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de Souza Moreira FM, Cabral Michel D, Marques Cardoso R. The elite strain INPA03-11B approved as a cowpea inoculant in Brazil represents a new Bradyrhizobium species and it has high adaptability to stressful soil conditions. Braz J Microbiol 2024:10.1007/s42770-024-01280-7. [PMID: 38393616 DOI: 10.1007/s42770-024-01280-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 02/04/2024] [Indexed: 02/25/2024] Open
Abstract
The strain INPA03-11BT, isolated in the 1980s from nodules of Centrosema sp. collected in Manaus, Amazonas, Brazil, was approved by the Brazilian Ministry of Agriculture as a cowpea inoculant in 2004. Since then, several studies have been conducted regarding its phenotypic, genetic, and symbiotic characteristics under axenic and field conditions. Phenotypic features demonstrate its high adaptability to stressful soil conditions, such as tolerance to acidity, high temperatures, and 13 antibiotics, and, especially, its high symbiotic efficiency with cowpea and soybean, proven in the field. The nodC and nifH phylogenies placed the INPA strain in the same clade as the species B. macuxiense BR 10303T which was also isolated from the Amazon region. The sequencing of the 16S rRNA ribosomal gene and housekeeping genes, as well as BOX-PCR profiles, showed its potential as a new species, which was confirmed by a similarity percentage of 94.7% and 92.6% in Average Nucleotide Identity with the closest phylogenetically related species Bradyrhizobium tropiciagri CNPSo1112T and B. viridifuturi SEMIA690T, respectively. dDDH values between INPA03-11BT and both CNPSo 1112T and SEMIA690T were respectively 58.5% and 48.1%, which are much lower than the limit for species boundary (70%). Therefore, we propose the name Bradyrhizobium amazonense for INPA03-11BT (= BR3301 = SEMIA6463).
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Affiliation(s)
- Fatima Maria de Souza Moreira
- Setor de Biologia, Microbiologia e Processos Biológicos do Solo, Universidade Federal de Lavras, Lavras, MG, CEP 37200-900, Brazil.
| | - Daniele Cabral Michel
- Setor de Biologia, Microbiologia e Processos Biológicos do Solo, Universidade Federal de Lavras, Lavras, MG, CEP 37200-900, Brazil
| | - Raysa Marques Cardoso
- Setor de Biologia, Microbiologia e Processos Biológicos do Solo, Universidade Federal de Lavras, Lavras, MG, CEP 37200-900, Brazil
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Lindner BG, Gerhardt K, Feistel DJ, Rodriguez-R LM, Hatt JK, Konstantinidis KT. A user's guide to the bioinformatic analysis of shotgun metagenomic sequence data for bacterial pathogen detection. Int J Food Microbiol 2024; 410:110488. [PMID: 38035404 DOI: 10.1016/j.ijfoodmicro.2023.110488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 09/15/2023] [Accepted: 11/11/2023] [Indexed: 12/02/2023]
Abstract
Metagenomics, i.e., shotgun sequencing of the total microbial community DNA from a sample, has become a mature technique but its application to pathogen detection in clinical, environmental, and food samples is far from common or standardized. In this review, we summarize ongoing developments in metagenomic sequence analysis that facilitate its wider application to pathogen detection. We examine theoretical frameworks for estimating the limit of detection for a particular level of sequencing effort, current approaches for achieving species and strain analytical resolution, and discuss some relevant modern tools for these tasks. While these recent advances are significant and establish metagenomics as a powerful tool to provide insights not easily attained by culture-based approaches, metagenomics is unlikely to emerge as a widespread, routine monitoring tool in the near future due to its inherently high detection limits, cost, and inability to easily distinguish between viable and non-viable cells. Instead, metagenomics seems best poised for applications involving special circumstances otherwise challenging for culture-based and molecular (e.g., PCR-based) approaches such as the de novo detection of novel pathogens, cases of co-infection by more than one pathogen, and situations where it is important to assess the genomic composition of the pathogenic population(s) and/or its impact on the indigenous microbiome.
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Affiliation(s)
- Blake G Lindner
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Kenji Gerhardt
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Dorian J Feistel
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Luis M Rodriguez-R
- Department of Microbiology, Digital Science Center (DiSC), University of Innsbruck, Innsbruck, Austria
| | - Janet K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA; School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
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Kaur J, Sood U, Talwar C, Whitman WB, Lal R. Phylogenomics-based reclassifications in the genus Psychrobacter including emended descriptions of Psychrobacter pacificensis, Psychrobacter proteolyticus and Psychrobacter submarinus. Antonie Van Leeuwenhoek 2023; 116:1113-1121. [PMID: 37640969 DOI: 10.1007/s10482-023-01871-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 08/09/2023] [Indexed: 08/31/2023]
Abstract
The taxonomic status of 43 Psychrobacter species was examined based upon the genome sequences of their type strains. Three groups of type strains were found to be conspecific, Psychrobacter salsus Shivaji et al. (Syst Appl Microbiol 27:628-635, 2004. 10.1078/0723202042369956) and Psychrobacter submarinus Romanenko et al. (Int J Syst Evol Microbiol 52:1291-1297, 2002. 10.1099/00207713-52-4-1291); Psychrobacter oceani Matsuyama et al. (Int J Syst Evol Microbiol 65:1450-1455, 2015. 10.1099/ijs.0.000118) and Psychrobacter pacificensis Maruyama et al. (Int J Syst Evol Microbiol 50:835-846, 2000. 10.1099/00207713-50-2-835); and Psychrobacter proteolyticus Denner et al. (Syst Appl Microbiol 24:44-53, 2001. 10.1078/0723-2020-00006), Psychrobacter marincola Romanenko et al. (Int J Syst Evol Microbiol 52:1291-1297, 2002. 10.1099/00207713-52-4-1291) and Psychrobacter adeliensis Shivaji et al. (Syst Appl Microbiol 27:628-635, 2004. 10.1078/0723202042369956). For all three groups, the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values are > 97.69% and > 80.2%, respectively. This conclusion is supported by similarities in morphology, growth properties, and fatty acid compositions. Based on this evidence, we propose the reclassification of Psychrobacter salsus Shivaji et al. (Syst Appl Microbiol 27:628-635, 2004. 10.1078/0723202042369956) as a later heterotypic synonym of Psychrobacter submarinus Romanenko et al. (Int J Syst Evol Microbiol 52:1291-1297, 2002. 10.1099/00207713-52-4-1291); Psychrobacter oceani Matsuyama et al. (Int J Syst Evol Microbiol 65:1450-1455, 2015. 10.1099/ijs.0.000118) as a later heterotypic synonym of Psychrobacter pacificensis Maruyama et al. (Int J Syst Evol Microbiol 50:835-846, 2000. 10.1099/00207713-50-2-835), and Psychrobacter marincola Romanenko et al. (Int J Syst Evol Microbiol 52:1291-1297, 2002. 10.1099/00207713-52-4-1291) and Psychrobacter adeliensis Shivaji et al. (Syst Appl Microbiol 27:628-635, 2004. 10.1078/0723202042369956) as later heterotypic synonyms of Psychrobacter proteolyticus Denner et al. (Syst Appl Microbiol 24:44-53, 2001. 10.1078/0723-2020-00006).
