOI: 10.1016/j.ijmm.2019.151355] [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: 06/05/2019] [Revised: 08/29/2019] [Accepted: 09/04/2019] [Indexed: 11/16/2022] Open
Abstract
Staphylococcus petrasii is recently described coagulase negative staphylococcal species and an opportunistic human pathogen, still often misidentified in clinical specimens. Four subspecies are distinguished in S. petrasii by polyphasic taxonomical analyses, however a comparative study has still not been done on the majority of isolates and their genome properties have not yet been thoroughly analysed. Here, we describe the phenotypic and genotypic characteristics of 65 isolates and the results of de novo sequencing, whole genome assembly and annotation of draft genomes of five strains. The strains were identified by MALDI-TOF mass spectrometry to the species level and the majority of the strains were identified to the subspecies level by fingerprinting methods, (GTG)5 repetitive PCR and ribotyping. Macrorestriction profiling by pulsed-field gel electrophoresis was confirmed to be a suitable strain typing method. Comparative genomics revealed the presence of new mobile genetic elements carrying antimicrobial resistance factors such as staphylococcal cassette chromosome (SCC) mec, transposones, phage-inducible genomic islands, and plasmids. Their mosaic structure and similarity across coagulase-negative staphylococci and Staphylococcus aureus suggest the possible exchange of these elements. Numerous putative virulence factors such as adhesins, autolysins, exoenzymes, capsule formation genes, immunomodulators, the phage-associated sasX gene, and SCC-associated spermidine N-acetyltransferase gene, pseudouridine and sorbitol utilization operons might explain clinical manifestations of S. petrasii isolates. The increasing recovery of S. petrasii isolates from human clinical material, the multi-drug resistance including methicillin resistance of S. petrasii subsp. jettensis strains, and virulence factors homologous to other pathogenic staphylococci demonstrate the importance of the species in human disease.
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Affiliation(s)
- Veronika Vrbovská
- Division of Genetics and Molecular Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Vojtěch Kovařovic
- Division of Genetics and Molecular Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Ivana Mašlaňová
- Division of Genetics and Molecular Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Adéla Indráková
- Division of Genetics and Molecular Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Petr Petráš
- Reference Laboratory for Staphylococci, National Institute of Public Health, Šrobárova 48, 100 42 Praha 10, Czech Republic
| | - Ondrej Šedo
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Pavel Švec
- Czech Collection of Microorganisms, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Lenka Fišarová
- Division of Genetics and Molecular Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Marta Šiborová
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Kamil Mikulášek
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; National Centre for Biomolecular Research, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Ivo Sedláček
- Czech Collection of Microorganisms, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jiří Doškař
- Division of Genetics and Molecular Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Roman Pantůček
- Division of Genetics and Molecular Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic.
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Tan X, Qiu H, Li F, Cheng D, Zheng X, Wang B, Huang M, Li W, Li Y, Sang K, Song B, Du J, Chen H, Xie C. Complete Genome Sequence of Sequevar 14M Ralstonia solanacearum Strain HA4-1 Reveals Novel Type III Effectors Acquired Through Horizontal Gene Transfer. Front Microbiol 2019; 10:1893. [PMID: 31474968 PMCID: PMC6703095 DOI: 10.3389/fmicb.2019.01893] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 07/31/2019] [Indexed: 01/08/2023] Open
Abstract
Ralstonia solanacearum, which causes bacterial wilt in a broad range of plants, is considered a "species complex" due to its significant genetic diversity. Recently, we have isolated a new R. solanacearum strain HA4-1 from Hong'an county in Hubei province of China and identified it being phylotype I, sequevar 14M (phylotype I-14M). Interestingly, we found that it can cause various disease symptoms among different potato genotypes and display different pathogenic behavior compared to a phylogenetically related strain, GMI1000. To dissect the pathogenic mechanisms of HA4-1, we sequenced its whole genome by combined sequencing technologies including Illumina HiSeq2000, PacBio RS II, and BAC-end sequencing. Genome assembly results revealed the presence of a conventional chromosome, a megaplasmid as well as a 143 kb plasmid in HA4-1. Comparative genome analysis between HA4-1 and GMI1000 shows high conservation of the general virulence factors such as secretion systems, motility, exopolysaccharides (EPS), and key regulatory factors, but significant variation in the repertoire and structure of type III effectors, which could be the determinants of their differential pathogenesis in certain potato species or genotypes. We have identified two novel type III effectors that were probably acquired through horizontal gene transfer (HGT). These novel R. solanacearum effectors display homology to several YopJ and XopAC family members. We named them as RipBR and RipBS. Notably, the copy of RipBR on the plasmid is a pseudogene, while the other on the megaplasmid is normal. For RipBS, there are three copies located in the megaplasmid and plasmid, respectively. Our results have not only enriched the genome information on R. solanacearum species complex by sequencing the first sequevar 14M strain and the largest plasmid reported in R. solanacearum to date but also revealed the variation in the repertoire of type III effectors. This will greatly contribute to the future studies on the pathogenic evolution, host adaptation, and interaction between R. solanacearum and potato.
