51
|
Carvalho R, Aburjaile F, Canario M, Nascimento AMA, Chartone-Souza E, de Jesus L, Zamyatnin AA, Brenig B, Barh D, Ghosh P, Goes-Neto A, Figueiredo HCP, Soares S, Ramos R, Pinto A, Azevedo V. Genomic Characterization of Multidrug-Resistant Escherichia coli BH100 Sub-strains. Front Microbiol 2021; 11:549254. [PMID: 33584554 PMCID: PMC7874104 DOI: 10.3389/fmicb.2020.549254] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 12/09/2020] [Indexed: 01/17/2023] Open
Abstract
The rapid emergence of multidrug-resistant (MDR) bacteria is a global health problem. Mobile genetic elements like conjugative plasmids, transposons, and integrons are the major players in spreading resistance genes in uropathogenic Escherichia coli (UPEC) pathotype. The E. coli BH100 strain was isolated from the urinary tract of a Brazilian woman in 1974. This strain presents two plasmids carrying MDR cassettes, pBH100, and pAp, with conjugative and mobilization properties, respectively. However, its transposable elements have not been characterized. In this study, we attempted to unravel the factors involved in the mobilization of virulence and drug-resistance genes by assessing genomic rearrangements in four BH100 sub-strains (BH100 MG2014, BH100 MG2017, BH100L MG2017, and BH100N MG2017). Therefore, the complete genomes of the BH100 sub-strains were achieved through Next Generation Sequencing and submitted to comparative genomic analyses. Our data shows recombination events between the two plasmids in the sub-strain BH100 MG2017 and between pBH100 and the chromosome in BH100L MG2017. In both cases, IS3 and IS21 elements were detected upstream of Tn21 family transposons associated with MDR genes at the recombined region. These results integrated with Genomic island analysis suggest pBH100 might be involved in the spreading of drug resistance through the formation of resistance islands. Regarding pathogenicity, our results reveal that BH100 strain is closely related to UPEC strains and contains many IS3 and IS21-transposase-enriched genomic islands associated with virulence. This study concludes that those IS elements are vital for the evolution and adaptation of BH100 strain.
Collapse
Affiliation(s)
- Rodrigo Carvalho
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Flavia Aburjaile
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Departamento de Genética, Universidade Federal de Pernambuco, Recife, Brazil
| | - Marcus Canario
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Andréa M A Nascimento
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Edmar Chartone-Souza
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Luis de Jesus
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Andrey A Zamyatnin
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Bertram Brenig
- Institute of Veterinary Medicine, University of Göttingen, Göttingen, Germany
| | - Debmalya Barh
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Institute of Integrative Omics and Applied Biotechnology, Purba Medinipur, India
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, United States
| | - Aristoteles Goes-Neto
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Henrique C P Figueiredo
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Siomar Soares
- Departmento de Microbiologia, Imunologia e Parasitologia, Universidade Federal do Triangulo Mineiro, Uberaba, Brazil
| | | | - Anne Pinto
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Vasco Azevedo
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| |
Collapse
|
52
|
Motyka-Pomagruk A, Zoledowska S, Kabza M, Lojkowska E. PacBio-Based Protocol for Bacterial Genome Assembly. Methods Mol Biol 2021; 2242:3-14. [PMID: 33961214 DOI: 10.1007/978-1-0716-1099-2_1] [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: 06/12/2023]
Abstract
Acquisition of high-quality bacterial genomes is fundamental, while having in mind investigation of subtitle intraspecies variation in addition to development of sensitive species-specific tools for detection and identification of the pathogens. In this view, Pacific Biosciences technology seems highly tempting taking into consideration over 10,000 bp length of the generated reads. In this work, we describe a bacterial genome assembly pipeline based on open-source software that might be handled also by non-bioinformaticians interested in transformation of sequencing data into reliable biological information. With the use of this method, we successfully closed six Dickeya solani genomes, while the assembly process was run just on a slightly improved desktop computer.
Collapse
Affiliation(s)
- Agata Motyka-Pomagruk
- Department of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk & Medical University of Gdansk, University of Gdansk, Gdansk, Poland
| | - Sabina Zoledowska
- Department of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk & Medical University of Gdansk, University of Gdansk, Gdansk, Poland
- Institute of Biotechnology and Molecular Medicine, Gdansk, Poland
| | - Michal Kabza
- Department of Integrative Genomics, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Ewa Lojkowska
- Department of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk & Medical University of Gdansk, University of Gdansk, Gdansk, Poland.
| |
Collapse
|
53
|
Jones C, Webster G, Mullins AJ, Jenner M, Bull MJ, Dashti Y, Spilker T, Parkhill J, Connor TR, LiPuma JJ, Challis GL, Mahenthiralingam E. Kill and cure: genomic phylogeny and bioactivity of Burkholderia gladioli bacteria capable of pathogenic and beneficial lifestyles. Microb Genom 2021; 7:mgen000515. [PMID: 33459584 PMCID: PMC8115902 DOI: 10.1099/mgen.0.000515] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 12/22/2020] [Indexed: 01/22/2023] Open
Abstract
Burkholderia gladioli is a bacterium with a broad ecology spanning disease in humans, animals and plants, but also encompassing multiple beneficial interactions. It is a plant pathogen, a toxin-producing food-poisoning agent, and causes lung infections in people with cystic fibrosis (CF). Contrasting beneficial traits include antifungal production exploited by insects to protect their eggs, plant protective abilities and antibiotic biosynthesis. We explored the genomic diversity and specialized metabolic potential of 206 B. gladioli strains, phylogenomically defining 5 clades. Historical disease pathovars (pv.) B. gladioli pv. allicola and B. gladioli pv. cocovenenans were distinct, while B. gladioli pv. gladioli and B. gladioli pv. agaricicola were indistinguishable; soft-rot disease and CF infection were conserved across all pathovars. Biosynthetic gene clusters (BGCs) for toxoflavin, caryoynencin and enacyloxin were dispersed across B. gladioli, but bongkrekic acid and gladiolin production were clade-specific. Strikingly, 13 % of CF infection strains characterized were bongkrekic acid-positive, uniquely linking this food-poisoning toxin to this aspect of B. gladioli disease. Mapping the population biology and metabolite production of B. gladioli has shed light on its diverse ecology, and by demonstrating that the antibiotic trimethoprim suppresses bongkrekic acid production, a potential therapeutic strategy to minimize poisoning risk in CF has been identified.
Collapse
Affiliation(s)
- Cerith Jones
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
- Present address: School of Applied Sciences, Faculty of Computing, Engineering and Science, University of South Wales, Pontypridd, CF37 4BD, UK
| | - Gordon Webster
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
| | - Alex J. Mullins
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
| | - Matthew Jenner
- Department of Chemistry and Warwick Integrative Synthetic Biology Centre, University of Warwick, CV4 7AL, UK
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, UK
| | - Matthew J. Bull
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
- Present address: Pathogen Genomics Unit, Public Health Wales Microbiology Cardiff, University Hospital of Wales, Cardiff, CF14 4XW, UK
| | - Yousef Dashti
- Department of Chemistry and Warwick Integrative Synthetic Biology Centre, University of Warwick, CV4 7AL, UK
- Present address: The Centre for Bacterial Cell Biology, Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4AX, UK
| | - Theodore Spilker
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Present address: Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Thomas R. Connor
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
| | - John J. LiPuma
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Gregory L. Challis
- Department of Chemistry and Warwick Integrative Synthetic Biology Centre, University of Warwick, CV4 7AL, UK
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, UK
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Eshwar Mahenthiralingam
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
| |
Collapse
|
54
|
Shieh YK, Liu SC, Lung Lu C. Scaffolding Contigs Using Multiple Reference Genomes. Comput Biol Chem 2020. [DOI: 10.5772/intechopen.93456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Scaffolding is an important step of the genome assembly and its function is to order and orient the contigs in the assembly of a draft genome into larger scaffolds. Several single reference-based scaffolders have currently been proposed. However, a single reference genome may not be sufficient alone for a scaffolder to correctly scaffold a target draft genome, especially when the target genome and the reference genome have distant evolutionary relationship or some rearrangements. This motivates researchers to develop the so-called multiple reference-based scaffolders that can utilize multiple reference genomes, which may provide different but complementary types of scaffolding information, to scaffold the target draft genome. In this chapter, we will review some of the state-of-the-art multiple reference-based scaffolders, such as Ragout, MeDuSa and Multi-CAR, and give a complete introduction to Multi-CSAR, an improved extension of Multi-CAR.
Collapse
|
55
|
Storey N, Rabiey M, Neuman BW, Jackson RW, Mulley G. Genomic Characterisation of Mushroom Pathogenic Pseudomonads and Their Interaction with Bacteriophages. Viruses 2020; 12:E1286. [PMID: 33182769 PMCID: PMC7696170 DOI: 10.3390/v12111286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/02/2020] [Accepted: 11/05/2020] [Indexed: 01/16/2023] Open
Abstract
Bacterial diseases of the edible white button mushroom Agaricus bisporus caused by Pseudomonas species cause a reduction in crop yield, resulting in considerable economic loss. We examined bacterial pathogens of mushrooms and bacteriophages that target them to understand the disease and opportunities for control. The Pseudomonastolaasii genome encoded a single type III protein secretion system (T3SS), but contained the largest number of non-ribosomal peptide synthase (NRPS) genes, multimodular enzymes that can play a role in pathogenicity, including a putative tolaasin-producing gene cluster, a toxin causing blotch disease symptom. However, Pseudomonasagarici encoded the lowest number of NRPS and three putative T3SS while non-pathogenic Pseudomonas sp. NS1 had intermediate numbers. Potential bacteriophage resistance mechanisms were identified in all three strains, but only P. agarici NCPPB 2472 was observed to have a single Type I-F CRISPR/Cas system predicted to be involved in phage resistance. Three novel bacteriophages, NV1, ϕNV3, and NV6, were isolated from environmental samples. Bacteriophage NV1 and ϕNV3 had a narrow host range for specific mushroom pathogens, whereas phage NV6 was able to infect both mushroom pathogens. ϕNV3 and NV6 genomes were almost identical and differentiated within their T7-like tail fiber protein, indicating this is likely the major host specificity determinant. Our findings provide the foundations for future comparative analyses to study mushroom disease and phage resistance.
Collapse
Affiliation(s)
- Nathaniel Storey
- School of Biological Sciences, Whiteknights Campus, University of Reading, Reading RG6 6AJ, UK; (N.S.); (R.W.J.); (G.M.)
| | - Mojgan Rabiey
- School of Biological Sciences, Whiteknights Campus, University of Reading, Reading RG6 6AJ, UK; (N.S.); (R.W.J.); (G.M.)
- School of Biosciences and Birmingham Institute of Forest Research, University of Birmingham, Birmingham B15 2TT, UK
| | - Benjamin W. Neuman
- Biology Department, College of Arts, Sciences and Education, TAMUT, Texarkana, TX 75503, USA;
| | - Robert W. Jackson
- School of Biological Sciences, Whiteknights Campus, University of Reading, Reading RG6 6AJ, UK; (N.S.); (R.W.J.); (G.M.)
- School of Biosciences and Birmingham Institute of Forest Research, University of Birmingham, Birmingham B15 2TT, UK
| | - Geraldine Mulley
- School of Biological Sciences, Whiteknights Campus, University of Reading, Reading RG6 6AJ, UK; (N.S.); (R.W.J.); (G.M.)
| |
Collapse
|
56
|
Hanachi M, Kiran A, Cornick J, Harigua-Souiai E, Everett D, Benkahla A, Souiai O. Genomic Characteristics of Invasive Streptococcus pneumoniae Serotype 1 in New Caledonia Prior to the Introduction of PCV13. Bioinform Biol Insights 2020; 14:1177932220962106. [PMID: 33088176 PMCID: PMC7545519 DOI: 10.1177/1177932220962106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 08/31/2020] [Indexed: 12/17/2022] Open
Abstract
Streptococcus pneumoniae serotype 1 is a common cause of global invasive pneumococcal disease. In New Caledonia, serotype 1 is the most prevalent serotype and led to two major outbreaks reported in the 2000s. The pneumococcal conjugate vaccine 13 (PCV13) was introduced into the vaccination routine, intending to prevent the expansion of serotype 1 in New Caledonia. Aiming to provide a baseline for monitoring the post-PCV13 changes, we performed a whole-genome sequence analysis on 67 serotype 1 isolates collected prior to the PCV13 introduction. To highlight the S. pneumoniae serotype 1 population structure, we performed a multilocus sequence typing (MLST) analysis revealing that NC serotype 1 consisted of 2 sequence types: ST3717 and the highly dominant ST306. Both sequence types harbored the same resistance genes to beta-lactams, macrolide, streptogramin B, fluoroquinolone, and lincosamide antibiotics. We have also identified 36 virulence genes that were ubiquitous to all the isolates. Among these virulence genes, the pneumolysin sequence presented an allelic profile associated with disease outbreaks and reduced hemolytic activity. Moreover, recombination hotspots were identified in 4 virulence genes and more notably in the cps locus (cps2L), potentially leading to capsular switching, a major mechanism of the emergence of nonvaccine types. In summary, this study represents the first overview of the genomic characteristics of S. pneumoniae serotype 1 in New Caledonia prior to the introduction of PCV13. This preliminary description represents a baseline to assess the impact of PCV13 on serotype 1 population structure and genomic diversity.