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Affiliation(s)
- Jasvinder Kaur
- Gargi College, University of Delhi, Siri Fort Road, New Delhi, 110 049, India
| | - Utkarsh Sood
- Department of Zoology, Kirori Mal College, University of Delhi, Delhi, 110007, India.
| | - Chandni Talwar
- Department of Zoology, University of Delhi, Delhi, 110007, India
- Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, GA, 30602, USA
| | - Rup Lal
- Acharya Narendra Dev College, University of Delhi, New Delhi, 110019, India.
- PhixGen Private Limited, Gurugram, Haryana, 122001, India.
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Akita H, Shinto Y, Kimura ZI. Isolation, draft genome sequence, and identification of Paenibacillus glycanilyticus subsp. hiroshimensis CCS26. J Genomics 2023; 11:48-51. [PMID: 37915958 PMCID: PMC10615617 DOI: 10.7150/jgen.87229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 09/15/2023] [Indexed: 11/03/2023] Open
Abstract
To isolate the useful strain for fermentation to produce bioactive compounds, we screened oligotrophic bacteria, and then strain CCS26 was isolated from leaf soil collected in Japan. This strain was capable of growth on low-nutrient medium. To elucidate the taxonomy of strain CCS26, we determined the 16S rRNA gene and draft genome sequences, respectively. A phylogenetic tree based on 16S rRNA gene sequences showed that strain CCS26 clustered with Paenibacillus species. The draft genome sequence of strain CCS26 consisted of a total of 90 contigs containing 6,957,994 bp, with a GC content of 50.8% and comprising 6,343 predicted coding sequences. Based on analysis of the average nucleotide identity with the draft genome sequence, the strain was identified as P. glycanilyticus subsp. hiroshimensis CCS26.
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Affiliation(s)
- Hironaga Akita
- College of Industrial Technology, Nihon University, 1-2-1 Izumi-cho, Narashino, Chiba 275-8575, Japan
| | - Yoshiki Shinto
- Department of Civil and Environmental Engineering, National Institute of Technology, Kure College, 2-2-11 Aga-minami, Kure, Hiroshima 737-8506, Japan
| | - Zen-ichiro Kimura
- Department of Civil and Environmental Engineering, National Institute of Technology, Kure College, 2-2-11 Aga-minami, Kure, Hiroshima 737-8506, Japan
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Daliri EBM, Balnionytė T, Lastauskienė E, Burokas A. Draft genome sequence dataset of Latilactobacillus curvatus PN39MY isolated from fermented vegetables. Data Brief 2023; 49:109436. [PMID: 37501729 PMCID: PMC10369389 DOI: 10.1016/j.dib.2023.109436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/14/2023] [Accepted: 07/17/2023] [Indexed: 07/29/2023] Open
Abstract
Here we report the draft genome sequence of the Latilactobacillus curvatus PN39MY strain. The strain was isolated from Lithuanian traditionally (homemade) fermented cucumber. The genome consisted of 83 contigs with a total size of 1,899,018 bp, an N50 of 40562 and a GC% of 42.1. After sequence trimming, 83 contigs were annotated and 1910 genes were coding sequences. The average nucleotide identity (ANI) between PN39MY and Latilactobacillus curvatus_ZJUNIT8 was 99.45% identifying the strain as Latilactobacillus curvatus. No genes related to antimicrobial resistance or virulence factors were found. The data presented here can be used in comparative genomics to identify antimicrobial resistant genes, plasmids and/or virulence factors that may be present in related Latilactobacillus species. The draft genome sequence data was deposited at NCBI under Bioproject with the accession number PRJNA941180.
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Affiliation(s)
- Eric Banan-Mwine Daliri
- Department of Biological Models, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio Ave. 7, LT, Vilnius 10257, Lithuania
| | - Toma Balnionytė
- Department of Biological Models, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio Ave. 7, LT, Vilnius 10257, Lithuania
| | - Eglė Lastauskienė
- Department of Microbiology and Biotechnology, Institute of Biosciences, Life Sciences Center, Vilnius University, Sauletekio Ave. 7, LT, Vilnius 10257, Lithuania
| | - Aurelijus Burokas
- Department of Biological Models, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio Ave. 7, LT, Vilnius 10257, Lithuania
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Wang J, Zhang R, Ding G, Wang L, Wang W, Zhang Y, Zhu G. Comparative genomic analysis of five coprinoid mushrooms species. Funct Integr Genomics 2023; 23:159. [PMID: 37178396 PMCID: PMC10182949 DOI: 10.1007/s10142-023-01094-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 04/24/2023] [Accepted: 05/09/2023] [Indexed: 05/15/2023]
Abstract
Although coprinoid mushrooms are widely known for the phenomenon of deliquescence and production of fungal laccases and extracellular peroxygenases, the genome structure and genetic diversity of coprinoid mushroom species have not been extensively studied. To reveal the genomic structure and diversity in coprinoid mushroom species, the genomes of five coprinoid mushroom species were compared and analyzed. A total of 24,303 orthologous gene families, including 89,462 genes, were identified in the five species. The numbers of core, softcore, dispensable, and private genes were 5617 (25.6%), 1628 (7.4%), 2083 (9.5%), and 12,574 (57.4%), respectively. Differentiation time analysis revealed that Coprinellus micaceus and Coprinellus angulatus differentiated approximately 181.0 million years ago. Coprinopsis cinerea and Coprinopsis marcescibilis differentiated approximately 131.0 million years ago, and they were differentiated from Candolleomyces aberdarensis approximately 176.0 million years ago. Gene family contraction and expansion analyses showed that 1465 genes and 532 gene families were expanded, and 95 genes and 134 gene families were contracted. Ninety-five laccase-coding genes were detected in the five species, and the distribution of the laccase-coding genes in the five species was not uniform. These data provide a reference for a deeper understanding of the genetic structure of the genomes of coprinoid mushroom species. Furthermore, this study provides a reference for follow-up studies on the genome structure of coprinoid mushroom species and the diversity of specific functional genes.