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Affiliation(s)
- Xiaodan Tan
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- National Center for Vegetable Improvement (Central China), Wuhan, China
| | - Huishan Qiu
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- National Center for Vegetable Improvement (Central China), Wuhan, China
| | - Feng Li
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- National Center for Vegetable Improvement (Central China), Wuhan, China
| | - Dong Cheng
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- National Center for Vegetable Improvement (Central China), Wuhan, China
| | - Xueao Zheng
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- National Center for Vegetable Improvement (Central China), Wuhan, China
| | - Bingsen Wang
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- National Center for Vegetable Improvement (Central China), Wuhan, China
| | - Mengshu Huang
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- National Center for Vegetable Improvement (Central China), Wuhan, China
| | - Wenhao Li
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- National Center for Vegetable Improvement (Central China), Wuhan, China
| | - Yanping Li
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- National Center for Vegetable Improvement (Central China), Wuhan, China
| | - Kangqi Sang
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Botao Song
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- National Center for Vegetable Improvement (Central China), Wuhan, China
| | - Juan Du
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- National Center for Vegetable Improvement (Central China), Wuhan, China
| | - Huilan Chen
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- National Center for Vegetable Improvement (Central China), Wuhan, China
| | - Conghua Xie
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- National Center for Vegetable Improvement (Central China), Wuhan, China
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35
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González-Escalona N, Allard MA, Brown EW, Sharma S, Hoffmann M. Nanopore sequencing for fast determination of plasmids, phages, virulence markers, and antimicrobial resistance genes in Shiga toxin-producing Escherichia coli. PLoS One 2019; 14:e0220494. [PMID: 31361781 PMCID: PMC6667211 DOI: 10.1371/journal.pone.0220494] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 07/17/2019] [Indexed: 02/02/2023] Open
Abstract
Whole genome sequencing can provide essential public health information. However, it is now known that widely used short-read methods have the potential to miss some randomly-distributed segments of genomes. This can prevent phages, plasmids, and virulence factors from being detected or properly identified. Here, we compared assemblies of three complete Shiga toxin-producing Escherichia coli (STEC) O26:H11/H- genomes from two different sequence types (ST21 and 29), each acquired using the Nextera XT MiSeq, MinION nanopore-based sequencing, and Pacific Biosciences (PacBio) sequencing. Each closed genome consisted of a single chromosome, approximately 5.7 Mb for CFSAN027343, 5.6 Mb for CFSAN027346, and 5.4 MB for CFSAN027350. However, short-read whole genome sequencing (WGS) using Nextera XT MiSeq failed to identify some virulence genes in plasmids and on the chromosome, both of which were detected using the long-read platforms. Results from long-read MinION and PacBio allowed us to identify differences in plasmid content: a single 88 kb plasmid in CFSAN027343; a 157kb plasmid in CFSAN027350; and two plasmids in CFSAN027346 (one 95 Kb, one 72 Kb). These data enabled rapid characterization of the virulome, detection of antimicrobial genes, and composition/location of Stx phages. Taken together, positive correlations between the two long-read methods for determining plasmids, virulome, antimicrobial resistance genes, and phage composition support MinION sequencing as one accurate and economical option for closing STEC genomes and identifying specific virulence markers.
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Affiliation(s)
- Narjol González-Escalona
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States of America
- * E-mail:
| | - Marc A. Allard
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States of America
| | - Eric W. Brown
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States of America
| | - Shashi Sharma
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States of America
| | - Maria Hoffmann
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States of America
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36
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Bertelli C, Brinkman FSL. Improved genomic island predictions with IslandPath-DIMOB. Bioinformatics 2019; 34:2161-2167. [PMID: 29905770 PMCID: PMC6022643 DOI: 10.1093/bioinformatics/bty095] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 02/21/2018] [Indexed: 11/23/2022] Open
Abstract
Motivation Genomic islands (GIs) are clusters of genes of probable horizontal origin that play a major role in bacterial and archaeal genome evolution and microbial adaptability. They are of high medical and industrial interest, due to their enrichment in virulence factors, some antimicrobial resistance genes and adaptive metabolic pathways. The development of more sensitive but precise prediction tools, using either sequence composition-based methods or comparative genomics, is needed as large-scale analyses of microbial genomes increase. Results IslandPath-DIMOB, a leading GI prediction tool in the IslandViewer webserver, has now been significantly improved by modifying both the decision algorithm to determine sequence composition biases, and the underlying database of HMM profiles for associated mobility genes. The accuracy of IslandPath-DIMOB and other major software has been assessed using a reference GI dataset predicted by comparative genomics, plus a manually curated dataset from literature review. Compared to the previous version (v0.2.0), this IslandPath-DIMOB v1.0.0 achieves 11.7% and 5.3% increase in recall and precision, respectively. IslandPath-DIMOB has the highest Matthews correlation coefficient among individual prediction methods tested, combining one of the highest recall measures (46.9%) at high precision (87.4%). The only method with higher recall had notably lower precision (55.1%). This new IslandPath-DIMOB v1.0.0 will facilitate more accurate studies of GIs, including their key roles in microbial adaptability of medical, environmental and industrial interest. Availability and implementation IslandPath-DIMOB v1.0.0 is freely available through the IslandViewer webserver {{http://www.pathogenomics.sfu.ca/islandviewer/}} and as standalone software {{https://github.com/brinkmanlab/islandpath/}} under the GNU-GPLv3. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Claire Bertelli