Collapse
Affiliation(s)
- Mariem Hanachi
- Laboratory of Bioinformatics, Biomathematics and Biostatistics-LR16IPT09, Institut Pasteur de Tunis, University of Tunis El Manar (UTM), Tunis, Tunisia.,Faculty of Science of Bizerte, University of Carthage, Jarzouna, Tunisia
| | - Anmol Kiran
- Queens Research Institute, University of Edinburgh, Edinburgh, UK.,Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Jennifer Cornick
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi.,Departement of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Emna Harigua-Souiai
- Laboratory of Molecular Epidemiology and Experimental Pathology-LR16IPT04, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Dean Everett
- Queens Research Institute, University of Edinburgh, Edinburgh, UK.,Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Alia Benkahla
- Laboratory of Bioinformatics, Biomathematics and Biostatistics-LR16IPT09, Institut Pasteur de Tunis, University of Tunis El Manar (UTM), Tunis, Tunisia
| | - Oussama Souiai
- Laboratory of Bioinformatics, Biomathematics and Biostatistics-LR16IPT09, Institut Pasteur de Tunis, University of Tunis El Manar (UTM), Tunis, Tunisia.,Institut Supérieur des Technologies Médicales de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| |
Collapse
|
57
|
Ferreira LC, Maul JE, Viana MVC, de Sousa TJ, de Carvalho Azevedo VA, Roberts DP, de Souza JT. Complete genome sequence of the biocontrol agent Serratia marcescens strain N4-5 uncovers an assembly artefact. Braz J Microbiol 2020; 52:245-250. [PMID: 32965626 DOI: 10.1007/s42770-020-00382-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 09/15/2020] [Indexed: 10/23/2022] Open
Abstract
Serratia marcescens are gram-negative bacteria found in several environmental niches, including the plant rhizosphere and patients in hospitals. Here, we present the genome of Serratia marcescens strain N4-5 (=NRRL B-65519), which has a size of 5,074,473 bp (664-fold coverage) and contains 4840 protein coding genes, 21 RNA genes, and an average G + C content of 59.7%. N4-5 harbours a plasmid of 11,089 bp and 43.5% G + C content that encodes six unique CDS repeated 2.5× times totalling 13 CDS. Our genome assembly and manual curation uncovered the insertion of two extra copies of the 5S rRNA gene in the assembled sequence, which was confirmed by PCR and Sanger sequencing to be a misassembly. This artefact was subsequently removed from the final assembly. The occurrence of extra copies of the 5S rRNA gene was also observed in most complete genomes of Serratia spp. deposited in public databases in our comparative analysis. These elements, which also occur naturally, can easily be confused with true genetic variation. Efforts to discover and correct assembly artefacts should be made in order to generate genome sequences that represent the biological truth underlying the studied organism. We present the genome of N4-5 and discuss genes potentially involved in biological control activity against plant pathogens and also the possible mechanisms responsible for the artefact we observed in our initial assembly. This report raises awareness about the extra copies of the 5S rRNA gene in sequenced bacterial genomes as they may represent misassemblies and therefore should be verified experimentally.
Collapse
Affiliation(s)
- Larissa Carvalho Ferreira
- Plant Pathology Department, Federal University of Lavras, Lavras, MG, 37200-000, Brazil.,Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3DA, UK
| | - Jude E Maul
- Sustainable Agricultural Systems Laboratory, USDA-Agricultural Research Service, Beltsville, MD, 20705, USA
| | | | - Thiago Jesus de Sousa
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | | | - Daniel P Roberts
- Sustainable Agricultural Systems Laboratory, USDA-Agricultural Research Service, Beltsville, MD, 20705, USA
| | - Jorge Teodoro de Souza
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3DA, UK.
| |
Collapse
|
58
|
Rolland C, La Scola B, Levasseur A. How Tupanvirus Degrades the Ribosomal RNA of Its Amoebal Host? The Ribonuclease T2 Track. Front Microbiol 2020; 11:1691. [PMID: 32849355 PMCID: PMC7399046 DOI: 10.3389/fmicb.2020.01691] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 06/29/2020] [Indexed: 12/15/2022] Open
Abstract
Tupanviruses are giant viruses recently discovered in Brazil from extreme environments: Tupanvirus soda lake (TPV-SL) and Tupanvirus deep ocean (TPV-DO). Unexpected features in Tupanviruses is the cytotoxic effect observed during infection, where the virus degrades the ribosomal RNA (rRNA) of its amoebal host. Interestingly, only TPV-SL causes this rRNA shutdown. We performed a genomic comparison of the two strains to determine potential modifications explaining the absence of rRNA degradation by TPV-DO. Whole genome comparisons were performed as well as more in-depth analysis at the gene level. We also calculated selective pressure on the orthologous genes between the two viruses. Our computational and evolutionary investigations revealed a potential target: a ribonuclease T2. These enzymes are known to be involved in cellular RNA catabolism such as in lysosomal degradation of rRNA. Our results suggest a functional ribonuclease localized in acid compartment closely related to ribonuclease T2 from eukaryotes. Silencing of the RNAse T2 gene of TPV-SL abolished its rRNA shutdown ability thereby correlating in silico assumption to the experimental evidence. In conclusion, all our results pointed to RNAse T2 as a target for explaining the difference for rRNA degradation ability between both strains.
Collapse
Affiliation(s)
- Clara Rolland
- Aix-Marseille Université, UMR MEPHI (Microbes, Evolution, Phylogeny and Infections), IRD, APHM, Faculté de Médecine, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Bernard La Scola
- Aix-Marseille Université, UMR MEPHI (Microbes, Evolution, Phylogeny and Infections), IRD, APHM, Faculté de Médecine, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Anthony Levasseur
- Aix-Marseille Université, UMR MEPHI (Microbes, Evolution, Phylogeny and Infections), IRD, APHM, Faculté de Médecine, Marseille, France
- IHU Méditerranée Infection, Marseille, France
- Institut Universitaire de France, Paris, France
| |
Collapse
|
59
|
Weisberg AJ, Davis EW, Tabima J, Belcher MS, Miller M, Kuo CH, Loper JE, Grünwald NJ, Putnam ML, Chang JH. Unexpected conservation and global transmission of agrobacterial virulence plasmids. Science 2020; 368:368/6495/eaba5256. [PMID: 32499412 DOI: 10.1126/science.aba5256] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/28/2020] [Accepted: 04/27/2020] [Indexed: 12/21/2022]
Abstract
The accelerated evolution and spread of pathogens are threats to host species. Agrobacteria require an oncogenic Ti or Ri plasmid to transfer genes into plants and cause disease. We developed a strategy to characterize virulence plasmids and applied it to analyze hundreds of strains collected between 1927 and 2017, on six continents and from more than 50 host species. In consideration of prior evidence for prolific recombination, it was surprising that oncogenic plasmids are descended from a few conserved lineages. Characterization of a hierarchy of features that promote or constrain plasticity allowed inference of the evolutionary history across the plasmid lineages. We uncovered epidemiological patterns that highlight the importance of plasmid transmission in pathogen diversification as well as in long-term persistence and the global spread of disease.
Collapse
Affiliation(s)
- Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Edward W Davis
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.,Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR 97331, USA
| | - Javier Tabima
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Michael S Belcher
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Marilyn Miller
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Joyce E Loper
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.,Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR 97331, USA.,Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, OR 97331, USA
| | - Niklaus J Grünwald
- Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, OR 97331, USA
| | - Melodie L Putnam
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA. .,Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR 97331, USA.,Center for Genome Research and Biocomputing (CGRB), Oregon State University, Corvallis, OR 97331, USA
| |
Collapse
|
60
|
Near-Complete Genome Sequence of a 2019 Novel Coronavirus (SARS-CoV-2) Strain Causing a COVID-19 Case in Peru. Microbiol Resour Announc 2020; 9:9/19/e00303-20. [PMID: 32381617 PMCID: PMC7206495 DOI: 10.1128/mra.00303-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A near-complete genome sequence was obtained for a novel coronavirus (SARS-CoV-2) strain obtained from an oropharyngeal swab from a Peruvian patient with coronavirus syndrome (COVID-19) who had contact with an individual who had returned to Peru from travel to Italy.
Collapse
|
61
|
Jabbar Z, Mukhtar H, Tayyeb A, Manzoor A. Next-generation sequencing to elucidate adaptive stress response and plantaricin genes among Lactobacillus plantarum strains. Future Microbiol 2020; 15:333-348. [PMID: 32286104 DOI: 10.2217/fmb-2019-0158] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Aim: The objective of this study was to identify the genes involved in plantaricin synthesis and adaptive stress response in four Lactobacillus plantarum strains (AS-6, AS-8, AS-9 and AS-10) and one Lactobacillus paraplantarum strain (AS-7) for their usage in medicine and industry. Materials & methods: Whole genomes of these strains were sequenced by a high-throughput sequencing technique known as next-generation sequencing via Ilumina MiSeq platform and the genes were identified by using various bioinformatics tools and software. Results: Plantaricin genes (plnD, plnE, plnF, plnG, plnI) and genes regulating response to temperature, pH, bile salt, osmotic and oxidative stress were identified in all strains. Conclusion: Lactobacilli could be an option to combat antimicrobial resistance and might replace harmful antibiotics in future.
Collapse
Affiliation(s)
- Zuriat Jabbar
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
| | - Hamid Mukhtar
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
| | - Asima Tayyeb
- School of Biological Sciences, University of The Punjab, Lahore 54590, Pakistan
| | - Asma Manzoor
- Institute of Biochemistry & Biotechnology, University of The Punjab, Lahore 54590, Pakistan
| |
Collapse
|
62
|
Silva FDJ, Ferreira LC, Campos VP, Cruz-Magalhães V, Barros AF, Andrade JP, Roberts DP, de Souza JT. Complete Genome Sequence of the Biocontrol Agent Bacillus velezensis UFLA258 and Its Comparison with Related Species: Diversity within the Commons. Genome Biol Evol 2020; 11:2818-2823. [PMID: 31580420 PMCID: PMC6788494 DOI: 10.1093/gbe/evz208] [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: 09/20/2019] [Indexed: 01/24/2023] Open
Abstract
In this study, the full genome sequence of Bacillus velezensis strain UFLA258, a biological control agent of plant pathogens was obtained, assembled, and annotated. With a comparative genomics approach, in silico analyses of all complete genomes of B. velezensis and closely related species available in the database were performed. The genome of B. velezensis UFLA258 consisted of a single circular chromosome of 3.95 Mb in length, with a mean GC content of 46.69%. It contained 3,949 genes encoding proteins and 27 RNA genes. Analyses based on Average Nucleotide Identity and Digital DNA–DNA Hybridization and a phylogeny with complete sequences of the rpoB gene confirmed that 19 strains deposited in the database as Bacillus amyloliquefaciens were in fact B. velezensis. In total, 115 genomes were analyzed and taxonomically classified as follows: 105 were B. velezensis, 9 were B. amyloliquefaciens, and 1 was Bacillus siamensis. Although these species are phylogenetically close, the combined analyses of several genomic characteristics, such as the presence of biosynthetic genes encoding secondary metabolites, CRISPr/Cas arrays, Average Nucleotide Identity and Digital DNA–DNA Hybridization, and other information on the strains, including isolation source, allowed their unequivocal classification. This genomic analysis expands our knowledge about the closely related species, B. velezensis, B. amyloliquefaciens, and B. siamensis, with emphasis on their taxonomical status.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Daniel P Roberts
- USDA-Agricultural Research Service, Sustainable Agricultural Systems Laboratory, Beltsville, Maryland
| | | |
Collapse
|
63
|
Draft Genome Sequence of Stenotrophomonas maltophilia CRB139-1, Isolated from Poultry Meat in Japan. Microbiol Resour Announc 2020; 9:9/12/e00075-20. [PMID: 32193235 PMCID: PMC7082454 DOI: 10.1128/mra.00075-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Stenotrophomonas maltophilia is a nosocomial pathogen that primarily causes respiratory infection in humans. This pathogen is widely distributed in the environment, including in foods. Here, we report the draft genome sequence of S. maltophilia strain CRB139-1, isolated from poultry meat in Japan. The genome size was 4,619,918 bp at 90× coverage. Stenotrophomonas maltophilia is a nosocomial pathogen that primarily causes respiratory infection in humans. This pathogen is widely distributed in the environment, including in foods. Here, we report the draft genome sequence of S. maltophilia strain CRB139-1, isolated from poultry meat in Japan. The genome size was 4,619,918 bp at 90× coverage.