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Affiliation(s)
- Jingjing Wang
- Department of Life Science, Hefei Normal University, Hefei, 230061, China
- Anhui Engineering Laboratory for Medicinal and Food Homologous Natural Resources Exploration, Hefei, 230061, China
- Department of Life Science, Anhui University, Hefei, 230601, China
| | - Ran Zhang
- Department of Life Science, Hefei Normal University, Hefei, 230061, China
- Department of Life Science, Anhui University, Hefei, 230601, China
| | - Guoao Ding
- Department of Life Science, Hefei Normal University, Hefei, 230061, China
- Department of Life Science, Anhui University, Hefei, 230601, China
| | - Lingling Wang
- Department of Life Science, Hefei Normal University, Hefei, 230061, China
- Anhui Engineering Laboratory for Medicinal and Food Homologous Natural Resources Exploration, Hefei, 230061, China
| | - Wei Wang
- Department of Life Science, Hefei Normal University, Hefei, 230061, China
- Anhui Engineering Laboratory for Medicinal and Food Homologous Natural Resources Exploration, Hefei, 230061, China
| | - Yan Zhang
- Department of Life Science, Hefei Normal University, Hefei, 230061, China.
- Anhui Engineering Laboratory for Medicinal and Food Homologous Natural Resources Exploration, Hefei, 230061, China.
- Department of Life Science, Anhui University, Hefei, 230601, China.
| | - GuiLan Zhu
- Department of Life Science, Hefei Normal University, Hefei, 230061, China.
- Anhui Engineering Laboratory for Medicinal and Food Homologous Natural Resources Exploration, Hefei, 230061, China.
- Department of Life Science, Anhui University, Hefei, 230601, China.
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Albert MJ, Al-Hashem G, Rotimi VO. Multiplex gyrB PCR Assay for Identification of Acinetobacter baumannii Is Validated by Whole Genome Sequence-Based Assays. Med Princ Pract 2022; 31:493-496. [PMID: 35944494 PMCID: PMC9801371 DOI: 10.1159/000526402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 08/07/2022] [Indexed: 01/02/2023] Open
Abstract
OBJECTIVE A multiplex gyrB PCR assay has been used to diagnose Acinetobacter baumannii. However, this assay has not been validated against the gold standard DNA-DNA hybridization assay, which is a laborious method. DNA-DNA hybridization assay is now replaced by whole genome sequence (WGS)-based methods. Two such methods are a k-mer-based search of sequence reads using the Kraken 2 program and average nucleotide identity (ANI). The objective was to validate the gyrB PCR assay with WGS-based methods. SUBJECTS AND METHODS We cultured 270 sequential A. baumannii isolates from the rectal swabs of 32 adult patients. The identity of the isolates was determined by gyrB PCR. The sequences of 269 isolates were determined by Illumina sequencing and the taxonomy was inferred by the Kraken 2 program and ANI. RESULTS All the 269 isolates were confirmed as A. baumannii by Kraken 2 and ANI. CONCLUSION The gyrB PCR assay is now validated for easy identification of A. baumannii in comparison with gold standard WGS-based assays.
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Arora PK, Saroj RS, Mishra R, Omar RA, Kumari P, Srivastava A, Garg SK, Singh VP. Draft genome sequence data of a 4-nitrophenol- degrading bacterium, Pseudomonas alloputida strain PNP. Data Brief 2021; 38:107390. [PMID: 34589566 PMCID: PMC8461342 DOI: 10.1016/j.dib.2021.107390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 09/06/2021] [Accepted: 09/09/2021] [Indexed: 11/24/2022] Open
Abstract
A 4-nitrophenol-degrading bacterial strain PNP was isolated from pesticide-contaminated soil collected from Lucknow. Strain PNP utilized 0.5 mM 4-nitrophenol as its carbon source and degraded it completely within 24 h with stoichiometric release of nitrite ions. Strain PNP was associated with the genus Pseudomonas in a phylogentic tree and exhibited highest 16S rRNA gene sequence similarity to Pseudomonas juntendi BML3 (99.79%) and Pseudomonas inefficax JV551A3 (99.79%). Based on values of average nucleotide identity and digital DNA-DNA hybridization among strain PNP and its closely related type strains, it concluded that strain PNP belongs to Pseudomonas alloputida. The Illumina HiSeq platform was used to sequence the PNP genome. The draft genome sequence of Pseudomonas alloputida PNP was presented here. The total size of the draft assembly was 6,087,340 bp, distributed into 87 contigs with N50 value of 139502. The genome has an average GC content of 61.7% and contains 5461 coding sequences and 77 putative RNA genes. This Whole Genome Shotgun project has been submitted at DDBJ/ENA/GenBank under the accession JAGKJH000000000.
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Affiliation(s)
- Pankaj Kumar Arora
- Department of Environmnetal Microbiology, Babasaheb Bhimrao Ambedkar University, Lucknow 226025, India
| | - Raj Shekhar Saroj
- Department of Environmnetal Microbiology, Babasaheb Bhimrao Ambedkar University, Lucknow 226025, India
| | - Rupali Mishra
- Department of Environmnetal Microbiology, Babasaheb Bhimrao Ambedkar University, Lucknow 226025, India
| | - Rishabh Anand Omar
- Department of Environmnetal Microbiology, Babasaheb Bhimrao Ambedkar University, Lucknow 226025, India
| | - Puja Kumari
- Department of Environmnetal Microbiology, Babasaheb Bhimrao Ambedkar University, Lucknow 226025, India
| | - Alok Srivastava
- Department of Plant Science, Faculty of Applied Sciences, MJP Rohilkhand University, Bareilly, India
| | - Sanjay Kumar Garg
- Department of Plant Science, Faculty of Applied Sciences, MJP Rohilkhand University, Bareilly, India
| | - Vijay Pal Singh
- Department of Plant Science, Faculty of Applied Sciences, MJP Rohilkhand University, Bareilly, India
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Song HC, Yang BT, Zhao T, Sun YF, Zhou JH, Shan XF, Qian AD, Sun WC, Kang YH. Comparative genomics analysis of strains from diverse sources reveals the evolutionary relationship of Aeromonas veronii. Microb Pathog 2021; 159:105134. [PMID: 34400283 DOI: 10.1016/j.micpath.2021.105134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 07/27/2021] [Accepted: 08/07/2021] [Indexed: 10/20/2022]
Abstract
Aeromonas veronii (A. veronii, AV) strains are emerging zoonotic and aquatic pathogens, yet we know very little about their genomics. This study aims to utilize comparative genomics to investigate the intraspecific genetic diversity, differences in virulence factors and evolutionary mechanisms of A. veronii strains from diverse sources and to fundamentally demonstrate their pathogenic mechanisms. We conducted comparative genomics analysis of 39 A. veronii strains from different sources and found that 1993 core genes are shared by these strains and that these shared core genes may be necessary to maintain the basic characteristics of A. veronii. Additionally, phylogenetic relationship analysis based on these shared genes revealed that a distant relationship between the AMC34 strain and the other 38 strains but that, the genetic relationship among the 38 strains is relatively close, indicating that AMC34 may not belong to A. veronii. Furthermore, analysis of shared core genes and average nucleotide identity (ANI) values showed no obvious correlation with the location of A. veronii isolation and genetic relationship. Our research indicates the evolutionary mechanism of A. veronii from different sources and provides new insights for a deeper understanding of its pathogenic mechanism.