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Fiona S L Brinkman
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
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37
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Bertelli C, Laird MR, Williams KP, Lau BY, Hoad G, Winsor GL, Brinkman FSL. IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets. Nucleic Acids Res 2019; 45:W30-W35. [PMID: 28472413 PMCID: PMC5570257 DOI: 10.1093/nar/gkx343] [Citation(s) in RCA: 913] [Impact Index Per Article: 182.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 04/18/2017] [Indexed: 11/14/2022] Open
Abstract
IslandViewer (http://www.pathogenomics.sfu.ca/islandviewer/) is a widely-used webserver for the prediction and interactive visualization of genomic islands (GIs, regions of probable horizontal origin) in bacterial and archaeal genomes. GIs disproportionately encode factors that enhance the adaptability and competitiveness of the microbe within a niche, including virulence factors and other medically or environmentally important adaptations. We report here the release of IslandViewer 4, with novel features to accommodate the needs of larger-scale microbial genomics analysis, while expanding GI predictions and improving its flexible visualization interface. A user management web interface as well as an HTTP API for batch analyses are now provided with a secured authentication to facilitate the submission of larger numbers of genomes and the retrieval of results. In addition, IslandViewer's integrated GI predictions from multiple methods have been improved and expanded by integrating the precise Islander method for pre-computed genomes, as well as an updated IslandPath-DIMOB for both pre-computed and user-supplied custom genome analysis. Finally, pre-computed predictions including virulence factors and antimicrobial resistance are now available for 6193 complete bacterial and archaeal strains publicly available in RefSeq. IslandViewer 4 provides key enhancements to facilitate the analysis of GIs and better understand their role in the evolution of successful environmental microbes and pathogens.
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Affiliation(s)
- Claire Bertelli
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Matthew R Laird
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kelly P Williams
- Systems Biology Department, Sandia National Laboratories, Livermore, CA 94551, USA
| | | | - Britney Y Lau
- Systems Biology Department, Sandia National Laboratories, Livermore, CA 94551, USA
| | - Gemma Hoad
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Geoffrey L Winsor
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Fiona S L Brinkman
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
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Subhadra B, Surendran S, Lim BR, Yim JS, Kim DH, Woo K, Han K, Oh MH, Choi CH. Complete genome sequence and phylogenetic analysis of nosocomial pathogen Acinetobacter nosocomialis strain NCTC 8102. Genes Genomics 2019; 41:1063-1075. [PMID: 31177378 DOI: 10.1007/s13258-019-00834-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 05/20/2019] [Indexed: 10/26/2022]
Abstract
BACKGROUND Acinetobacter has emerged recently as one of the most challenging nosocomial pathogens because of its increased rate of antimicrobial resistance. The genetic complexity and genome diversity, as well as the lack of adequate knowledge on the pathogenic determinants of Acinetobacter strains often hinder with pathogenesis studies for the development of better therapeutics to tackle this nosocomial pathogen. OBJECTIVES In this study, we comparatively analyzed the whole genome sequence of a virulent Acinetobacternosocomialis strain NCTC 8102. METHODS The genomic DNA of A. nosocomialis NCTC 8102 was isolated and sequenced using PacBio RS II platform. The sequenced genome was functionally annotated and gene prediction was carried out using the program, Glimmer 3. The phylogenetic analysis of the genome was performed using Mega 6 program and the comparative genome analysis was carried out by BLAST (Basic Local Alignment Search Tool). RESULTS The complete genome analysis depicted that the genome consists of a circular chromosome with an average G + C content of 38.7%. The genome comprises 3700 protein-coding genes, 96 RNA genes (18 rRNA, 74 tRNA and 4 ncRNA genes), and 91 pseudogenes. In addition, 6 prophage regions comprising 2 intact, 1 incomplete and 3 questionable ones and 18 genomic islands were identified in the genome, suggesting the possible occurrence of horizontal gene transfer in this strain. Comparative genome analysis of A. nosocomialis NCTC 8102 genome with the already sequenced A. nosocomialis strain SSA3 showed an average nucleotide identity of 99.0%. In addition, the number of prophages and genomic islands were higher in the A. nosocomialis NCTC 8102 genome compared to that of the strain SSA3. 14 of the genomic islands were unique to A. nosocomialis NCTC 8102 compared to strain SSA3 and they harbored genes which are involved in virulence, multidrug resistance, biofilm formation and bacterial pathogenesis. CONCLUSION We sequenced the whole genome of A. nosocomialis strain NCTC 8102 followed by comparatively genome analysis. The study provides valuable information on the genetic features of A. nosocomialis strain and the data from this study would assist in further studies for the development of control measures for this nosocomial pathogen.