Collapse
|
64
|
Goonetilleke SN, Croxford AE, March TJ, Wirthensohn MG, Hrmova M, Mather DE. Variation among S-locus haplotypes and among stylar RNases in almond. Sci Rep 2020; 10:583. [PMID: 31953457 PMCID: PMC6969032 DOI: 10.1038/s41598-020-57498-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 12/31/2019] [Indexed: 11/23/2022] Open
Abstract
In many plant species, self-incompatibility systems limit self-pollination and mating among relatives. This helps maintain genetic diversity in natural populations but imposes constraints in agriculture and plant breeding. In almond [Prunus dulcis (Mill.) D.A. Webb], the specificity of self-incompatibility is mainly determined by stylar ribonuclease (S-RNase) and S-haplotype-specific F-box (SFB) proteins, both encoded within a complex locus, S. Prior to this research, a nearly complete sequence was available for one S-locus haplotype. Here, we report complete sequences for four haplotypes and partial sequences for 11 haplotypes. Haplotypes vary in sequences of genes (particularly S-RNase and SFB), distances between genes and numbers and positions of long terminal repeat transposons. Haplotype variation outside of the S-RNase and SFB genes may help maintain functionally important associations between S-RNase and SFB alleles. Fluorescence-based assays were developed to distinguish among some S-RNase alleles. With three-dimensional modelling of five S-RNase proteins, conserved active sites were identified and variation was observed in electrostatic potential and in the numbers, characteristics and positions of secondary structural elements, loop anchoring points and glycosylation sites. A hypervariable region on the protein surface and differences in the number, location and types of glycosylation sites may contribute to determining S-RNase specificity.
Collapse
Affiliation(s)
- Shashi N Goonetilleke
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia
| | - Adam E Croxford
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia
| | - Timothy J March
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia
| | - Michelle G Wirthensohn
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia
| | - Maria Hrmova
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia.,School of Life Sciences, Huaiyin Normal University, Huai'an, 223300, China
| | - Diane E Mather
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia.
| |
Collapse
|
65
|
Nethery MA, Henriksen ED, Daughtry KV, Johanningsmeier SD, Barrangou R. Comparative genomics of eight Lactobacillus buchneri strains isolated from food spoilage. BMC Genomics 2019; 20:902. [PMID: 31775607 PMCID: PMC6881996 DOI: 10.1186/s12864-019-6274-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 11/12/2019] [Indexed: 12/22/2022] Open
Abstract
Abstract Background Lactobacillus buchneri is a lactic acid bacterium frequently associated with food bioprocessing and fermentation and has been found to be either beneficial or detrimental to industrial food processes depending on the application. The ability to metabolize lactic acid into acetic acid and 1,2-propandiol makes L. buchneri invaluable to the ensiling process, however, this metabolic activity leads to spoilage in other applications, and is especially damaging to the cucumber fermentation industry. This study aims to augment our genomic understanding of L. buchneri in order to make better use of the species in a wide range of applicable industrial settings. Results Whole-genome sequencing (WGS) was performed on seven phenotypically diverse strains isolated from spoiled, fermented cucumber and the ATCC type strain for L. buchneri, ATCC 4005. Here, we present our findings from the comparison of eight newly-sequenced and assembled genomes against two publicly available closed reference genomes, L. buchneri CD034 and NRRL B-30929. Overall, we see ~ 50% of all coding sequences are conserved across these ten strains. When these coding sequences are clustered by functional description, the strains appear to be enriched in mobile genetic elements, namely transposons. All isolates harbor at least one CRISPR-Cas system, and many contain putative prophage regions, some of which are targeted by the host’s own DNA-encoded spacer sequences. Conclusions Our findings provide new insights into the genomics of L. buchneri through whole genome sequencing and subsequent characterization of genomic features, building a platform for future studies and identifying elements for potential strain manipulation or engineering.
Collapse
Affiliation(s)
- Matthew A Nethery
- Genomic Sciences Graduate Program, North Carolina State University, Raleigh, NC, USA.,Department of Food, Bioprocessing & Nutrition Sciences, North Carolina State University, Raleigh, NC, USA
| | | | - Katheryne V Daughtry
- Department of Food, Bioprocessing & Nutrition Sciences, North Carolina State University, Raleigh, NC, USA.,United States Department of Agriculture, Agricultural Research Service, Southeast Area, Food Science Research Unit, North Carolina State University, 322 Schaub Hall, Box 7624, Raleigh, NC, 27695-7624, USA
| | - Suzanne D Johanningsmeier
- United States Department of Agriculture, Agricultural Research Service, Southeast Area, Food Science Research Unit, North Carolina State University, 322 Schaub Hall, Box 7624, Raleigh, NC, 27695-7624, USA
| | - Rodolphe Barrangou
- Genomic Sciences Graduate Program, North Carolina State University, Raleigh, NC, USA. .,Department of Food, Bioprocessing & Nutrition Sciences, North Carolina State University, Raleigh, NC, USA.
| |
Collapse
|
66
|
Massicotte MA, Vincent AT, Schneider A, Paquet VE, Frenette M, Charette SJ. One Aeromonas salmonicida subsp. salmonicida isolate with a pAsa5 variant bearing antibiotic resistance and a pRAS3 variant making a link with a swine pathogen. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 690:313-320. [PMID: 31299566 DOI: 10.1016/j.scitotenv.2019.06.456] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/24/2019] [Accepted: 06/26/2019] [Indexed: 06/10/2023]
Abstract
The Gram-negative bacterium Aeromonas salmonicida subsp. salmonicida is an aquatic pathogen which causes furunculosis to salmonids, especially in fish farms. The emergence of strains of this bacterium exhibiting antibiotic resistance is increasing, limiting the effectiveness of antibiotherapy as a treatment against this worldwide disease. In the present study, we discovered an isolate of A. salmonicida subsp. salmonicida that harbors two novel plasmids variants carrying antibiotic resistance genes. The use of long-read sequencing (PacBio) allowed us to fully characterize those variants, named pAsa5-3432 and pRAS3-3432, which both differ from their classic counterpart through their content in mobile genetic elements. The plasmid pAsa5-3432 carries a new multidrug region composed of multiple mobile genetic elements, including a Class 1 integron similar to an integrated element of Salmonella enterica. With this new region, probably acquired through plasmid recombination, pAsa5-3432 is the first reported plasmid of this bacterium that bears both an essential virulence factor (the type three secretion system) and multiple antibiotic resistance genes. As for pRAS3-3432, compared to the classic pRAS3, it carries a new mobile element that has only been identified in Chlamydia suis. Hence, with the identification of those two novel plasmids harboring mobile genetic elements that are normally encountered in other bacterial species, the present study puts emphasis on the important impact of mobile genetic elements in the genomic plasticity of A. salmonicida subsp. salmonicida and suggests that this aquatic bacterium could be an important reservoir of antibiotic resistance genes that can be exchanged with other bacteria, including human and animal pathogens.
Collapse
Affiliation(s)
- Marie-Ange Massicotte
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City G1V 0A6, Quebec, Canada; Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Hôpital Laval, Quebec City, Quebec G1V 4G5, Canada; Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval; Quebec City G1V 0A6, Quebec, Canada
| | - Antony T Vincent
- INRS-Institut Armand-Frappier, Bacterial Symbionts Evolution, Laval City H7V 1B7, QC, Canada
| | - Anna Schneider
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City G1V 0A6, Quebec, Canada; Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval; Quebec City G1V 0A6, Quebec, Canada
| | - Valérie E Paquet
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City G1V 0A6, Quebec, Canada; Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Hôpital Laval, Quebec City, Quebec G1V 4G5, Canada; Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval; Quebec City G1V 0A6, Quebec, Canada
| | - Michel Frenette
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval; Quebec City G1V 0A6, Quebec, Canada; Groupe de Recherche en Écologie Buccale (GREB), Faculté de médecine dentaire; Université Laval; Quebec City G1V 0A6, Quebec, Canada
| | - Steve J Charette
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City G1V 0A6, Quebec, Canada; Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Hôpital Laval, Quebec City, Quebec G1V 4G5, Canada; Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval; Quebec City G1V 0A6, Quebec, Canada.
| |
Collapse
|
67
|
Imanishi I, Nicolas A, Caetano ACB, Castro TLDP, Tartaglia NR, Mariutti R, Guédon E, Even S, Berkova N, Arni RK, Seyffert N, Azevedo V, Nishifuji K, Le Loir Y. Exfoliative toxin E, a new Staphylococcus aureus virulence factor with host-specific activity. Sci Rep 2019; 9:16336. [PMID: 31704997 PMCID: PMC6841975 DOI: 10.1038/s41598-019-52777-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 10/21/2019] [Indexed: 11/24/2022] Open
Abstract
Exfoliative toxins (ETs) are secreted virulence factors produced by staphylococci. These serine proteases specifically cleave desmoglein 1 (Dsg1) in mammals and are key elements in staphylococcal skin infections. We recently identified a new et gene in S. aureus O46, a strain isolated from ovine mastitis. In the present study, we characterized the new et gene at a genetic level and the enzymatic activity of the deduced protein. The S. aureus O46 genome was re-assembled, annotated and compared with other publicly available S. aureus genomes. The deduced amino acid sequence of the new et gene shared 40%, 53% and 59% sequence identity to those of ETA, ETB and ETD, respectively. The new et gene shared the same genetic vicinity and was similar in other S. aureus strains bearing this gene. The recombinant enzyme of the new et gene caused skin exfoliation in vivo in neonatal mice. The new et-gene was thus named ete, encoding a new type (type E) of exfoliative toxin. We showed that ETE degraded the extracellular segments of Dsg1 in murine, ovine and caprine epidermis, as well as in ovine teat canal epithelia, but not that in bovine epidermis. We further showed that it directly hydrolyzed human and swine Dsg1 as well as murine Dsg1α and Dsg1β, but not canine Dsg1 or murine Dsg1γ. Molecular modeling revealed a correlation between the preferred orientation of ETE docking on its Dsg1 cleavage site and species-specific cleavage activity, suggesting that the docking step preceding cleavage accounts for the ETE species-specificity. This new virulence factor may contribute to the bacterial colonization on the stratified epithelia in certain ruminants with mastitis.