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Affiliation(s)
- Hai-Chao Song
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Bin-Tong Yang
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Tong Zhao
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Yu-Feng Sun
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Jin-Hua Zhou
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Xiao-Feng Shan
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Ai-Dong Qian
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Wen-Chao Sun
- Institute of Virology, Wenzhou University, Wenzhou, Zhejiang, 325035, China.
| | - Yuan-Huan Kang
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, Jilin, 130118, China.
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Redondo-Salvo S, Bartomeus-Peñalver R, Vielva L, Tagg KA, Webb HE, Fernández-López R, de la Cruz F. COPLA, a taxonomic classifier of plasmids. BMC Bioinformatics 2021; 22:390. [PMID: 34332528 PMCID: PMC8325299 DOI: 10.1186/s12859-021-04299-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 07/12/2021] [Indexed: 11/10/2022] Open
Abstract
Background Plasmids are mobile genetic elements, key in the dissemination of antibiotic resistance, virulence determinants and other adaptive traits in bacteria. Obtaining a robust method for plasmid classification is necessary to better understand the genetics and epidemiology of many pathogens. Until now, plasmid classification systems focused on specific traits, which limited their precision and universality. The definition of plasmid taxonomic units (PTUs), based on average nucleotide identity metrics, allows the generation of a universal plasmid classification scheme, applicable to all bacterial taxa. Here we present COPLA, a software able to assign plasmids to known and novel PTUs, based on their genomic sequence. Results We implemented an automated pipeline able to assign a given plasmid DNA sequence to its cognate PTU, and assessed its performance using a sample of 1000 unclassified plasmids. Overall, 41% of the samples could be assigned to a previously defined PTU, a number that reached 63% in well-known taxa such as the Enterobacterales order. The remaining plasmids represent novel PTUs, indicating that a large fraction of plasmid backbones is still uncharacterized. Conclusions COPLA is a bioinformatic tool for universal, species-independent, plasmid classification. Offered both as an automatable pipeline and an open web service, COPLA will help bacterial geneticists and clinical microbiologists to quickly classify plasmids. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04299-x.
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Affiliation(s)
- Santiago Redondo-Salvo
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain
| | - Roger Bartomeus-Peñalver
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain
| | - Luis Vielva
- Departamento de Ingeniería de las Comunicaciones, Universidad de Cantabria, Santander, Spain
| | - Kaitlin A Tagg
- Centers for Disease Control and Prevention, Atlanta, USA.,WDS, Inc., Atlanta, USA
| | - Hattie E Webb
- Centers for Disease Control and Prevention, Atlanta, USA.,WDS, Inc., Atlanta, USA
| | - Raúl Fernández-López
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain
| | - Fernando de la Cruz
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain.
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Hudson LK, Orellana LAG, Bryan DW, Moore A, Munafo JP, den Bakker HC, Denes TG. Phylogeny of the Bacillus altitudinis Complex and Characterization of a Newly Isolated Strain with Antilisterial Activity. J Food Prot 2021; 84:1321-1332. [PMID: 33793813 DOI: 10.4315/jfp-20-498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 03/27/2021] [Indexed: 11/11/2022]
Abstract
ABSTRACT Bacillus strain UTK D1-0055 was isolated from a laboratory environment and appeared to have antilisterial activity. The genome was sequenced, the strain was identified as Bacillus altitudinis, and a high-quality complete annotated genome was produced. The taxonomy was evaluated for this and related Bacillus species (B. aerophilus, B. pumilus, B. safensis, B. stratosphericus, and B. xiamenensis) because the taxonomy is unclear and contains errors in public databases such as NCBI. The included strains grouped into seven clusters based on average nucleotide identity. Strains designated as B. aerophilus, B. altitudinis, and B. stratosphericus grouped together in the cluster containing the B. altitudinis type strain, suggesting that these three species should be considered a single species, B. altitudinis. The antimicrobial activity of UTK D1-0055 was evaluated against a panel of 15 Listeria strains (nine Listeria monocytogenes serotypes, Listeria innocua, and Listeria marthii), other foodborne pathogens (six Salmonella enterica serotypes and Escherichia coli), and three representative fungi (Saccharomyces cerevisiae, Botrytis cinerea, and Hyperdermium pulvinatum). Antibacterial activity was observed against all Listeria strains, but no antibacterial effects were found against the other tested bacterial and fungal strains. Biosynthetic gene clusters were identified in silico that may be related to the observed antibacterial activity, and these clusters included genes that putatively encode bacteriocins and nonribosomally synthesized peptides. The B. altitudinis strain identified in this investigation had a broad range of antilisterial activity, suggesting that it and other related strains may be useful for biocontrol in the food industry. HIGHLIGHTS
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Affiliation(s)
- Lauren K Hudson
- Department of Food Science, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Leticia A G Orellana
- Department of Food Science, University of Tennessee, Knoxville, Tennessee 37996, USA.,Zamorano Pan-American Agricultural School, San Antonio de Oriente, Francisco Morazán, Honduras
| | - Daniel W Bryan
- Department of Food Science, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Andrew Moore
- Department of Food Science, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - John P Munafo
- Department of Food Science, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Henk C den Bakker
- Center for Food Safety and Department of Food Science and Technology, University of Georgia, Griffin, Georgia 30602, USA
| | - Thomas G Denes
- Department of Food Science, University of Tennessee, Knoxville, Tennessee 37996, USA