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Affiliation(s)
- Bindu Subhadra
- Department of Microbiology and Medical Science, Chungnam National University School of Medicine, 266 Munwha-ro, Jung-gu, Daejeon, 35015, South Korea
| | - Surya Surendran
- Department of Microbiology and Medical Science, Chungnam National University School of Medicine, 266 Munwha-ro, Jung-gu, Daejeon, 35015, South Korea
| | - Bo Ra Lim
- Department of Microbiology and Medical Science, Chungnam National University School of Medicine, 266 Munwha-ro, Jung-gu, Daejeon, 35015, South Korea
| | - Jong-Sung Yim
- Department of Microbiology and Medical Science, Chungnam National University School of Medicine, 266 Munwha-ro, Jung-gu, Daejeon, 35015, South Korea
| | - Dong Ho Kim
- Department of Microbiology and Medical Science, Chungnam National University School of Medicine, 266 Munwha-ro, Jung-gu, Daejeon, 35015, South Korea
| | - Kyungho Woo
- Department of Microbiology and Medical Science, Chungnam National University School of Medicine, 266 Munwha-ro, Jung-gu, Daejeon, 35015, South Korea
| | - Kyudong Han
- Department of Nanobiomedical Science, Dankook University, 119 Dandae-ro, Dongnam-gu, Cheonan, 31116, South Korea.,BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, South Korea
| | - Man Hwan Oh
- Department of Nanobiomedical Science, Dankook University, 119 Dandae-ro, Dongnam-gu, Cheonan, 31116, South Korea.
| | - Chul Hee Choi
- Department of Microbiology and Medical Science, Chungnam National University School of Medicine, 266 Munwha-ro, Jung-gu, Daejeon, 35015, South Korea.
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Nusrat S, Harbig T, Gehlenborg N. Tasks, Techniques, and Tools for Genomic Data Visualization. COMPUTER GRAPHICS FORUM : JOURNAL OF THE EUROPEAN ASSOCIATION FOR COMPUTER GRAPHICS 2019; 38:781-805. [PMID: 31768085 PMCID: PMC6876635 DOI: 10.1111/cgf.13727] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Genomic data visualization is essential for interpretation and hypothesis generation as well as a valuable aid in communicating discoveries. Visual tools bridge the gap between algorithmic approaches and the cognitive skills of investigators. Addressing this need has become crucial in genomics, as biomedical research is increasingly data-driven and many studies lack well-defined hypotheses. A key challenge in data-driven research is to discover unexpected patterns and to formulate hypotheses in an unbiased manner in vast amounts of genomic and other associated data. Over the past two decades, this has driven the development of numerous data visualization techniques and tools for visualizing genomic data. Based on a comprehensive literature survey, we propose taxonomies for data, visualization, and tasks involved in genomic data visualization. Furthermore, we provide a comprehensive review of published genomic visualization tools in the context of the proposed taxonomies.
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Affiliation(s)
- S Nusrat
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - T Harbig
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - N Gehlenborg
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
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Duprey A, Taib N, Leonard S, Garin T, Flandrois JP, Nasser W, Brochier-Armanet C, Reverchon S. The phytopathogenic nature of Dickeya aquatica 174/2 and the dynamic early evolution of Dickeya pathogenicity. Environ Microbiol 2019; 21:2809-2835. [PMID: 30969462 DOI: 10.1111/1462-2920.14627] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/04/2019] [Accepted: 04/08/2019] [Indexed: 12/13/2022]
Abstract
Dickeya is a genus of phytopathogenic enterobacterales causing soft rot in a variety of plants (e.g. potato, chicory, maize). Among the species affiliated to this genus, Dickeya aquatica, described in 2014, remained particularly mysterious because it had no known host. Furthermore, while D. aquatica was proposed to represent a deep-branching species among Dickeya genus, its precise phylogenetic position remained elusive. Here, we report the complete genome sequence of the D. aquatica type strain 174/2. We demonstrate the affinity of D. aquatica strain 174/2 for acidic fruits such as tomato and cucumber and show that exposure of this bacterium to acidic pH induces twitching motility. An in-depth phylogenomic analysis of all available Dickeya proteomes pinpoints D. aquatica as the second deepest branching lineage within this genus and reclassifies two lineages that likely correspond to new genomospecies (gs.): Dickeya gs. poaceaephila (Dickeya sp NCPPB 569) and Dickeya gs. undicola (Dickeya sp 2B12), together with a new putative genus, tentatively named Prodigiosinella. Finally, from comparative analyses of Dickeya proteomes, we infer the complex evolutionary history of this genus, paving the way to study the adaptive patterns and processes of Dickeya to different environmental niches and hosts. In particular, we hypothesize that the lack of xylanases and xylose degradation pathways in D. aquatica could reflect adaptation to aquatic charophyte hosts which, in contrast to land plants, do not contain xyloglucans.
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Affiliation(s)
- Alexandre Duprey
- Univ Lyon, Université Claude Bernard Lyon 1, INSA-Lyon, CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, 10 Rue Raphaël Dubois, 69622, Villeurbanne, France
| | - Najwa Taib
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, 69622, Villeurbanne, France
| | - Simon Leonard
- Univ Lyon, Université Claude Bernard Lyon 1, INSA-Lyon, CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, 10 Rue Raphaël Dubois, 69622, Villeurbanne, France
| | - Tiffany Garin
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, 69622, Villeurbanne, France
| | - Jean-Pierre Flandrois
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, 69622, Villeurbanne, France
| | - William Nasser
- Univ Lyon, Université Claude Bernard Lyon 1, INSA-Lyon, CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, 10 Rue Raphaël Dubois, 69622, Villeurbanne, France
| | - Céline Brochier-Armanet
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, 69622, Villeurbanne, France
| | - Sylvie Reverchon
- Univ Lyon, Université Claude Bernard Lyon 1, INSA-Lyon, CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, 10 Rue Raphaël Dubois, 69622, Villeurbanne, France
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Abstract
Whole-cell and acellular pertussis vaccines are used globally against Bordetella pertussis. Various vaccine reference strains are used globally for the production of such vaccines. Whole-cell and acellular pertussis vaccines are used globally against Bordetella pertussis. Various vaccine reference strains are used globally for the production of such vaccines. We report here a draft genome sequence for Bordetella pertussis strain BP 165, which is used by the Serum Institute of India in the production of acellular pertussis vaccine.