Collapse
Affiliation(s)
- Ichiro Imanishi
- Laboratory of Veterinary Internal Medicine, Division of Animal Life Science, Graduate School, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | | | - Ana-Carolina Barbosa Caetano
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, 270-901, Brazil
| | - Thiago Luiz de Paula Castro
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, 270-901, Brazil.,Institute of Health Sciences, Federal University of Bahia, Salvador, BA, 40110-100, Brazil
| | - Natayme Rocha Tartaglia
- STLO, INRA, Agrocampus Ouest, F-35042, Rennes, France.,Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, 270-901, Brazil
| | | | - Eric Guédon
- STLO, INRA, Agrocampus Ouest, F-35042, Rennes, France
| | - Sergine Even
- STLO, INRA, Agrocampus Ouest, F-35042, Rennes, France
| | - Nadia Berkova
- STLO, INRA, Agrocampus Ouest, F-35042, Rennes, France
| | | | - Nubia Seyffert
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, 270-901, Brazil.,Institute of Biology, Federal University of Bahia, Salvador, BA, 40170-115, Brazil
| | - Vasco Azevedo
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, 270-901, Brazil
| | - Koji Nishifuji
- Laboratory of Veterinary Internal Medicine, Division of Animal Life Science, Graduate School, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | - Yves Le Loir
- STLO, INRA, Agrocampus Ouest, F-35042, Rennes, France.
| |
Collapse
|
68
|
Knab R, Petersen H, Lin HJ, Meixner M, Rautenschlein S, Jung A. In vitro characterization and genetic diversity of Bordetella avium field strains. Avian Pathol 2019; 49:36-46. [PMID: 31456417 DOI: 10.1080/03079457.2019.1660305] [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] [Indexed: 10/26/2022]
Abstract
Bordetella avium (BA) is a respiratory pathogen of particular importance for turkeys. Specific adherence and damage to the respiratory epithelia are crucial steps of the pathogenesis, but knowledge about the mechanisms and the variety of virulence in field strains is limited. We analysed 17 BA field strains regarding their in vitro virulence-associated properties in tracheal organ cultures (TOC) of turkey embryos, and their genetic diversity. The TOC adherence assay indicated that BA field strains differ considerably in their ability to adhere to the tracheal mucosa, while the TOC ciliostasis assay illustrated a high degree of diversity in ciliostatic effects. These two virulence-associated properties were associated with each other in the investigated strains. Three of the investigated strains displayed significantly (P > 0.05) lower in vitro virulence in comparison to other strains. Genetic diversity of BA strains was analysed by core genome multilocus sequence typing (cgMLST). We applied a cgMLST scheme comprising 2667 targets of the reference genome (77.3% of complete genome, BA strain 197N). The results showed a broad genetic diversity in BA field strains but did not demonstrate a correlation between sequence type and virulence-associated properties. The cgMLST analysis revealed that strains with less marked virulence-associated properties had a variety of mutations in the putative filamentous haemagglutinin gene. Likewise, amino acid sequence alignment indicated variations in the protein. The results from our study showed that both adherence and ciliostasis assay can be used for virulence characterization of BA. Variations in the filamentous haemagglutinin protein may be responsible for reduced virulence of BA field strains.
Collapse
Affiliation(s)
- Rebecca Knab
- Clinic for Poultry, University of Veterinary Medicine, Hannover, Germany
| | - Henning Petersen
- Clinic for Poultry, University of Veterinary Medicine, Hannover, Germany
| | - Hsuen-Ju Lin
- Amedes Genetics, MVZ Endokrinologikum Berlin, Berlin, Germany
| | - Martin Meixner
- Amedes Genetics, MVZ Endokrinologikum Berlin, Berlin, Germany
| | | | - Arne Jung
- Clinic for Poultry, University of Veterinary Medicine, Hannover, Germany
| |
Collapse
|
69
|
Raj I, Bansiwal A, Vaidya AN. Kinetic evaluation for rapid degradation of dimethylamine enriched with Agromyces and Ochrobactrum sp. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 245:322-329. [PMID: 31158684 DOI: 10.1016/j.jenvman.2019.05.074] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 05/13/2019] [Accepted: 05/19/2019] [Indexed: 06/09/2023]
Abstract
Dimethylamine (DMA) possesses an obnoxious odor which has resulted in public concern during the past several decades. A rare bacterial species proficient to degrade DMA, designated IR-26, was isolated from Indian Oil Corporation Limited (IOCL) and identified as Agromyces and Ochrobactrum sp., which has presented a rapid degradation when compared to other bacterial species which were capable to degrade DMA. The removal efficiency of 100% has been calculated in different concentration of DMA. The kinetic study reveals the maximum reduction rate of DMA was 0.11 per hour and the maximum growth rate of biomass was 0.013 per hour respectively. The saturation constant of DMA was around 1.96 mg/L which shows a high affinity of DMA. The importance of these analyses is offered and conversed in this paper.
Collapse
Affiliation(s)
- Ishan Raj
- Environmental Biotechnology and Genomics Division, CSIR-NEERI, Nagpur, India; Academy of Scientific and Innovative Research, CSIR-NEERI, Nagpur, 440020 Maharashtra, India.
| | - Amit Bansiwal
- Environmental Material Division, CSIR-NEERI, Nagpur, India
| | - A N Vaidya
- Solid and Hazardous Waste Management Division, CSIR-NEERI, Nagpur, India
| |
Collapse
|
70
|
Chen KT, Lu CL. CSAR-web: a web server of contig scaffolding using algebraic rearrangements. Nucleic Acids Res 2019; 46:W55-W59. [PMID: 29733393 PMCID: PMC6030906 DOI: 10.1093/nar/gky337] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 04/19/2018] [Indexed: 01/23/2023] Open
Abstract
CSAR-web is a web-based tool that allows the users to efficiently and accurately scaffold (i.e. order and orient) the contigs of a target draft genome based on a complete or incomplete reference genome from a related organism. It takes as input a target genome in multi-FASTA format and a reference genome in FASTA or multi-FASTA format, depending on whether the reference genome is complete or incomplete, respectively. In addition, it requires the users to choose either ‘NUCmer on nucleotides’ or ‘PROmer on translated amino acids’ for CSAR-web to identify conserved genomic markers (i.e. matched sequence regions) between the target and reference genomes, which are used by the rearrangement-based scaffolding algorithm in CSAR-web to order and orient the contigs of the target genome based on the reference genome. In the output page, CSAR-web displays its scaffolding result in a graphical mode (i.e. scalable dotplot) allowing the users to visually validate the correctness of scaffolded contigs and in a tabular mode allowing the users to view the details of scaffolds. CSAR-web is available online at http://genome.cs.nthu.edu.tw/CSAR-web.
Collapse
Affiliation(s)
- Kun-Tze Chen
- Department of Computer Science, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Chin Lung Lu
- Department of Computer Science, National Tsing Hua University, Hsinchu 30013, Taiwan
| |
Collapse
|
71
|
De novo genome assembly and comparative annotation reveals metabolic versatility in cellulolytic bacteria from cropland and forest soils. Funct Integr Genomics 2019; 20:89-101. [PMID: 31378834 DOI: 10.1007/s10142-019-00704-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 07/09/2019] [Accepted: 07/24/2019] [Indexed: 10/26/2022]
Abstract
Cellulose, the most abundant polysaccharide in nature, is a rich source of renewable energy and sustains soil nutrients. Among the microorganisms known to degrade cellulose, bacteria are less studied compared to fungi. In the present work, we have investigated the culturable bacteria actively involved in cellulose degradation in forest and crop field soils. Based on clear zone formation and enzyme activity assay, we identified 7 bacterial strains positive for cellulose degradation. Of these, two most efficient strains (Bacillus cereus strains BHU1 and BHU2) were selected for whole genome sequencing, annotation, and information regarding GC content, number of genes, total subsystems, starch, and cellulose degradation pathways. Average nucleotide identity (ANI) showed more than 90% similarity between both the strains (BHU1 and BHU2) and with B. cereus ATCC 14579. Both the strains have genes and enzyme families like endoglucanase and β-glucosidase as evident from whole genome sequence. Cellulase containing gene families (GH5, GH8, GH1), and many other carbohydrate-degrading enzymes, were present in both the bacterial strains. Taken together, the results suggest that the strains were efficient in cellulose degradation, and can be used for energy generation and production of value-added product.
Collapse
|
72
|
Waters NR, Abram F, Brennan F, Holmes A, Pritchard L. riboSeed: leveraging prokaryotic genomic architecture to assemble across ribosomal regions. Nucleic Acids Res 2019; 46:e68. [PMID: 29608703 PMCID: PMC6009695 DOI: 10.1093/nar/gky212] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 03/12/2018] [Indexed: 11/12/2022] Open
Abstract
The vast majority of bacterial genome sequencing has been performed using Illumina short reads. Because of the inherent difficulty of resolving repeated regions with short reads alone, only ∼10% of sequencing projects have resulted in a closed genome. The most common repeated regions are those coding for ribosomal operons (rDNAs), which occur in a bacterial genome between 1 and 15 times, and are typically used as sequence markers to classify and identify bacteria. Here, we exploit the genomic context in which rDNAs occur across taxa to improve assembly of these regions relative to de novo sequencing by using the conserved nature of rDNAs across taxa and the uniqueness of their flanking regions within a genome. We describe a method to construct targeted pseudocontigs generated by iteratively assembling reads that map to a reference genome’s rDNAs. These pseudocontigs are then used to more accurately assemble the newly sequenced chromosome. We show that this method, implemented as riboSeed, correctly bridges across adjacent contigs in bacterial genome assembly and, when used in conjunction with other genome polishing tools, can assist in closure of a genome.
Collapse
Affiliation(s)
- Nicholas R Waters
- Microbiology, School of Natural Sciences, National University of Ireland, Galway, H91 TK33, Ireland.,Information and Computational Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland
| | - Florence Abram
- Microbiology, School of Natural Sciences, National University of Ireland, Galway, H91 TK33, Ireland
| | - Fiona Brennan
- Microbiology, School of Natural Sciences, National University of Ireland, Galway, H91 TK33, Ireland.,Soil and Environmental Microbiology, Environmental Research Centre, Teagasc, Johnstown Castle, Wexford, Y35 TC97, Ireland
| | - Ashleigh Holmes
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland
| | - Leighton Pritchard
- Information and Computational Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland
| |
Collapse
|
73
|
Draft Genome Sequences of 16 Strains of Escherichia Cryptic Clade II Isolated from Intertidal Sediment in Hong Kong. Microbiol Resour Announc 2019; 8:8/29/e00416-19. [PMID: 31320428 PMCID: PMC6639607 DOI: 10.1128/mra.00416-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The genus Escherichia includes several cryptic clades. Among them, the members of cryptic clade II have rarely been found, and their genome sequences remain largely uninvestigated. Here, we report the draft genome sequences of 16 strains of Escherichia cryptic clade II that were isolated from intertidal sediment in Hong Kong.
Collapse
|
74
|
Srivastava AK, Saxena P, Sharma A, Srivastava R, Jamali H, Bharati AP, Yadav J, Srivastava AK, Kumar M, Chakdar H, Kashyap PL, Saxena AK. Draft genome sequence of a cold-adapted phosphorous-solubilizing Pseudomonas koreensis P2 isolated from Sela Lake, India. 3 Biotech 2019; 9:256. [PMID: 31192081 DOI: 10.1007/s13205-019-1784-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 05/30/2019] [Indexed: 12/20/2022] Open
Abstract
The draft genome sequence of a cold-adapted phosphorus-solubilizing strain Pseudomonas koreensis P2 isolated from the Sela Lake contains 6,436,246 bp with G + C content of 59.8%. The genome sequence includes 5743 protein coding genes, 68 non-protein coding genes, 1007 putative proteins, 5 rRNA genes, 64 tRNAs and two prophage regions in 40 contigs. Besides these, genes involved in phosphate solubilization, siderophore production, iron uptake, heat shock and cold shock tolerance, multidrug resistance and glycine-betaine production were also identified.
Collapse
|
75
|
Genome analysis of urease positive Serratia marcescens, co-producing SRT-2 and AAC(6′)-Ic with multidrug efflux pumps for antimicrobial resistance. Genomics 2019; 111:653-660. [DOI: 10.1016/j.ygeno.2018.04.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 12/13/2017] [Accepted: 04/03/2018] [Indexed: 11/22/2022]
|
76
|
Draft Genome Sequence of Streptococcus suis S10, a Virulent Strain Used in Experimental Pig Infections. Microbiol Resour Announc 2019; 8:8/23/e00227-19. [PMID: 31171613 PMCID: PMC6554600 DOI: 10.1128/mra.00227-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, we report the draft whole-genome sequence of Streptococcus suis strain S10, isolated from the tonsils of a healthy pig. S. suis S10 belongs to the highly virulent serotype 2, which includes isolates that cause infectious diseases, including meningitis, in pigs and human. The genome contains a complete prophage that encodes a candidate virulence gene.