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Kang Y, Chen Y, Zhang Z, Shen H, Zhou W, Wu C. A case of peritoneal dialysis-associated peritonitis caused by Rhodococcus kroppenstedtii. BMC Infect Dis 2021; 21:565. [PMID: 34120601 PMCID: PMC8201711 DOI: 10.1186/s12879-021-06280-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 06/03/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rhodococcus kroppenstedtii is an aerobic, gram-positive bacterium firstly identified in the environment, which has not been reported in human-related infection. Herein, we reported the first case of peritoneal dialysis (PD)-associated peritonitis caused by R. kroppenstedtii which was identified by whole genome sequencing. CASE PRESENTATION A 69-year-old man was admitted to hospital with abdominal pain and fever. Over the last 2 years, he had been undergoing continuous ambulatory peritoneal dialysis (CAPD) due to end-stage renal disease. Clinical symptom and sign in combination with laboratory examinations supported the clinical diagnosis of PD-associated peritonitis. Thus, ceftizoxime and teicoplanin were empirically used after PD effluent was collected for bacterial culture. A gram-positive bacterium was found from the PD effluent culture, which could not be identified by either Vitek 2 Compact ANC card or matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The strain was finally confirmed to be R. kroppenstedtii by whole genome sequencing (WGS) through the average nucleotide identity (ANI) analysis. With a continuous treatment with teicoplanin and imipenem for 15 days and intraperitoneal catheter removed, the infection symptom was improved evidenced by a normal body temperature, also with white blood cell count (WBC), procalcitonin (PCT) and C-reactive protein (CRP) dropped to normal levels. Peritoneal dialysis effluent culture showed a negative result. Then, hemodialysis and arteriovenous fistula angioplasty were performed, but the patient developed a progressive blood pressure loss, accompanied by multiple organ disorder, and died on Feb 25, 2020. CONCLUSIONS To the best of our knowledge, this is the first time to report a peritoneal dialysis-associated peritonitis caused by R. kroppenstedtii which was identified by average nucleotide identity analysis based on WGS.
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Affiliation(s)
- Yi Kang
- Department of Infectious Diseases, Nanjing Drum Tower Hospital, Clinical College of Nanjing Medical University, 321# Zhongshan Road, Gulou District, Nanjing City, Jiangsu Province, 210008, P. R. China
| | - Yuxin Chen
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu Province, 210008, P. R. China
| | - Zhifeng Zhang
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu Province, 210008, P. R. China
| | - Han Shen
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu Province, 210008, P. R. China
| | - Wanqing Zhou
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu Province, 210008, P. R. China.
| | - Chao Wu
- Department of Infectious Diseases, Nanjing Drum Tower Hospital, Clinical College of Nanjing Medical University, 321# Zhongshan Road, Gulou District, Nanjing City, Jiangsu Province, 210008, P. R. China.
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Bian DR, Xue H, Wang GM, Piao CG, Li Y. Affinibrenneria salicis gen. nov. sp. nov. isolated from Salix matsudana bark canker. Arch Microbiol 2021; 203:3473-81. [PMID: 33903975 DOI: 10.1007/s00203-021-02323-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 04/03/2021] [Accepted: 04/08/2021] [Indexed: 10/21/2022]
Abstract
L3-3HAT, a Gram-negative-staining, facultatively anaerobic, motile bacterial strain, was isolated from the symptomatic bark of Salix matsudana canker in China. 16S rRNA gene analysis revealed that the novel strain shares the highest sequence similarity with Brenneria goodwinii FRB141T (95.5%). In phylogenetic trees based on four housekeeping genes (gyrB, rpoB, atpD, and infB) and the 16S rRNA gene sequence, the novel strain formed a separate branch from the five genera of the family Pectobacteriaceae (Lonsdalea, Brenneria, Dickeya, Pectobacterium, and Sodalis), suggesting that the novel strain should belong to a novel species of a novel genus within the family Pectobacteriaceae. The result was also supported by phylogenomics, amino acid identity and average nucleotide identity. The major fatty acids were C14:0, C16:0, C17:0 cyclo, and C19:0 cyclo ɷ8c. Genome analysis showed that the novel strain has a large genome (5.89 Mb) with 5,052 coding genes, including 181 virulence genes by searching the pathogen-host interactions database (PHI-base), indicating that the novel strain is a potential pathogen of plants and animals. Based on phenotypic and genotypic characteristics, the L3-3HAT strain represents a novel species of a novel genus in the Pectobacteriaceae family, for which the name Affinibrenneria salicis gen nov. sp. nov. is proposed. The strain type is L3-3HAT (= CFCC 15588T = LMG 31209T).
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Lee SD, Yang HL, Kim IS. Rouxiella aceris sp. nov., isolated from tree sap and the emended description of the genus Rouxiella. Antonie Van Leeuwenhoek 2021; 114:1013-24. [PMID: 33842994 DOI: 10.1007/s10482-021-01572-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/01/2021] [Indexed: 10/21/2022]
Abstract
Polyphasic taxonomic studies were performed for the seven strains, which were isolated from sap extracted from Acer pictum in Mt. Halla in Jeju, Republic of Korea. Cells of all the isolates were Gram-reaction-negative, facultatively anaerobic, short rods and contained the major isoprenoid quinone of Q-8, the predominant fatty acids of C16:0 and C17:0 cyclo and the major polar lipids including phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospholipid. The G + C contents of the genomic DNAs were 50.6-51.3%.The 16S rRNA gene-based phylogeny exhibited that the seven isolates formed two distinct sublines within the family Yersiniaceae. In the 92 core gene analysis, strain SAP-1T formed a subline at the base of radiation of the genus Rouxiella and its assignment to the genus Rouxiella was supported by high amino acid identity values (82.0-83.4%), albeit with sharing low 16S rRNA gene identities (96.0-96.9%). The average nucleotide identity and digital DNA-DNA hybridisation values together with phenotypic differences showed that strains SAP-1T, SAP-7, SAP-8 and SAP-13 belonged to a new species of the genus Rouxiella, while strains SAP-2, SAP-3 and SAP-27 were strains of Rouxiella silvae. On the basis of data obtained here, Rouxiella aceris sp. nov. (type strain, SAP-1T = KCTC 72599T = CCM 9078T) is proposed, with the emended description of the genus Rouxiella.