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Du Y, Ma J, Yin Z, Liu K, Yao G, Xu W, Fan L, Du B, Ding Y, Wang C. Comparative genomic analysis of Bacillus paralicheniformis MDJK30 with its closely related species reveals an evolutionary relationship between B. paralicheniformis and B. licheniformis. BMC Genomics 2019; 20:283. [PMID: 30975079 PMCID: PMC6458615 DOI: 10.1186/s12864-019-5646-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 03/27/2019] [Indexed: 02/03/2023] Open
Abstract
Background Members of the genus Bacillus are important plant growth-promoting rhizobacteria that serve as biocontrol agents. Bacillus paralicheniformis MDJK30 is a PGPR isolated from the peony rhizosphere and can suppress plant-pathogenic bacteria and fungi. To further uncover the genetic mechanism of the plant growth-promoting traits of MDJK30 and its closely related strains, we used comparative genomics to provide insights into the genetic diversity and evolutionary relationship between B. paralicheniformis and B. licheniformis. Results A comparative genomics analysis based on B. paralicheniformis MDJK30 and 55 other previously reported Bacillus strains was performed. The evolutionary position of MDJK30 and the evolutionary relationship between B. paralicheniformis and B. licheniformis were evaluated by studying the phylogeny of the core genomes, a population structure analysis and ANI results. Comparative genomic analysis revealed various features of B. paralicheniformis that contribute to its commensal lifestyle in the rhizosphere, including an opening pan genome, a diversity of transport and the metabolism of the carbohydrates and amino acids. There are notable differences in the numbers and locations of the insertion sequences, prophages, genomic islands and secondary metabolic synthase operons between B. paralicheniformis and B. licheniformis. In particular, we found most gene clusters of Fengycin, Bacitracin and Lantipeptide were only present in B. paralicheniformis and were obtained by horizontal gene transfer (HGT), and these clusters may be used as genetic markers for distinguishing B. paralicheniformis and B. licheniformis. Conclusions This study reveals that MDJK30 and the other strains of lineage paralicheniformis present plant growth-promoting traits at the genetic level and can be developed and commercially formulated in agriculture as PGPR. Core genome phylogenies and population structure analysis has proven to be a powerful tool for differentiating B. paralicheniformis and B. licheniformis. Comparative genomic analyses illustrate the genetic differences between the paralicheniformis-licheniformis group with respect to rhizosphere adaptation. Electronic supplementary material The online version of this article (10.1186/s12864-019-5646-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuhui Du
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, TEDA College, Nankai University, Tianjin, People's Republic of China
| | - Jinjin Ma
- College of Life Sciences / National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources / Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an, People's Republic of China
| | - Zhiqiu Yin
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, TEDA College, Nankai University, Tianjin, People's Republic of China
| | - Kai Liu
- College of Life Sciences / National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources / Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an, People's Republic of China
| | - Gan Yao
- College of Life Sciences / National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources / Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an, People's Republic of China
| | - Wenfeng Xu
- State Key Laboratory of Nutrition Resources Integrated Utilization, Linshu, People's Republic of China
| | - Lingchao Fan
- State Key Laboratory of Nutrition Resources Integrated Utilization, Linshu, People's Republic of China
| | - Binghai Du
- College of Life Sciences / National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources / Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an, People's Republic of China
| | - Yanqin Ding
- College of Life Sciences / National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources / Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an, People's Republic of China.
| | - Chengqiang Wang
- College of Life Sciences / National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources / Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an, People's Republic of China.
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Nawaz F, Khan MN, Javed A, Ahmed I, Ali N, Ali MI, Bakhtiar SM, Imran M. Genomic and Functional Characterization of Enterococcus mundtii QAUEM2808, Isolated From Artisanal Fermented Milk Product Dahi. Front Microbiol 2019; 10:434. [PMID: 30972030 PMCID: PMC6443856 DOI: 10.3389/fmicb.2019.00434] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 02/19/2019] [Indexed: 12/15/2022] Open
Abstract
Microbial strains with a unique combination of technological and bioactive properties are preferred for industrial applications. The present study was conducted to evaluate the potential use of Enterococcus mundtii QAUEM2808 (NCBI Accession Number: LSMC00000000) in milk fermentation. This strain was isolated from Dahi, an indigenous fermented milk product of South-East Asia. The in vitro study confirmed the acidification ability as well as the proteolytic, cellulolytic, and amylolytic enzyme activities of this strain. It also produced a substantial amount of the folate in laboratory media and no physiological dysfunctions in laboratory animals was observed in feeding trials. All these properties were confirmed by in silico genome analysis. The Enterococcus mundtii QAUEM2808 genome consisted of a single, circular chromosome comprising 2,957,300-bp, 2,587 genes with GC content of 38.5%. Moreover, 16t RNAs, 1, 3 (16S, 23S) rRNAs, 4 ncRNAs, and 91 pseudo genes were also predicted. The majority of genome encode genes for protein, amino acids, carbohydrate, cell wall DNA and RNA metabolisms including all genes required for conversion of lactose to lactic acid. It also exhibited antimicrobial activity against E. coli ATCC 10536, S. aureus ATCC 6538, P. aeruginosa ATCC 9027, and L. monocytogenes ATCC 13932 and was found to be sensitive to commonly used antibiotics. The in silico analysis revealed the presence of genes for mundaticin and enterocin production, and CRISPER regions, however, the genes for antibiotic resistance were absent. No genes related to the pathogenicity island and prophages were detected by genome mining. Therefore, it could be inferened that Enterococcus mundtii QAUEM2808 has the potential to be used in milk fermentation as adjunct culture.