Collapse
|
77
|
Data on the polymorphic sites in the chloroplast genomes of the sunflower alloplasmic CMS lines. Data Brief 2019; 25:104072. [PMID: 31211212 PMCID: PMC6562223 DOI: 10.1016/j.dib.2019.104072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 02/07/2019] [Accepted: 05/20/2019] [Indexed: 01/29/2023] Open
Abstract
Data presents the chloroplast genome sequences of the five sunflower alloplasmic cytoplasmic male sterility (CMS) lines obtained with using the Illumina MiSeq, HiSeq and NextSeq platforms. The sunflower alloplasmic CMS lines has the same nuclear genome from line HA89, but they differ in cytoplasmic genomes, inherited from annual (PET1, PET2 - H. petiolaris, ANN2 - H. annuus) and perennial (MAX1 - H. maximilliani) species of the genus Helianthus L. The chloroplast genomes were annotated. Also presented is a dataset of variable sites such as single nucleotide polymorphism (SNP), simple sequence repeat (SSR), insertion and deletion (INDEL) in the chloroplast genome of the sequenced alloplasmic lines. The raw reads are available in FIGSHARE (https://doi.org/10.6084/m9.figshare.7520183). The complete chloroplast genome sequences for the sunflower alloplasmic lines are available in GenBank NCBI under the accessions MK341448.1-MK341452.1; the remaining data are provided with this article.
Collapse
|
78
|
Pasari N, Gupta M, Eqbal D, Yazdani SS. Genome analysis of Paenibacillus polymyxa A18 gives insights into the features associated with its adaptation to the termite gut environment. Sci Rep 2019; 9:6091. [PMID: 30988376 PMCID: PMC6465253 DOI: 10.1038/s41598-019-42572-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 04/03/2019] [Indexed: 01/17/2023] Open
Abstract
Paenibacillus polymyxa A18 was isolated from termite gut and was identified as a potential cellulase and hemicellulase producer in our previous study. Considering that members belonging to genus Paenibacillus are mostly free-living in soil, we investigated here the essential genetic features that helped P. polymyxa A18 to survive in gut environment. Genome sequencing and analysis identified 4608 coding sequences along with several elements of horizontal gene transfer, insertion sequences, transposases and integrated phages, which add to its genetic diversity. Many genes coding for carbohydrate-active enzymes, including the enzymes responsible for woody biomass hydrolysis in termite gut, were identified in P. polymyxa A18 genome. Further, a series of proteins conferring resistance to 11 antibiotics and responsible for production of 4 antibiotics were also found to be encoded, indicating selective advantage for growth and colonization in the gut environment. To further identify genomic regions unique to this strain, a BLAST-based comparative analysis with the sequenced genomes of 47 members belonging to genus Paenibacillus was carried out. Unique regions coding for nucleic acid modifying enzymes like CRISPR/Cas and Type I Restriction-Modification enzymes were identified in P. polymyxa A18 genome suggesting the presence of defense mechanism to combat viral infections in the gut. In addition, genes responsible for the formation of biofilms, such as Type IV pili and adhesins, which might be assisting P. polymyxa A18 in colonizing the gut were also identified in its genome. In situ colonization experiment further confirmed the ability of P. polymyxa A18 to colonize the gut of termite.
Collapse
Affiliation(s)
- Nandita Pasari
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.,DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Mayank Gupta
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.,DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Danish Eqbal
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Syed Shams Yazdani
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India. .,DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.
| |
Collapse
|
79
|
Draft Genome Sequence of Halotolerant Bacterium Chromohalobacter salexigens ANJ207, Isolated from Salt Crystal Deposits in Pipelines. Microbiol Resour Announc 2019; 8:8/15/e00049-19. [PMID: 30975796 PMCID: PMC6460019 DOI: 10.1128/mra.00049-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Chromohalobacter salexigens ANJ207 was isolated from a salt crystal and is known to tolerate up to 30% NaCl concentration. Here, we report the de novo draft assembly of C. salexigens ANJ207. Chromohalobacter salexigens ANJ207 was isolated from a salt crystal and is known to tolerate up to 30% NaCl concentration. Here, we report the de novo draft assembly of C. salexigens ANJ207. The genome was determined to have 3.66 Mb represented in 13 scaffolds, with a total of 3,406 genes predicted.
Collapse
|
80
|
Schmidt R, Durling MB, de Jager V, Menezes RC, Nordkvist E, Svatoš A, Dubey M, Lauterbach L, Dickschat JS, Karlsson M, Garbeva P. Deciphering the genome and secondary metabolome of the plant pathogen Fusarium culmorum. FEMS Microbiol Ecol 2019; 94:4990469. [PMID: 29718180 DOI: 10.1093/femsec/fiy078] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 04/27/2018] [Indexed: 01/01/2023] Open
Abstract
Fusarium culmorum is one of the most important fungal plant pathogens that causes diseases on a wide diversity of cereal and non-cereal crops. We report herein for the first time the genome sequence of F. culmorum strain PV and its associated secondary metabolome that plays a role in the interaction with other microorganisms and contributes to its pathogenicity on plants. The genome revealed the presence of two terpene synthases, trichodiene and longiborneol synthase, which generate an array of volatile terpenes. Furthermore, we identified two gene clusters, deoxynivalenol and zearalenone, which encode for the production of mycotoxins. Linking the production of mycotoxins with in vitro bioassays, we found high virulence of F. culmorum PV on maize, barley and wheat. By using ultra-performance liquid chromatography-mass spectrometry, we confirmed several compounds important for the behaviour and lifestyle of F. culmorum. This research sets the basis for future studies in microbe-plant interactions.
Collapse
Affiliation(s)
- Ruth Schmidt
- Department of Microbial Ecology, Netherlands Institute of Ecology, Droevendaalsesteeg 10,6708 PB Wageningen, the Netherlands
| | - Mikael B Durling
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 75007 Uppsala, Sweden
| | - Victor de Jager
- Department of Microbial Ecology, Netherlands Institute of Ecology, Droevendaalsesteeg 10,6708 PB Wageningen, the Netherlands
| | - Riya C Menezes
- Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany
| | | | - Aleš Svatoš
- Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany
| | - Mukesh Dubey
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 75007 Uppsala, Sweden
| | - Lukas Lauterbach
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, D-53121 Bonn, Germany
| | - Jeroen S Dickschat
- Department of Microbial Ecology, Netherlands Institute of Ecology, Droevendaalsesteeg 10,6708 PB Wageningen, the Netherlands.,Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, D-53121 Bonn, Germany
| | - Magnus Karlsson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 75007 Uppsala, Sweden
| | - Paolina Garbeva
- Department of Microbial Ecology, Netherlands Institute of Ecology, Droevendaalsesteeg 10,6708 PB Wageningen, the Netherlands
| |
Collapse
|
81
|
Mullins AJ, Murray JAH, Bull MJ, Jenner M, Jones C, Webster G, Green AE, Neill DR, Connor TR, Parkhill J, Challis GL, Mahenthiralingam E. Genome mining identifies cepacin as a plant-protective metabolite of the biopesticidal bacterium Burkholderia ambifaria. Nat Microbiol 2019; 4:996-1005. [PMID: 30833726 PMCID: PMC6544543 DOI: 10.1038/s41564-019-0383-z] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 01/22/2019] [Indexed: 11/09/2022]
Abstract
Beneficial microorganisms are widely used in agriculture for control of plant pathogens but a lack of efficacy and safety information has limited the exploitation of multiple promising biopesticides. We applied phylogeny-led genome mining, metabolite analyses and biological control assays to define the efficacy of Burkholderia ambifaria, a naturally beneficial bacterium with proven biocontrol properties, but potential pathogenic risk. A panel of 64 B. ambifaria strains demonstrated significant antimicrobial activity against priority plant pathogens. Genome sequencing, specialized metabolite biosynthetic gene cluster mining and metabolite analysis revealed an armoury of known and unknown pathways within B. ambifaria. The biosynthetic gene cluster responsible for the production of the metabolite, cepacin, was identified and directly shown to mediate protection of germinating crops against Pythium damping-off disease. B. ambifaria maintained biopesticidal protection and overall fitness in soil after deletion of its third replicon, a non-essential plasmid associated with virulence in B. cepacia complex bacteria. Removal of the third replicon reduced B. ambifaria persistence in a murine respiratory infection model. Here we show that by using interdisciplinary phylogenomic, metabolomic and functional approaches, the mode of action of natural biological control agents related to pathogens can be systematically established to facilitate their future exploitation.
Collapse
Affiliation(s)
- Alex J Mullins
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, UK.
| | - James A H Murray
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, UK
| | - Matthew J Bull
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, UK
| | - Matthew Jenner
- Department of Chemistry and Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, UK
| | - Cerith Jones
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, UK.,Faculty of Computing, Engineering and Science, University of South Wales, Pontypridd, UK
| | - Gordon Webster
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, UK
| | - Angharad E Green
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Daniel R Neill
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Thomas R Connor
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, UK
| | - Julian Parkhill
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Gregory L Challis
- Department of Chemistry and Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, UK.,Department of Biochemistry and Molecular Biology,Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Eshwar Mahenthiralingam
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, UK.
| |
Collapse
|
82
|
Diancourt L, Sautereau J, Criscuolo A, Popoff MR. Two Clostridiumperfringens Type E Isolates in France. Toxins (Basel) 2019; 11:E138. [PMID: 30823654 PMCID: PMC6468631 DOI: 10.3390/toxins11030138] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 02/22/2019] [Accepted: 02/23/2019] [Indexed: 12/03/2022] Open
Abstract
Clostridiumperfringens type E is a less frequently isolated C.perfringens type and has not previously been reported in France. We have characterized two recent type E isolates, C.perfringens 508.17 from the intestinal content of a calf that died of enterotoxemia, and 515.17 from the stool of a 60-year-old woman, subsequent to food poisoning, which contained the plasmid pCPPB-1 with variant iota toxin and C. perfringens enterotoxin genes.
Collapse
Affiliation(s)
- Laure Diancourt
- CNR Bactéries anaérobies et Botulisme, Institut Pasteur, 75015 Paris, France.
| | - Jean Sautereau
- CNR Bactéries anaérobies et Botulisme, Institut Pasteur, 75015 Paris, France.
| | - Alexis Criscuolo
- Hub de Bioinformatique et Biostatistique-C3BI, Institut Pasteur, USR 3756, CNRS, 75015 Paris, France.
| | - Michel R Popoff
- Bacterial Toxins, Institut Pasteur, ERL 6002, 75015 Paris, France.
| |
Collapse
|
83
|
Genome Sequence of Bacillus subtilis subsp. subtilis Strain IITK SM1, Isolated from Kitchen Waste Compost. Microbiol Resour Announc 2019; 8:MRA01330-18. [PMID: 30746513 PMCID: PMC6368648 DOI: 10.1128/mra.01330-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 01/09/2019] [Indexed: 11/26/2022] Open
Abstract
We report here the complete genome sequence of Bacillus subtilis subsp. subtilis strain IITK SM1, isolated from kitchen waste compost. We report here the complete genome sequence of Bacillus subtilis subsp. subtilis strain IITK SM1, isolated from kitchen waste compost. We have sequenced the whole genome of this strain to identify and characterize the enzymes that participate in efficient composting activity.
Collapse
|
84
|
Yang Y, Luo M, Zhou H, Li C, Luk A, Zhao G, Fung K, Ip M. Role of Two-Component System Response Regulator bceR in the Antimicrobial Resistance, Virulence, Biofilm Formation, and Stress Response of Group B Streptococcus. Front Microbiol 2019; 10:10. [PMID: 30728810 PMCID: PMC6351488 DOI: 10.3389/fmicb.2019.00010] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 01/07/2019] [Indexed: 01/31/2023] Open
Abstract
Group B Streptococcus (GBS; Streptococcus agalactiae) is a leading cause of sepsis in neonates and pregnant mothers worldwide. Whereas the hyper-virulent serogroup III clonal cluster 17 has been associated with neonatal disease and meningitis, serogroup III ST283 was recently implicated in invasive disease among non-pregnant adults in Asia. Here, through comparative genome analyses of invasive and non-invasive ST283 strains, we identified a truncated DNA-binding regulator of a two-component system in a non-invasive strain that was homologous to Bacillus subtilis bceR, encoding the bceRSAB response regulator, which was conserved among GBS strains. Using isogenic knockout and complementation mutants of the ST283 strain, we demonstrated that resistance to bacitracin and the human antimicrobial peptide cathelicidin LL-37 was reduced in the ΔbceR strain with MICs changing from 64 and 256 μg/ml to 0.25 and 64 μg/ml, respectively. Further, the ATP-binding cassette transporter was upregulated by sub-inhibitory concentrations of bacitracin in the wild-type strain. Upregulation of dltA in the wild-type strain was also observed and thought to explain the increased resistance to antimicrobial peptides. DltA, an enzyme involved in D-alanylation during the synthesis of wall teichoic acids, which mediates reduced antimicrobial susceptibility, was previously shown to be regulated by the bceR-type regulator in Staphylococcus aureus. In a murine infection model, we found that the ΔbceR mutation significantly reduced the mortality rate compared to that with the wild-type strain (p < 0.01). Moreover, this mutant was more susceptible to oxidative stress compared to the wild-type strain (p < 0.001) and was associated with reduced biofilm formation (p < 0.0001). Based on 2-DGE and mass spectrometry, we showed that downregulation of alkyl hydroperoxide reductase (AhpC), a Gls24 family stress protein, and alcohol dehydrogenase (Adh) in the ΔbceR strain might explain the attenuated virulence and compromised stress response. Together, we showed for the first time that the bceR regulator in GBS plays an important role in bacitracin and antimicrobial peptide resistance, virulence, survival under oxidative stress, and biofilm formation.