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Tian L, Mazloom R, Heath LS, Vinatzer BA. LINflow: a computational pipeline that combines an alignment-free with an alignment-based method to accelerate generation of similarity matrices for prokaryotic genomes. PeerJ 2021; 9:e10906. [PMID: 33828908 PMCID: PMC8000461 DOI: 10.7717/peerj.10906] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 01/14/2021] [Indexed: 01/21/2023] Open
Abstract
Background Computing genomic similarity between strains is a prerequisite for genome-based prokaryotic classification and identification. Genomic similarity was first computed as Average Nucleotide Identity (ANI) values based on the alignment of genomic fragments. Since this is computationally expensive, faster and computationally cheaper alignment-free methods have been developed to estimate ANI. However, these methods do not reach the level of accuracy of alignment-based methods. Methods Here we introduce LINflow, a computational pipeline that infers pairwise genomic similarity in a set of genomes. LINflow takes advantage of the speed of the alignment-free sourmash tool to identify the genome in a dataset that is most similar to a query genome and the precision of the alignment-based pyani software to precisely compute ANI between the query genome and the most similar genome identified by sourmash. This is repeated for each new genome that is added to a dataset. The sequentially computed ANI values are stored as Life Identification Numbers (LINs), which are then used to infer all other pairwise ANI values in the set. We tested LINflow on four sets, 484 genomes in total, and compared the needed time and the generated similarity matrices with other tools. Results LINflow is up to 150 times faster than pyani and pairwise ANI values generated by LINflow are highly correlated with those computed by pyani. However, because LINflow infers most pairwise ANI values instead of computing them directly, ANI values occasionally depart from the ANI values computed by pyani. In conclusion, LINflow is a fast and memory-efficient pipeline to infer similarity among a large set of prokaryotic genomes. Its ability to quickly add new genome sequences to an already computed similarity matrix makes LINflow particularly useful for projects when new genome sequences need to be regularly added to an existing dataset.
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Affiliation(s)
- Long Tian
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Reza Mazloom
- Department of Computer Science, Virginia Tech, Blacksburg, VA, USA
| | - Lenwood S Heath
- Department of Computer Science, Virginia Tech, Blacksburg, VA, USA
| | - Boris A Vinatzer
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
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16
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Park CJ, Caimi NA, Buecher DC, Valdez EW, Northup DE, Andam CP. Unexpected genomic, biosynthetic and species diversity of Streptomyces bacteria from bats in Arizona and New Mexico, USA. BMC Genomics 2021; 22:247. [PMID: 33827425 PMCID: PMC8028829 DOI: 10.1186/s12864-021-07546-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/19/2021] [Indexed: 11/10/2022] Open
Abstract
Background Antibiotic-producing Streptomyces bacteria are ubiquitous in nature, yet most studies of its diversity have focused on free-living strains inhabiting diverse soil environments and those in symbiotic relationship with invertebrates. Results We studied the draft genomes of 73 Streptomyces isolates sampled from the skin (wing and tail membranes) and fur surfaces of bats collected in Arizona and New Mexico. We uncovered large genomic variation and biosynthetic potential, even among closely related strains. The isolates, which were initially identified as three distinct species based on sequence variation in the 16S rRNA locus, could be distinguished as 41 different species based on genome-wide average nucleotide identity. Of the 32 biosynthetic gene cluster (BGC) classes detected, non-ribosomal peptide synthetases, siderophores, and terpenes were present in all genomes. On average, Streptomyces genomes carried 14 distinct classes of BGCs (range = 9–20). Results also revealed large inter- and intra-species variation in gene content (single nucleotide polymorphisms, accessory genes and singletons) and BGCs, further contributing to the overall genetic diversity present in bat-associated Streptomyces. Finally, we show that genome-wide recombination has partly contributed to the large genomic variation among strains of the same species. Conclusions Our study provides an initial genomic assessment of bat-associated Streptomyces that will be critical to prioritizing those strains with the greatest ability to produce novel antibiotics. It also highlights the need to recognize within-species variation as an important factor in genetic manipulation studies, diversity estimates and drug discovery efforts in Streptomyces. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07546-w.
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Affiliation(s)
- Cooper J Park
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
| | - Nicole A Caimi
- Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | | | - Ernest W Valdez
- Department of Biology, University of New Mexico, Albuquerque, NM, USA.,U.S. Geological Survey, Fort Collins Science Center, Fort Collins, CO, USA
| | - Diana E Northup
- Department of Biology, University of New Mexico, Albuquerque, NM, USA.
| | - Cheryl P Andam
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA.
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Hodgeman R, Mann R, Savin K, Djitro N, Rochfort S, Rodoni B. Molecular characterisation of Mycobacterium avium subsp. paratuberculosis in Australia. BMC Microbiol 2021; 21:101. [PMID: 33789575 PMCID: PMC8012159 DOI: 10.1186/s12866-021-02140-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 02/23/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mycobacterium avium subsp. paratuberculosis (Map) causes Johne's disease (JD), a chronic enteritis widespread in ruminants, resulting in substantial economic losses, especially to the dairy industry. Understanding the genetic diversity of Map in Australia will assist epidemiological studies for tracking disease transmission and identify subtype characteristics for use in development of improved diagnostic typing methods. Here we investigated the phylogenetic relationships of 351 Map isolates and compared different subtyping methods to assess their suitability for use in diagnostics and accuracy. RESULTS SNP-based phylogenetic analysis of 228 Australian isolates and 123 publicly available international isolates grouped Type S and Type C strains into two distinct lineages. Type C strains were highly monomorphic with only 20 SNP differences separating them. Type S strains, when aligned separately to the Telford strain, fell into two distinct clades: The first clade contained seven international isolates while the second clade contained one international isolate from Scotland and all 59 Australian isolates. The Australian Type B strain clustered with US bison strains. IS1311 PCR and Restriction Enzyme Analysis (REA) intermittently generated incorrect results when compared to Long Sequence Polymorphism (LSP) analysis, whole genome SNP-based phylogenetic analysis, IS1311 sequence alignment and average nucleotide identity (ANI). These alternative methods generated consistent Map typing results. A published SNP based assay for genotyping Map was found to be unsuitable for differentiating between Australian and international strain types of Map. CONCLUSION This is the first phylogenetic analysis of Australian Map isolates. The Type C lineage was highly monomorphic, and the Type S lineage clustered all Australian isolates into one clade with a single Scottish sheep strain. The Australian isolate classified as Type B by IS1311 PCR and REA is likely to be descended from bison and most closely related to US bison strains. Limitations of the current typing methods were identified in this study.