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Affiliation(s)
- Farah Nawaz
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Nadeem Khan
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Aqib Javed
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Ibrar Ahmed
- Alpha Genomics Private Limited, Islamabad, Pakistan
| | - Naeem Ali
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Ishtiaq Ali
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Syeda Mariam Bakhtiar
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, Pakistan
| | - Muhammad Imran
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
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Coagulase-Negative Staphylococci Pathogenomics. Int J Mol Sci 2019; 20:ijms20051215. [PMID: 30862021 PMCID: PMC6429511 DOI: 10.3390/ijms20051215] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 02/28/2019] [Accepted: 03/07/2019] [Indexed: 01/16/2023] Open
Abstract
Coagulase-negative Staphylococci (CoNS) are skin commensal bacteria. Besides their role in maintaining homeostasis, CoNS have emerged as major pathogens in nosocomial settings. Several studies have investigated the molecular basis for this emergence and identified multiple putative virulence factors with regards to Staphylococcus aureus pathogenicity. In the last decade, numerous CoNS whole-genome sequences have been released, leading to the identification of numerous putative virulence factors. Koch’s postulates and the molecular rendition of these postulates, established by Stanley Falkow in 1988, do not explain the microbial pathogenicity of CoNS. However, whole-genome sequence data has shed new light on CoNS pathogenicity. In this review, we analyzed the contribution of genomics in defining CoNS virulence, focusing on the most frequent and pathogenic CoNS species: S. epidermidis, S. haemolyticus, S. saprophyticus, S. capitis, and S. lugdunensis.
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Li J, Tai C, Deng Z, Zhong W, He Y, Ou HY. VRprofile: gene-cluster-detection-based profiling of virulence and antibiotic resistance traits encoded within genome sequences of pathogenic bacteria. Brief Bioinform 2019; 19:566-574. [PMID: 28077405 DOI: 10.1093/bib/bbw141] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Indexed: 11/13/2022] Open
Abstract
VRprofile is a Web server that facilitates rapid investigation of virulence and antibiotic resistance genes, as well as extends these trait transfer-related genetic contexts, in newly sequenced pathogenic bacterial genomes. The used backend database MobilomeDB was firstly built on sets of known gene cluster loci of bacterial type III/IV/VI/VII secretion systems and mobile genetic elements, including integrative and conjugative elements, prophages, class I integrons, IS elements and pathogenicity/antibiotic resistance islands. VRprofile is thus able to co-localize the homologs of these conserved gene clusters using HMMer or BLASTp searches. With the integration of the homologous gene cluster search module with a sequence composition module, VRprofile has exhibited better performance for island-like region predictions than the other widely used methods. In addition, VRprofile also provides an integrated Web interface for aligning and visualizing identified gene clusters with MobilomeDB-archived gene clusters, or a variety set of bacterial genomes. VRprofile might contribute to meet the increasing demands of re-annotations of bacterial variable regions, and aid in the real-time definitions of disease-relevant gene clusters in pathogenic bacteria of interest. VRprofile is freely available at http://bioinfo-mml.sjtu.edu.cn/VRprofile.
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Affiliation(s)
- Jun Li
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P.R.China
| | - Cui Tai
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zixin Deng
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Weihong Zhong
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P.R.China
| | - Yongqun He
- Department of microbiology and immunology research, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Hong-Yu Ou
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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Waghmode S, Suryavanshi M, Dama L, Kansara S, Ghattargi V, Das P, Banpurkar A, Satpute SK. Genomic Insights of Halophilic Planococcus maritimus SAMP MCC 3013 and Detail Investigation of Its Biosurfactant Production. Front Microbiol 2019; 10:235. [PMID: 30863371 PMCID: PMC6399143 DOI: 10.3389/fmicb.2019.00235] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 01/28/2019] [Indexed: 01/02/2023] Open
Abstract
Moderate halophilic bacteria thrive in saline conditions and produce biosurfactant (BS) which facilitates the oil scavenging activity in the oil polluted surroundings. Production of such unusual bioactive molecules plays a vital role for their survival in an extreme and adverse environment. Current research deals with isolation of Planococcus maritimus strain SAMP MCC 3013 from Indian Arabian coastline sea water for BS production. The bacterium tolerated up to 2.7 M NaCl demonstrating osmotic stress bearable physiological systems. We used integrated approach to explore the genomic insight of the strain SAMP and displayed the presence of gene for BS biosynthesis. The genome analysis revealed this potential to be intrinsic to the strain. Preliminary screening techniques viz., surface tension (SFT), drop collapse (DC) and oil displacement (OD) showed SAMP MCC 3013 as a potent BS producer. BS reduced SFT of phosphate buffer saline (PBS) pH: 7.0 from 72 to 30 mN/m with a critical micelle concentration (CMC) value of 1.3 mg/mL. Subsequent investigation on chemical characterization, using thin layer chromatography (TLC), Fourier transform infrared spectroscopy (FT-IR), nuclear magnetic resonance (1H NMR and 13C NMR) and liquid chromatography mass spectrometry (LC-MS) revealed terpene containing BS having sugar, lipid moieties. The genomic sequence analysis of P. maritimus SAMP showed complete genes in the pathway for the synthesis of terpenoid. Probably terpenoid is the accountable backbone molecule for the BS production, but the later stages of terpenoid conversion to the BS could not be found. Moreover, it is important to highlight that till today; no single report documents the in-detailed physico-chemical characterization of BS from Planococcus sp. Based on genomic and functional properties, the term terpene containing BS is denoted for the surfactant produced by P. maritimus.