Collapse
Affiliation(s)
- Ying Yang
- Department of Microbiology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Mingjing Luo
- Department of Microbiology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Haokui Zhou
- Department of Microbiology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Carmen Li
- Department of Microbiology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Alison Luk
- Department of Microbiology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - GuoPing Zhao
- Department of Microbiology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Kitty Fung
- Department of Microbiology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Margaret Ip
- Department of Microbiology, The Chinese University of Hong Kong, Shatin, Hong Kong
| |
Collapse
|
85
|
Draft genome sequence data of Lactobacillus paracasei strain DTA83 isolated from infant stools. Data Brief 2019; 22:1064-1067. [PMID: 30740494 PMCID: PMC6356017 DOI: 10.1016/j.dib.2019.01.041] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 01/08/2019] [Accepted: 01/18/2019] [Indexed: 11/22/2022] Open
Abstract
Here the draft genome sequence of Lactobacillus paracasei strain DTA83, isolated from stools of healthy infants in Rio de Janeiro (Brazil), is reported. The 2.8-Mb genome possesses 2825 protein-coding sequences distributed on 330 SEED subsystems. This strain belongs to a set of potentially probiotic Lactobacillus spp. strains used to study genetic factors related to antibiotic resistance after stress conditions, such as simulated gastrointestinal conditions. The complete genome data have been deposited in GenBank under the accession number QRBH00000000, https://www.ncbi.nlm.nih.gov/nuccore/QRBH00000000.
Collapse
|
86
|
Genome analysis provides insights into crude oil degradation and biosurfactant production by extremely halotolerant Halomonas desertis G11 isolated from Chott El-Djerid salt-lake in Tunisian desert. Genomics 2018; 111:1802-1814. [PMID: 30529640 DOI: 10.1016/j.ygeno.2018.12.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 09/05/2018] [Accepted: 12/04/2018] [Indexed: 01/10/2023]
Abstract
Here, we report the genomic features and the bioremediation potential of Halomonas desertis G11, a new halophilic species which uses crude oil as a carbon and energy source and displays intrinsic resistance to salt stress conditions (optimum growth at 10% NaCl). G11 genome (3.96 Mb) had a mean GC content of 57.82%, 3622 coding sequences, 480 subsystems and 64 RNA genes. Annotation predicted 38 genes involved in osmotic stress including the biosynthesis of osmoprotectants glycine-betaine, ectoine and osmoregulated periplasmic glucans. Genome analysis revealed also the versatility of the strain for emulsifying crude oil and metabolizing hydrocarbons. The ability of G11 to degrade crude oil components and to secrete a glycolipid biosurfactant with satisfying properties was experimentally confirmed and validated. Our results help to explain the exceptional capacity of G11 to survive at extreme desertic conditions, and highlight the metabolic features of this organism that has biotechnological and ecological potentialities.
Collapse
|
87
|
Draft Genome Sequence of Bacillus subtilis Strain FB6-3, Isolated from Fermented Bamboo Shoot. Microbiol Resour Announc 2018; 7:MRA01319-18. [PMID: 30533791 PMCID: PMC6256478 DOI: 10.1128/mra.01319-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 10/22/2018] [Indexed: 11/20/2022] Open
Abstract
Here, we report the draft genome sequence of Bacillus subtilis strain FB6-3, isolated from fermented bamboo shoot samples (Soibum) from Manipur, India. The genome was constructed to facilitate studies in evolution of the genetic code. The de novo assembly resulted in a chromosome size of 4,192,717 bp and 3,885 coding sequences.
Collapse
|
88
|
Daas MS, Rosana ARR, Acedo JZ, Douzane M, Nateche F, Kebbouche-Gana S, Vederas JC. Insights into the draft genome sequence of bioactives-producing Bacillus thuringiensis DNG9 isolated from Algerian soil-oil slough. Stand Genomic Sci 2018; 13:25. [PMID: 30344888 PMCID: PMC6186030 DOI: 10.1186/s40793-018-0331-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 09/28/2018] [Indexed: 12/16/2022] Open
Abstract
Bacillus thuringiensis is widely used as a bioinsecticide due to its ability to form parasporal crystals containing proteinaceous toxins. It is a member of the Bacillus cereus sensu lato, a group with low genetic diversity but produces several promising antimicrobial compounds. B. thuringiensis DNG9, isolated from an oil-contaminated slough in Algeria, has strong antibacterial, antifungal and biosurfactant properties. Here, we report the 6.06 Mbp draft genome sequence of B. thuringiensis DNG9. The genome encodes several gene inventories for the biosynthesis of bioactive compounds such as zwittermycin A, petrobactin, insecticidal toxins, polyhydroxyalkanoates and multiple bacteriocins. We expect the genome information of strain DNG9 will provide another model system to study pathogenicity against insect pests, plant diseases, and antimicrobial compound mining and comparative phylogenesis among the Bacillus cereus sensu lato group.
Collapse
Affiliation(s)
- Mohamed Seghir Daas
- Valcore Laboratory, Department of Biology, University M’Hamed Bougara of Boumerdes, 35000 Boumerdes, Algeria
- Food Technology Research Division, Institut National de la Recherche Agronomique d’Algérie, 16200, El Harrach, Algiers, Algeria
| | | | - Jeella Z. Acedo
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2 Canada
| | - Malika Douzane
- Food Technology Research Division, Institut National de la Recherche Agronomique d’Algérie, 16200, El Harrach, Algiers, Algeria
| | - Farida Nateche
- Microbiology Group, Laboratory of Cellular and Molecular Biology, Faculty of Biological Sciences, University of Science and Technology–Houari Boumediene, 16111, Bab Ezzouar, Algiers, Algeria
| | - Salima Kebbouche-Gana
- Valcore Laboratory, Department of Biology, University M’Hamed Bougara of Boumerdes, 35000 Boumerdes, Algeria
| | - John C. Vederas
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2 Canada
| |
Collapse
|
89
|
Parise D, Parise MTD, Viana MVC, Muñoz-Bucio AV, Cortés-Pérez YA, Arellano-Reynoso B, Díaz-Aparicio E, Dorella FA, Pereira FL, Carvalho AF, Figueiredo HCP, Ghosh P, Barh D, Gomide ACP, Azevedo VAC. First genome sequencing and comparative analyses of Corynebacterium pseudotuberculosis strains from Mexico. Stand Genomic Sci 2018; 13:21. [PMID: 30338024 PMCID: PMC6180578 DOI: 10.1186/s40793-018-0325-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 09/24/2018] [Indexed: 12/20/2022] Open
Abstract
Corynebacterium pseudotuberculosis is a pathogenic bacterium which has been rapidly spreading all over the world, causing economic losses in the agricultural sector and sporadically infecting humans. Six C. pseudotuberculosis strains were isolated from goats, sheep, and horses with distinct abscess locations. For the first time, Mexican genomes of this bacterium were sequenced and studied in silico. All strains were sequenced using Ion Personal Genome Machine sequencer, assembled using Newbler and SPAdes software. The automatic genome annotation was done using the software RAST and in-house scripts for transference, followed by manual curation using Artemis software and BLAST against NCBI and UniProt databases. The six genomes are publicly available in NCBI database. The analysis of nucleotide sequence similarity and the generated phylogenetic tree led to the observation that the Mexican strains are more similar between strains from the same host, but the genetic structure is probably more influenced by transportation of animals between farms than host preference. Also, a putative drug target was predicted and in silico analysis of 46 strains showed two gene clusters capable of differentiating the biovars equi and ovis: Restriction Modification system and CRISPR-Cas cluster.
Collapse
Affiliation(s)
- Doglas Parise
- Laboratory of Cellular and Molecular Genetics, Institute of Biologic Sciences, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
| | - Mariana T D Parise
- Laboratory of Cellular and Molecular Genetics, Institute of Biologic Sciences, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
| | - Marcus V C Viana
- Laboratory of Cellular and Molecular Genetics, Institute of Biologic Sciences, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
| | - Adrian V Muñoz-Bucio
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine and Zootechnics, National Autonomous University of Mexico, Mexico City, Mexico
| | - Yazmin A Cortés-Pérez
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine and Zootechnics, National Autonomous University of Mexico, Mexico City, Mexico
| | - Beatriz Arellano-Reynoso
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine and Zootechnics, National Autonomous University of Mexico, Mexico City, Mexico
| | - Efrén Díaz-Aparicio
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine and Zootechnics, National Autonomous University of Mexico, Mexico City, Mexico
| | - Fernanda A Dorella
- Aquacen - National Reference Laboratory for Aquatic Animal Diseases, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
| | - Felipe L Pereira
- Aquacen - National Reference Laboratory for Aquatic Animal Diseases, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
| | - Alex F Carvalho
- Aquacen - National Reference Laboratory for Aquatic Animal Diseases, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
| | - Henrique C P Figueiredo
- Aquacen - National Reference Laboratory for Aquatic Animal Diseases, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA-23284 USA
| | - Debmalya Barh
- Laboratory of Cellular and Molecular Genetics, Institute of Biologic Sciences, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, West Bengal 721172 India
- Division of Bioinformatics and Computational Genomics, NITTE University Center for Science Education and Research (NUCSER), NITTE (Deemed to be University), Deralakatte, Mangaluru, Karnataka India
| | - Anne C P Gomide
- Laboratory of Cellular and Molecular Genetics, Institute of Biologic Sciences, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
| | - Vasco A C Azevedo
- Laboratory of Cellular and Molecular Genetics, Institute of Biologic Sciences, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
| |
Collapse
|
90
|
Pathogenicity, Phylogenetic relationship and NGS based identification and assembly of tumorigenic Agrobacterium radiabacter plasmidic and chromosomic reads isolated from Prunus duclcis. Genomics 2018; 111:1423-1430. [PMID: 30287402 DOI: 10.1016/j.ygeno.2018.09.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 09/25/2018] [Indexed: 11/22/2022]
Abstract
Although many Agrobacterium radiobacter strains have already been identified, only a few genomes of strains belonging to genomovar G4 have been sequenced so far. In this study, we report the first virulent genome sequence of Agrobacterium radiobacter strain tun 183, which is highly virulent to almond specie. The genome size was estimated to be 5.53 Mb, with 57.9%GC content. In total, 6486 genes encoding proteins and 61 genes encoding RNAs were identified in this genome. Comparisons with the available sequenced genomes of genomovar G4 as well as with other A. sp. were conducted, revealing a hexapartite genome containing circular and linear chromosomes in addition to two accessory plasmids and a tumor inducing plasmid (pTi) in strain tun 183. The phylogenetic analysis of recA gene clearly showed the clustering of tun 183 strain within genomovar G4, supporting the monophyly within this genomovar.
Collapse
|
91
|
First De Novo Draft Genome Sequence of the Pathogenic Fungus Fusarium udum F02845, Associated with Pigeonpea (Cajanus cajan L. Millspaugh) Wilt. Microbiol Resour Announc 2018; 7:MRA01001-18. [PMID: 30533683 PMCID: PMC6256552 DOI: 10.1128/mra.01001-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 09/08/2018] [Indexed: 11/20/2022] Open
Abstract
Fusarium udum F02845 is a destructive fungal pathogen which causes pigeonpea (Cajanus cajan L. Millspaugh) wilt. Fusarium udum F02845 is a destructive fungal pathogen which causes pigeonpea (Cajanus cajan L. Millspaugh) wilt. Here we report the first de novo draft assembly of Fusarium udum F02845, isolated from an infected pigeonpea stem. The genome was determined to be 56.38 Mb in size, with a G+C content of 42.44%, and predicted to have 712 scaffolds with a total number of 11,829 genes.