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Affiliation(s)
- Rachel Hodgeman
- Agriculture Victoria, AgriBio, La Trobe University, Bundoora, Victoria, Australia. .,School of Applied Systems Biology, AgriBio, La Trobe University, Bundoora, Victoria, Australia.
| | - Rachel Mann
- Agriculture Victoria, AgriBio, La Trobe University, Bundoora, Victoria, Australia
| | - Keith Savin
- Agriculture Victoria, AgriBio, La Trobe University, Bundoora, Victoria, Australia
| | - Noel Djitro
- School of Applied Systems Biology, AgriBio, La Trobe University, Bundoora, Victoria, Australia
| | - Simone Rochfort
- Agriculture Victoria, AgriBio, La Trobe University, Bundoora, Victoria, Australia.,School of Applied Systems Biology, AgriBio, La Trobe University, Bundoora, Victoria, Australia
| | - Brendan Rodoni
- Agriculture Victoria, AgriBio, La Trobe University, Bundoora, Victoria, Australia.,School of Applied Systems Biology, AgriBio, La Trobe University, Bundoora, Victoria, Australia
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18
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Cornelius AJ, Huq M, On SLW, French NP, Vandenberg O, Miller WG, Lastovica AJ, Istivan T, Biggs PJ. Genetic characterisation of Campylobacter concisus: Strategies for improved genomospecies discrimination. Syst Appl Microbiol 2021; 44:126187. [PMID: 33677170 DOI: 10.1016/j.syapm.2021.126187] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 02/03/2021] [Accepted: 02/08/2021] [Indexed: 02/08/2023]
Abstract
Although at least two genetically distinct groups, or genomospecies, have been well documented for Campylobacter concisus, no phenotype has yet been identified for their differentiation and thus formal description as separate species. C. concisus has been isolated from a variety of sites in the human body, including saliva and stool samples from both healthy and diarrhoeic individuals. We evaluated the ability of a range of whole genome-based tools to distinguish between the two C. concisus genomospecies (GS) using a collection of 190 C. concisus genomes. Nine genomes from related Campylobacter species were included in some analyses to provide context. Analyses incorporating sequence analysis of multiple ribosomal genes generated similar levels of C. concisus GS discrimination as genome-wide comparisons. The C. concisus genomes formed two groups; GS1 represented by ATCC 33237T and GS2 by CCUG 19995. The two C. concisus GS were separated from the nine genomes of related species. GS1 and GS2 also differed in G+C content with medians of 37.56% and 39.51%, respectively. The groups are consistent with previously established GS and are supported by DNA reassociation results. Average Nucleotide Identity using MUMmer (ANIm) and Genome BLAST Distance Phylogeny generated in silico DNA-DNA hybridisation (isDDH) (against ATCC 33237T and CCUG 19995), plus G+C content provides cluster-independent GS discrimination suitable for routine use. Pan-genomic analysis identified genes specific to GS1 and GS2. WGS data and genomic species identification methods support the existence of two GS within C. concisus. These data provide genome-level metrics for strain identification to genomospecies level.
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Affiliation(s)
- Angela J Cornelius
- Institute of Environmental Science and Research Ltd, P.O. Box 29181, Christchurch 8540, New Zealand.
| | - Mohsina Huq
- School of Science, RMIT University, G.P.O. Box 2476, Bundoora, Victoria 3001, Australia
| | - Stephen L W On
- Lincoln University, P.O. Box 85084, Lincoln 7647, New Zealand
| | - Nigel P French
- Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
| | - Olivier Vandenberg
- National Reference Centre for Campylobacter, Laboratoire Hospitalier Universitaire de Bruxelles, 322 rue Haute, 1000 Brussels, Belgium; School of Public Health, Campus Erasme - Bâtiment A, Route de Lennik 808 - CP591, Université Libre de Bruxelles, 1070 Bruxelles, Belgium
| | - William G Miller
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, United States Department of Agriculture, 800 Buchanan Street, Albany, CA 94710, USA
| | - Albert J Lastovica
- University of Western Cape, Private Bag X17, Bellville 7535, South Africa
| | - Taghrid Istivan
- School of Science, RMIT University, G.P.O. Box 2476, Bundoora, Victoria 3001, Australia
| | - Patrick J Biggs
- Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
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Yamada K, Aoki K, Nagasawa T, Sasaki M, Murakami H, Ishii T, Ujiie S, Morita T, Ishii Y, Tateda K. Complete whole-genome sequence of the novel Pseudomonas species strain TUM18999, isolated from a patient with a burn wound in Japan. J Glob Antimicrob Resist 2021; 24:395-7. [PMID: 33577996 DOI: 10.1016/j.jgar.2021.01.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/30/2020] [Accepted: 01/18/2021] [Indexed: 11/22/2022] Open
Abstract
OBJECTIVES Pseudomonas is a Gram-negative bacterial genus with numerous member species. In this study, using whole-genome sequencing, we characterized a novel Pseudomonas sp. strain TUM18999, isolated as a pathogen from a human patient. METHODS The TUM18999 strain was isolated from a patient's burn wound. Minimum inhibitory concentrations (MICs) were determined using the broth microdilution method. The whole-genome sequence was obtained using Miseq and MinION, and we conducted phylogenetic analysis based on single nucleotide polymorphisms of the core genome. RESULTS Antimicrobial susceptibility testing revealed a high ceftazidime MIC (32 mg/L). Moreover, carbapenemase production was confirmed using the modified carbapenem inactivation method. We found that the complete genome of TUM18999 was 6,826,062 bp long, with 6175 coding sequences (CDS) and a DNA G+C content (non-plasmid) of 66.4 mol%. Consistent with the high similarities with the 16S rRNA sequences of P. otitidis MCC10330 (98.6%) and P. alcaligenes NBRC 14159 (99.2%), similarities (<90%) were also observed with the gyrB genes of both strains. The average nucleotide identities for P. alcaligenes NBRC 14159 and P. otitidis MCC10330 were also <90%. The core-genome single nucleotide polymorphism phylogenetic tree indicated that the TUM18999 strain was most closely related to P. otitidis MCC10330. In addition, the TUM18999 strain carried the novel gene, species-specific subclass B3 metallo-β-lactamase (MBL), and its similarities with P. alcaligenes metallo-β-lactamase-1 (PAM-1) and P. otitidis metallo-β-lactamase-1 (POM-1) were 90.24% and 73.14%, respectively. CONCLUSION We characterized the complete whole genome sequence of the novel Pseudomonas sp. TUM18999 carrying the novel gene species-specific subclass B3 MBL.