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Affiliation(s)
- Samadhan Waghmode
- Department of Microbiology, Elphinstone College, University of Mumbai, Mumbai, India
| | - Mangesh Suryavanshi
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Laxmikant Dama
- Department of Zoology, DBF Dayanand College, University of Solapur, Solapur, India
| | - Shraddha Kansara
- Department of Microbiology, Savitribai Phule Pune University, Pune, India
| | - Vikas Ghattargi
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Parijat Das
- Department of Microbiology, Savitribai Phule Pune University, Pune, India
| | - Arun Banpurkar
- Department of Physics, Savitribai Phule Pune University, Pune, India
| | - Surekha K. Satpute
- Department of Microbiology, Savitribai Phule Pune University, Pune, India
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Aswani V, Najar F, Pantrangi M, Mau B, Schwan WR, Shukla SK. Virulence factor landscape of a Staphylococcus aureus sequence type 45 strain, MCRF184. BMC Genomics 2019; 20:123. [PMID: 30736742 PMCID: PMC6368776 DOI: 10.1186/s12864-018-5394-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 12/18/2018] [Indexed: 11/10/2022] Open
Abstract
Background We describe the virulence factors of a methicillin-sensitive Staphylococcus aureus sequence type (ST) 45 strain, MCRF184, (spa type t917), that caused severe necrotizing fasciitis in a 72-year-old diabetic male. The genome of MCRF184 possesses three genomic islands: a relatively large type III νSaα with 42 open reading frames (ORFs) that includes superantigen- and lipoprotein-like genes, a truncated νSaβ that consists mostly of the enterotoxin gene cluster (egc), and a νSaγ island with 18 ORFs including α-toxin. Additionally, the genome has two phage-related regions: phage φSa3 with three genes of the immune evasion cluster (IEC), and an incomplete phage that is distinct from other S. aureus phages. Finally, the region between orfX and orfY harbors a putative efflux pump, acetyltransferase, regulators, and mobilization genes instead of genes of SCCmec. Results Virulence factors included phenol soluble modulins (PSMs) α1 through α4 and PSMs β1 and β2. Ten ORFs identified in MCRF184 had not been reported in previously sequenced S. aureus strains. Conclusion The dire clinical outcome in the patient and the described virulence factors all suggest that MCRF184, a ST45 strain is a highly virulent strain of S. aureus. Electronic supplementary material The online version of this article (10.1186/s12864-018-5394-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vijay Aswani
- Department of Internal Medicine & Pediatrics, University at Buffalo, Buffalo, New York, USA
| | - Fares Najar
- Department of Chemistry & Biochemistry, University of Oklahoma, Norman, OK, USA
| | - Madhulatha Pantrangi
- Center for Human Genetics, 1000 North Oak Avenue # MLR, Marshfield, WI, 54449, USA
| | - Bob Mau
- Wisconsin Institute for Discovery, University of Wisconsin, Madison, WI, USA
| | - William R Schwan
- Department of Microbiology, University of Wisconsin -La Crosse, La Crosse, WI, USA
| | - Sanjay K Shukla
- Center for Human Genetics, 1000 North Oak Avenue # MLR, Marshfield, WI, 54449, USA.
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Gislason AS, Turner K, Domaratzki M, Cardona ST. Comparative analysis of the Burkholderia cenocepacia K56-2 essential genome reveals cell envelope functions that are uniquely required for survival in species of the genus Burkholderia. Microb Genom 2019; 3. [PMID: 29208119 PMCID: PMC5729917 DOI: 10.1099/mgen.0.000140] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Burkholderia cenocepacia K56-2 belongs to the Burkholderia cepacia complex, a group of Gram-negative opportunistic pathogens that have large and dynamic genomes. In this work, we identified the essential genome of B. cenocepacia K56-2 using high-density transposon mutagenesis and insertion site sequencing (Tn-seq circle). We constructed a library of one million transposon mutants and identified the transposon insertions at an average of one insertion per 27 bp. The probability of gene essentiality was determined by comparing of the insertion density per gene with the variance of neutral datasets generated by Monte Carlo simulations. Five hundred and eight genes were not significantly disrupted, suggesting that these genes are essential for survival in rich, undefined medium. Comparison of the B. cenocepacia K56-2 essential genome with that of the closely related B. cenocepacia J2315 revealed partial overlapping, suggesting that some essential genes are strain-specific. Furthermore, 158 essential genes were conserved in B. cenocepacia and two species belonging to the Burkholderia pseudomallei complex, B. pseudomallei K96243 and Burkholderia thailandensis E264. Porins, including OpcC, a lysophospholipid transporter, LplT, and a protein involved in the modification of lipid A with aminoarabinose were found to be essential in Burkholderia genomes but not in other bacterial essential genomes identified so far. Our results highlight the existence of cell envelope processes that are uniquely essential in species of the genus Burkholderia for which the essential genomes have been identified by Tn-seq.