Collapse
|
92
|
Alfsnes K, Frye SA, Eriksson J, Eldholm V, Brynildsrud OB, Bohlin J, Harrison OB, Hood DW, Maiden MCJ, Tønjum T, Ambur OH. A genomic view of experimental intraspecies and interspecies transformation of a rifampicin-resistance allele into Neisseria meningitidis. Microb Genom 2018; 4. [PMID: 30251949 PMCID: PMC6321871 DOI: 10.1099/mgen.0.000222] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The spread of antibiotic resistance within and between different bacterial populations is a major health problem on a global scale. The identification of genetic transformation in genomic data from Neisseria meningitidis, the meningococcus (Mc), and other bacteria is problematic, since similar or even identical alleles may be involved. A particular challenge in naturally transformable bacteria generally is to distinguish between common ancestry and true recombined sites in sampled genome sequences. Furthermore, the identification of recombination following experimental transformation of homologous alleles requires identifiable differences between donor and recipient, which in itself influences the propensity for homologous recombination (HR). This study identifies the distribution of HR events following intraspecies and interspecies Mc transformations of rpoB alleles encoding rifampicin resistance by whole-genome DNA sequencing and single nucleotide variant analysis. The HR events analysed were confined to the genomic region surrounding the single nucleotide genetic marker used for selection. An exponential length distribution of these recombined events was found, ranging from a few nucleotides to about 72 kb stretches. The lengths of imported sequences were on average found to be longer following experimental transformation of the recipient with genomic DNA from an intraspecies versus an interspecies donor (P<0.001). The recombination events were generally observed to be mosaic, with donor sequences interspersed with recipient sequence. Here, we present four models to explain these observations, by fragmentation of the transformed DNA, by interruptions of the recombination mechanism, by secondary recombination of endogenous self-DNA, or by repair/replication mechanisms.
Collapse
Affiliation(s)
| | - Stephan A Frye
- 2Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway
| | - Jens Eriksson
- 2Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway
| | - Vegard Eldholm
- 3Department of Molecular Biology, Domain of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Ola Brønstad Brynildsrud
- 4Department of Methodology Research and Analysis, Domain of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Jon Bohlin
- 4Department of Methodology Research and Analysis, Domain of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Odile B Harrison
- 5The Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Derek W Hood
- 6Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, UK
| | - Martin C J Maiden
- 5The Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Tone Tønjum
- 2Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway.,7Department of Microbiology, University of Oslo, Oslo, Norway
| | - Ole Herman Ambur
- 2Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway.,8OsloMet - Oslo Metropolitan University, Oslo, Norway
| |
Collapse
|
93
|
do Carmo FLR, Silva WM, Tavares GC, Ibraim IC, Cordeiro BF, Oliveira ER, Rabah H, Cauty C, da Silva SH, Canário Viana MV, Caetano ACB, Dos Santos RG, de Oliveira Carvalho RD, Jardin J, Pereira FL, Folador EL, Le Loir Y, Figueiredo HCP, Jan G, Azevedo V. Mutation of the Surface Layer Protein SlpB Has Pleiotropic Effects in the Probiotic Propionibacterium freudenreichii CIRM-BIA 129. Front Microbiol 2018; 9:1807. [PMID: 30174657 PMCID: PMC6107788 DOI: 10.3389/fmicb.2018.01807] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 07/18/2018] [Indexed: 01/19/2023] Open
Abstract
Propionibacterium freudenreichii is a beneficial Gram-positive bacterium, traditionally used as a cheese-ripening starter, and currently considered as an emerging probiotic. As an example, the P. freudenreichii CIRM-BIA 129 strain recently revealed promising immunomodulatory properties. Its consumption accordingly exerts healing effects in different animal models of colitis, suggesting a potent role in the context of inflammatory bowel diseases. This anti-inflammatory effect depends on surface layer proteins (SLPs). SLPs may be involved in key functions in probiotics, such as persistence within the gut, adhesion to host cells and mucus, or immunomodulation. Several SLPs coexist in P. freudenreichii CIRM-BIA 129 and mediate immunomodulation and adhesion. A mutant P. freudenreichii CIRM-BIA 129ΔslpB (CB129ΔslpB) strain was shown to exhibit decreased adhesion to intestinal epithelial cells. In the present study, we thoroughly analyzed the impact of this mutation on cellular properties. Firstly, we investigated alterations of surface properties in CB129ΔslpB. Surface extractable proteins, surface charges (ζ-potential) and surface hydrophobicity were affected by the mutation. Whole-cell proteomics, using high definition mass spectrometry, identified 1,288 quantifiable proteins in the wild-type strain, i.e., 53% of the theoretical proteome predicted according to P. freudenreichii CIRM-BIA 129 genome sequence. In the mutant strain, we detected 1,252 proteins, including 1,227 proteins in common with the wild-type strain. Comparative quantitative analysis revealed 97 proteins with significant differences between wild-type and mutant strains. These proteins are involved in various cellular process like signaling, metabolism, and DNA repair and replication. Finally, in silico analysis predicted that slpB gene is not part of an operon, thus not affecting the downstream genes after gene knockout. This study, in accordance with the various roles attributed in the literature to SLPs, revealed a pleiotropic effect of a single slpB mutation, in the probiotic P. freudenreichii. This suggests that SlpB may be at a central node of cellular processes and confirms that both nature and amount of SLPs, which are highly variable within the P. freudenreichii species, determine the probiotic abilities of strains.
Collapse
Affiliation(s)
- Fillipe L R do Carmo
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Institut National de la Recherche Agronomique, UMR1253 Science & Technologie du Lait & de l'Oeuf, Rennes, France.,Agrocampus Ouest, UMR1253 Science & Technologie du Lait & de l'Oeuf, Rennes, France
| | - Wanderson M Silva
- Instituto de Biotecnología, CICVyA - Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Guilherme C Tavares
- AQUACEN, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Izabela C Ibraim
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Barbara F Cordeiro
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Emiliano R Oliveira
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Houem Rabah
- Institut National de la Recherche Agronomique, UMR1253 Science & Technologie du Lait & de l'Oeuf, Rennes, France.,Agrocampus Ouest, UMR1253 Science & Technologie du Lait & de l'Oeuf, Rennes, France
| | - Chantal Cauty
- Institut National de la Recherche Agronomique, UMR1253 Science & Technologie du Lait & de l'Oeuf, Rennes, France
| | - Sara H da Silva
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Marcus V Canário Viana
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ana C B Caetano
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Roselane G Dos Santos
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Julien Jardin
- Institut National de la Recherche Agronomique, UMR1253 Science & Technologie du Lait & de l'Oeuf, Rennes, France
| | - Felipe L Pereira
- AQUACEN, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Edson L Folador
- Centro de Biotecnologia, Universidade Federal da Paraíba, João Pessoa, Brazil
| | - Yves Le Loir
- Institut National de la Recherche Agronomique, UMR1253 Science & Technologie du Lait & de l'Oeuf, Rennes, France.,Agrocampus Ouest, UMR1253 Science & Technologie du Lait & de l'Oeuf, Rennes, France
| | - Henrique C P Figueiredo
- AQUACEN, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Gwénaël Jan
- Institut National de la Recherche Agronomique, UMR1253 Science & Technologie du Lait & de l'Oeuf, Rennes, France.,Agrocampus Ouest, UMR1253 Science & Technologie du Lait & de l'Oeuf, Rennes, France
| | - Vasco Azevedo
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| |
Collapse
|
94
|
Faria M, Bordin N, Kizina J, Harder J, Devos D, Lage OM. Planctomycetes attached to algal surfaces: Insight into their genomes. Genomics 2018; 110:231-238. [PMID: 29074368 DOI: 10.1016/j.ygeno.2017.10.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/06/2017] [Accepted: 10/21/2017] [Indexed: 01/03/2023]
Abstract
Planctomycetes are bacteria with complex molecular and cellular biology. They have large genomes, some over 7Mb, and complex life cycles that include motile cells and sessile cells. Some live on the complex biofilm of macroalgae. Factors governing their life in this environment were investigated at the genomic level. We analyzed the genomes of three planctomycetes isolated from algal surfaces. The genomes were 6.6Mbp to 8.1Mbp large. Genes for outer-membrane proteins, peptidoglycan and lipopolysaccharide biosynthesis were present. Rubripirellula obstinata LF1T, Roseimaritima ulvae UC8T and Mariniblastus fucicola FC18T shared with Rhodopirellula baltica and R. rubra SWK7 unique proteins related to metal binding systems, phosphate metabolism, chemotaxis, and stress response. These functions may contribute to their ecological success in such a complex environment. Exceptionally huge proteins (6000 to 10,000 amino-acids) with extracellular, periplasmic or membrane-associated locations were found which may be involved in biofilm formation or cell adhesion.
Collapse
Affiliation(s)
- Mafalda Faria
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Nicola Bordin
- Centro Andaluz de Biología del Desarollo, CSIC, Junta de Andalucía, Universidad Pablo de Olavide, Carretera de Utrera, Km. 1, 41013 Seville, Spain
| | - Jana Kizina
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany
| | - Jens Harder
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany
| | - Damien Devos
- Centro Andaluz de Biología del Desarollo, CSIC, Junta de Andalucía, Universidad Pablo de Olavide, Carretera de Utrera, Km. 1, 41013 Seville, Spain
| | - Olga M Lage
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal.
| |
Collapse
|
95
|
PirVP genes causing AHPND identified in a new Vibrio species (Vibrio punensis) within the commensal Orientalis clade. Sci Rep 2018; 8:13080. [PMID: 30166588 PMCID: PMC6117253 DOI: 10.1038/s41598-018-30903-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 08/03/2018] [Indexed: 11/20/2022] Open
Abstract
Acute hepatopancreatic necrosis disease (AHPND) has extended rapidly, causing alarming shrimp mortalities. Initially, the only known causative agent was Vibrio parahaemolyticus carrying a plasmid coding for the mortal toxins PirVP. Recently, it has been found that the plasmid and hence the disease, could be transferred among members of the Harveyi clade. The current study performs a genomic characterization of an isolate capable of developing AHPND in shrimp. Mortality studies and molecular and histopathological analyses showed the infection capacity of the strain. Multilocus sequence analysis placed the bacteria as a member of the Orientalis clade, well known for containing commensal and even probiotic bacteria used in the shrimp industry. Further whole genome comparative analyses, including Vibrio species from the Orientalis clade, and phylogenomic metrics (TETRA, ANI and DDH) showed that the isolate belongs to a previously unidentified species, now named Vibrio punensis sp. nov. strain BA55. Our findings show that the gene transfer capacity of Vibrio species goes beyond the clade classification, demonstrating a new pathogenic capacity to a previously known commensal clade. The presence of these genes in a different Vibrio clade may contribute to the knowledge of the Vibrio pathogenesis and has major implications for the spread of emerging diseases.
Collapse
|
96
|
Gomide ACP, Ibraim IC, Alves JTC, de Sá PG, de Oliveira Silva YR, Santana MP, Silva WM, Folador EL, Mariano DCB, de Paula Castro TL, Barbosa S, Dorella FA, Carvalho AF, Pereira FL, Leal CAG, Figueiredo HCP, Azevedo V, Silva A, Folador ARC. Transcriptome analysis of Corynebacterium pseudotuberculosis biovar Equi in two conditions of the environmental stress. Gene 2018; 677:349-360. [PMID: 30098432 DOI: 10.1016/j.gene.2018.08.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 07/10/2018] [Accepted: 08/06/2018] [Indexed: 11/30/2022]
Abstract
Corynebacterium pseudotuberculosis has been widely studied in an effort to understand its biological evolution. Transcriptomics has revealed possible candidates for virulence and pathogenicity factors of strain 1002 (biovar Ovis). Because C. pseudotuberculosis is classified into two biovars, Ovis and Equi, it was interesting to assess the transcriptional profile of biovar Equi strain 258, the causative agent of ulcerative lymphangitis. The genome of this strain was re-sequenced; the reassembly was completed using optical mapping technology, and the sequence was subsequently re-annotated. Two growth conditions that occur during the host infection process were simulated for the transcriptome: the osmotic and acid medium. Genes that may be associated with the microorganism's resilience under unfavorable conditions were identified through RNAseq, including genes present in pathogenicity islands. The RT-qPCR was performed to confirm the results in biological triplicate for each condition for some genes. The results extend our knowledge of the factors associated with the spread and persistence of C. pseudotuberculosis during the infection process and suggest possible avenues for studies related to the development of vaccines, diagnosis, and therapies that might help minimize damage to agribusinesses.
Collapse
Affiliation(s)
- Anne Cybelle Pinto Gomide
- Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Av. Antônio Carlos, Belo Horizonte 31.270-901, Brazil.
| | - Izabela Coimbra Ibraim
- Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Av. Antônio Carlos, Belo Horizonte 31.270-901, Brazil
| | - Jorianne T C Alves
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil, Rua Augusto Corrêa, Belém 66.075-110, Brazil
| | - Pablo Gomes de Sá
- Federal Rural University of Amazonia, Rodovia PA 140, 2428 Tomé-Açu, PA, Brazil
| | - Yuri Rafael de Oliveira Silva
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil, Rua Augusto Corrêa, Belém 66.075-110, Brazil
| | - Mariana Passos Santana
- Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Av. Antônio Carlos, Belo Horizonte 31.270-901, Brazil
| | - Wanderson Marques Silva
- National Institute of Agricultural Technology, Los Reseros y Nicolás Repetto, Hurlingham 1686, Argentina
| | - Edson Luiz Folador
- Biotechnology Center, Federal University of Paraíba, João Pessoa, Brazil.
| | - Diego C B Mariano
- Department of Computer Sciences, Institute of Exact Sciences, Federal University of Minas Gerais, Av. Antônio Carlos, Belo Horizonte 31.270-901, Brazil.
| | - Thiago Luiz de Paula Castro
- Department of Biointeraction, Institute of Health Sciences, Federal University of Bahia, Av. Reitor Miguel Calmon, s/n, Vale do Canela, Bahia, Brazil
| | - Silvanira Barbosa
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil, Rua Augusto Corrêa, Belém 66.075-110, Brazil
| | - Fernanda Alves Dorella
- AQUACEN - National Reference Laboratory of Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Alex F Carvalho
- AQUACEN - National Reference Laboratory of Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Felipe L Pereira
- AQUACEN - National Reference Laboratory of Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Brazil.
| | - Carlos A G Leal
- AQUACEN - National Reference Laboratory of Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Brazil.
| | - Henrique C P Figueiredo
- AQUACEN - National Reference Laboratory of Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Vasco Azevedo
- Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Av. Antônio Carlos, Belo Horizonte 31.270-901, Brazil.
| | - Artur Silva
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil, Rua Augusto Corrêa, Belém 66.075-110, Brazil.
| | - Adriana Ribeiro Carneiro Folador
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil, Rua Augusto Corrêa, Belém 66.075-110, Brazil.
| |
Collapse
|
97
|
Yadav S, Dubey SK. Cellulose degradation potential of Paenibacillus lautus strain BHU3 and its whole genome sequence. BIORESOURCE TECHNOLOGY 2018; 262:124-131. [PMID: 29702421 DOI: 10.1016/j.biortech.2018.04.067] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 04/15/2018] [Accepted: 04/17/2018] [Indexed: 06/08/2023]
Abstract
The aim of this work was to study cellulose degradation and whole genome sequence of Paenibacillus lautus BHU3 isolate. The 16S rRNA gene sequence analysis revealed genetic relatedness (99%) of Iso 7 with Paenibacillus lautus, Iso 8 with Paenibacillus lactis, and Iso 9 with Bacillus amyloliquefaciens. Clear zone formation followed by CMCase and FPase assays exhibited cellulolytic potential in the order: P. lautus > P. lactis > B. amyloliquefaciens. The most potent isolate, Paenibacillus lautus strain BHU3 was subjected to whole genome analysis with reference to the genomic basis of cellulose degradation. Results showed that P. lautus strain BHU3 contains 6234 protein coding genes of which, 316 were associated with the carbohydrate metabolism. Further, genomic CAZymes analysis indicated that the P. lautus strain BHU3 comprising a range of glycoside hydrolase (GH) family genes (143), may play the vital role(s) in enhancing the cellulolytic attributes, and could be the useful tool for lignocellulosic biomass degradation and waste management.
Collapse
Affiliation(s)
- Suman Yadav
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Suresh Kumar Dubey
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
| |
Collapse
|
98
|
Dantur KI, Chalfoun NR, Claps MP, Tórtora ML, Silva C, Jure Á, Porcel N, Bianco MI, Vojnov A, Castagnaro AP, Welin B. The Endophytic Strain Klebsiella michiganensis Kd70 Lacks Pathogenic Island-Like Regions in Its Genome and Is Incapable of Infecting the Urinary Tract in Mice. Front Microbiol 2018; 9:1548. [PMID: 30061870 PMCID: PMC6054940 DOI: 10.3389/fmicb.2018.01548] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 06/21/2018] [Indexed: 01/14/2023] Open
Abstract
Klebsiella spp. have been isolated from many different environmental habitats but have mainly been associated with nosocomial acquired diseases in humans. Although there are many recently published sequenced genomes of members of this genus, there are very few studies on whole genome comparisons between clinical and non-clinical isolates, and it is therefore still an open question if a strain found in nature is capable of infecting humans/animals. Klebsiella michiganensis Kd70 was isolated from the intestine of larvae of Diatraea saccharalis but genome analysis revealed multiple genes associated with colonization and growth promotion in plants suggesting an endophytic lifestyle. Kd70 cells labeled with gfp confirmed capability of root colonization and soil application of Kd70 promoted growth in greenhouse grown sugarcane. Further genomic analysis showed that the Kd70 genome harbored fewer mammalian virulence factors and no pathogen island-like regions when compared to clinical isolates of this species, suggesting attenuated animal/human pathogenicity. This postulation was corroborated by in vivo experiments in which it was demonstrated that Kd70 was unable to infect the mouse urinary tract. This is to the best of our knowledge the first experimental example of a member of a pathogenic Klebsiella spp. unable to infect a mammalian organism. A proteomic comparison deduced from the genomic sequence between Kd70 and several other K. michiganensis strains showed a high similarity with isolates from many different environments including clinical strains, and demonstrated the existence of conserved genetic lineages within this species harboring members from different ecological niches and geographical locations. Furthermore, most genetic differences were found to be associated with genomic islands of clinical isolates, suggesting that evolutionary adaptation of animal pathogenicity to a large extent has depended on horizontal gene transfer. In conclusion our results demonstrate the importance of conducting thorough in vivo pathogenicity studies before presupposing animal/human virulence of non-clinical bacterial isolates.
Collapse
Affiliation(s)
- Karina I. Dantur
- Instituto de Tecnología Agroindustrial del Noroeste Argentino, Estación Experimental Agroindustrial Obispo Colombres – Consejo Nacional de Investigaciones Científicas y Técnicas, Las Talitas, Argentina
| | - Nadia R. Chalfoun
- Instituto de Tecnología Agroindustrial del Noroeste Argentino, Estación Experimental Agroindustrial Obispo Colombres – Consejo Nacional de Investigaciones Científicas y Técnicas, Las Talitas, Argentina
| | - Maria P. Claps
- Instituto de Tecnología Agroindustrial del Noroeste Argentino, Estación Experimental Agroindustrial Obispo Colombres – Consejo Nacional de Investigaciones Científicas y Técnicas, Las Talitas, Argentina
| | - Maria L. Tórtora
- Instituto de Tecnología Agroindustrial del Noroeste Argentino, Estación Experimental Agroindustrial Obispo Colombres – Consejo Nacional de Investigaciones Científicas y Técnicas, Las Talitas, Argentina
| | - Clara Silva
- Instituto de Microbiología, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Tucumán, Argentina
| | - Ángela Jure
- Instituto de Microbiología, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Tucumán, Argentina
| | - Norma Porcel
- Instituto de Microbiología, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Tucumán, Argentina
| | - Maria I. Bianco
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará – Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Adrián Vojnov
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará – Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Atilio P. Castagnaro
- Instituto de Tecnología Agroindustrial del Noroeste Argentino, Estación Experimental Agroindustrial Obispo Colombres – Consejo Nacional de Investigaciones Científicas y Técnicas, Las Talitas, Argentina
| | - Björn Welin
- Instituto de Tecnología Agroindustrial del Noroeste Argentino, Estación Experimental Agroindustrial Obispo Colombres – Consejo Nacional de Investigaciones Científicas y Técnicas, Las Talitas, Argentina
| |
Collapse
|
99
|
Complete Genome Sequence of Bacillus velezensis LABIM40, an Effective Antagonist of Fungal Plant Pathogens. GENOME ANNOUNCEMENTS 2018; 6:6/25/e00595-18. [PMID: 29930076 PMCID: PMC6013614 DOI: 10.1128/genomea.00595-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bacillus velezensis strain LABIM40 holds high potential for biological control of plant pathogens. Its complete genome contains one chromosome of 3,972,310 bp with 3,777 DNA coding sequences and displays 33 gene clusters potentially involved in the suppression of fungal pathogens. Bacillus velezensis strain LABIM40 holds high potential for biological control of plant pathogens. Its complete genome contains one chromosome of 3,972,310 bp with 3,777 DNA coding sequences and displays 33 gene clusters potentially involved in the suppression of fungal pathogens.
Collapse
|
100
|
Tschitschko B, Erdmann S, DeMaere MZ, Roux S, Panwar P, Allen MA, Williams TJ, Brazendale S, Hancock AM, Eloe-Fadrosh EA, Cavicchioli R. Genomic variation and biogeography of Antarctic haloarchaea. MICROBIOME 2018; 6:113. [PMID: 29925429 PMCID: PMC6011602 DOI: 10.1186/s40168-018-0495-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 06/06/2018] [Indexed: 05/10/2023]
Abstract
BACKGROUND The genomes of halophilic archaea (haloarchaea) often comprise multiple replicons. Genomic variation in haloarchaea has been linked to viral infection pressure and, in the case of Antarctic communities, can be caused by intergenera gene exchange. To expand understanding of genome variation and biogeography of Antarctic haloarchaea, here we assessed genomic variation between two strains of Halorubrum lacusprofundi that were isolated from Antarctic hypersaline lakes from different regions (Vestfold Hills and Rauer Islands). To assess variation in haloarchaeal populations, including the presence of genomic islands, metagenomes from six hypersaline Antarctic lakes were characterised. RESULTS The sequence of the largest replicon of each Hrr. lacusprofundi strain (primary replicon) was highly conserved, while each of the strains' two smaller replicons (secondary replicons) were highly variable. Intergenera gene exchange was identified, including the sharing of a type I-B CRISPR system. Evaluation of infectivity of an Antarctic halovirus provided experimental evidence for the differential susceptibility of the strains, bolstering inferences that strain variation is important for modulating interactions with viruses. A relationship was found between genomic structuring and the location of variation within replicons and genomic islands, demonstrating that the way in which haloarchaea accommodate genomic variability relates to replicon structuring. Metagenome read and contig mapping and clustering and scaling analyses demonstrated biogeographical patterning of variation consistent with environment and distance effects. The metagenome data also demonstrated that specific haloarchaeal species dominated the hypersaline systems indicating they are endemic to Antarctica. CONCLUSION The study describes how genomic variation manifests in Antarctic-lake haloarchaeal communities and provides the basis for future assessments of Antarctic regional and global biogeography of haloarchaea.
Collapse
Affiliation(s)
- Bernhard Tschitschko
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
- Present Address: Climate Change Cluster, Department of Environmental Sciences, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Susanne Erdmann
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Matthew Z DeMaere
- i3 Institute, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Simon Roux
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Pratibha Panwar
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Michelle A Allen
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Timothy J Williams
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Sarah Brazendale
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
- , Present Address: 476 Lancaster Rd, Pegarah, Australia
| | - Alyce M Hancock
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
- Present Address: University of Tasmania Institute of Marine and Antarctic Studies, Antarctic Gateway Partnership and Antarctic Climate and Ecosystem Research Centre, Battery Point, Tasmania, Australia
| | | | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia.
| |
Collapse
|