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Affiliation(s)
- April S Gislason
- 1Department of Microbiology, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Keith Turner
- 2Monsanto Company, 700 Chesterfield Parkway W, Chesterfield, MO, 63017, USA
| | - Mike Domaratzki
- 3Department of Computer Science, University of Manitoba, Winnipeg, R3T 2N2, Canada
| | - Silvia T Cardona
- 4Department of Medical Microbiology & Infectious Diseases, University of Manitoba, Winnipeg, MB, R3E 0J9, Canada
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Wu X, Wu X, Shen L, Li J, Yu R, Liu Y, Qiu G, Zeng W. Whole Genome Sequencing and Comparative Genomics Analyses of Pandoraea sp. XY-2, a New Species Capable of Biodegrade Tetracycline. Front Microbiol 2019; 10:33. [PMID: 30761094 PMCID: PMC6361800 DOI: 10.3389/fmicb.2019.00033] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 01/10/2019] [Indexed: 02/06/2023] Open
Abstract
Few bacteria are resistant to tetracycline and can even biodegrade tetracycline in the environment. In this study, we isolated a bacterium Pandoraea sp. XY-2, which could biodegrade 74% tetracycline at pH 7.0 and 30°C within 6 days. Thereafter, we determined the whole genome sequence of Pandoraea sp. XY-2 genome is a single circular chromosome of 5.06 Mb in size. Genomic annotation showed that two AA6 family members-encoding genes and nine glutathione S-transferase (GSTs)-encoding genes could be relevant to tetracycline biodegradation. In addition, the average nucleotide identities (ANI) analysis between the genomes of Pandoraea sp. XY-2 and other Pandoraea spp. revealed that Pandoraea sp. XY-2 belongs to a new species. Moreover, comparative genome analysis of 36 Pandoraea strains identified the pan and specific genes, numerous single nucleotide polymorphisms (SNPs), insertions, and deletion variations (InDels) and different syntenial relationships in the genome of Pandoraea sp. XY-2. Finally, the evolution and the origin analysis of genes related to tetracycline resistance revealed that the six tetA(48) genes and two specificgenes tetG and tetR in Pandoraea sp. XY-2 were acquired by horizontal gene transfer (HGT) events from sources related to Paraburkholderia, Burkholderia, Caballeronia, Salmonella, Vibrio, Proteobacteria, Pseudomonas, Acinetobacter, Flavimaricola, and some unidentified sources. As a new species, Pandoraea sp. XY-2 will be an excellent resource for the bioremediation of tetracycline-contaminated environment.
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Affiliation(s)
- Xueling Wu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy, Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Xiaoyan Wu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Li Shen
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy, Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Jiaokun Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy, Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Runlan Yu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy, Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Yuandong Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy, Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Guanzhou Qiu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy, Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Weimin Zeng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy, Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
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Complete Genome Sequence Analysis and Characterization of Selected Iron Regulation Genes of Pasteurella Multocida Serotype A Strain PMTB2.1. Genes (Basel) 2019; 10:genes10020081. [PMID: 30691021 PMCID: PMC6409639 DOI: 10.3390/genes10020081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 12/23/2018] [Accepted: 01/08/2019] [Indexed: 11/25/2022] Open
Abstract
Although more than 100 genome sequences of Pasteurella multocida are available, comprehensive and complete genome sequence analysis is limited. This study describes the analysis of complete genome sequence and pathogenomics of P. multocida strain PMTB2.1. The genome of PMTB2.1 has 2176 genes with more than 40 coding sequences associated with iron regulation and 140 virulence genes including the complete tad locus. The tad locus includes several previously uncharacterized genes such as flp2, rcpC and tadV genes. A transposable phage resembling to Mu phages was identified in P. multocida that has not been identified in any other serotype yet. The multi-locus sequence typing analysis assigned the PMTB2.1 genome sequence as type ST101, while the comparative genome analysis showed that PMTB2.1 is closely related to other P. multocida strains with the genomic distance of less than 0.13. The expression profiling of iron regulating-genes of PMTB2.1 was characterized under iron-limited environment. Results showed significant changes in the expression profiles of iron-regulating genes (p < 0.05) whereas the highest expression of fecE gene (281 fold) at 30 min suggests utilization of the outer-membrane proteins system in iron acquisition at an early stage of growth. This study showed the phylogenomic relatedness of P. multocida and improved annotation of important genes and functional characterization of iron-regulating genes of importance to the bacterial growth.
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