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Tomida J, Akiyama-Miyoshi T, Tanaka K, Hayashi M, Kutsuna R, Fujiwara N, Kawamura Y. Fusobacterium watanabei sp. nov. As additional species within the genus Fusobacerium, isolated from human clinical specimens. Anaerobe 2021; 69:102323. [PMID: 33515720 DOI: 10.1016/j.anaerobe.2021.102323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 01/12/2021] [Accepted: 01/19/2021] [Indexed: 10/22/2022]
Abstract
Eight spindle-shaped bacteria were isolated from clinical samples in Japan and investigated for their taxonomic position. Phylogenetic trees (based on 16S rRNA, rpoB, zinc protease, and gyrB gene sequence comparisons) showed distinct clustering of eight strains with the type strain of Fusobacterium nucleatum and its closely related species. In silico whole genome comparison analysis based on average nucleotide index based on BLAST (ANIb) and digital DNA-DNA hybridization (dDDH) data between our clinical isolates (PAGU 1795, PAGU 1796T, and PAGU 1797) and the type strain of the closely related species showed values of less than 92.4% and 49.5%, respectively. On the basis of its phylogenetic and genomic distinctiveness together with differential phenotypic properties and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS) characteristic signal patterns, we propose Fusobacterium watanabei sp. nov., with the type strain PAGU 1796T (= GTC 21791T = CCUG 74246T).
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Affiliation(s)
- Junko Tomida
- Department of Microbiology, School of Pharmacy, Aichi Gakuin University, 1-100 Kusumoto-cho, Nagoya, Aichi, 464-8650, Japan.
| | - Toru Akiyama-Miyoshi
- Pathogenic Microbe Laboratory, Research Institute, National Center for Global Health and Medicine, Shinjuku, Tokyo, 162-8655, Japan.
| | - Kaori Tanaka
- Division of Anaerobe Research, Life Science Research Center, Gifu University, 1-1 Yanagido, Gifu, Gifu, 501-1194, Japan.
| | - Masahiro Hayashi
- Division of Anaerobe Research, Life Science Research Center, Gifu University, 1-1 Yanagido, Gifu, Gifu, 501-1194, Japan.
| | - Ryo Kutsuna
- Department of Microbiology, School of Pharmacy, Aichi Gakuin University, 1-100 Kusumoto-cho, Nagoya, Aichi, 464-8650, Japan.
| | - Nagatoshi Fujiwara
- Department of Food and Nutrition, Faculty of Contemporary Human Life Science, Tezukayama University, 3-1-3, Gakuen-Minami, Nara, Naraz, 631-8585, Japan.
| | - Yoshiaki Kawamura
- Department of Microbiology, School of Pharmacy, Aichi Gakuin University, 1-100 Kusumoto-cho, Nagoya, Aichi, 464-8650, Japan.
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Torres Manno MA, Repizo GD, Magni C, Dunlap CA, Espariz M. The assessment of leading traits in the taxonomy of the Bacillus cereus group. Antonie Van Leeuwenhoek 2020; 113:2223-2242. [PMID: 33179199 DOI: 10.1007/s10482-020-01494-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 10/23/2020] [Indexed: 12/18/2022]
Abstract
Bacillus cereus sensu lato strains (B. cereus group) are widely distributed in nature and have received interest for decades due to their importance in insect pest management, food production and their positive and negative repercussions in human health. Consideration of practical uses such as virulence, physiology, morphology, or ill-defined features have been applied to describe and classify species of the group. However, current comparative studies have exposed inconsistencies between evolutionary relatedness and biological significance among genomospecies of the B. cereus group. Here, the combined analyses of core-based phylogeny and all versus all Average Nucleotide Identity values based on 2116 strains were conducted to update the genomospecies circumscriptions within B. cereus group. These analyses suggested the existence of 57 genomospecies, 37 of which are novel, thus indicating that the taxonomic identities of more than 39% of the analyzed strains should be revised or updated. In addition, we found that whole-genome in silico analyses were suitable to differentiate genomospecies such as B. anthracis, B. cereus and B. thuringiensis. The prevalence of toxin and virulence factors coding genes in each of the genomospecies of the B. cereus group was also examined, using phylogeny-aware methods at wide-genome scale. Remarkably, Cry and emetic toxins, commonly assumed to be associated with B. thuringiensis and emetic B. paranthracis, respectively, did not show a positive correlation with those genomospecies. On the other hand, anthrax-like toxin and capsule-biosynthesis coding genes were positively correlated with B. anthracis genomospecies, despite not being present in all strains, and with presumably non-pathogenic genomospecies. Hence, despite these features have been so far considered relevant for industrial or medical classification of related species of the B. cereus group, they were inappropriate for their circumscription. In this study, genomospecies of the group were accurately affiliated and representative strains defined, generating a rational framework that will allow comparative analysis in epidemiological or ecological studies. Based on this classification the role of specific markers such as Type VII secretion system, cytolysin, bacillolysin, and siderophores such as petrobactin were pointed out for further analysis.
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Affiliation(s)
- Mariano A Torres Manno
- Laboratorio de Biotecnología e Inocuidad de los Alimentos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Municipalidad de Granadero Baigorria, Sede Suipacha 590, Rosario, Santa Fe, Argentina
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR - CONICET), sede FCByF - UNR, Rosario, Santa Fe, Argentina
- Área Estadística y Procesamiento de Datos, Departamento de Matemática y Estadística, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Guillermo D Repizo
- Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Rosario, Argentina
- Laboratorio de Resistencia bacteriana a antimicrobianos, Instituto de Biología Molecular y Celular de Rosario (IBR), sede FCByF - UNR, Rosario, Santa Fe, Argentina
| | - Christian Magni
- Laboratorio de Biotecnología e Inocuidad de los Alimentos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Municipalidad de Granadero Baigorria, Sede Suipacha 590, Rosario, Santa Fe, Argentina
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR - CONICET), sede FCByF - UNR, Rosario, Santa Fe, Argentina
| | - Christopher A Dunlap
- United States Department of Agriculture, Crop Bioprotection Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, 1815 North University Street, Peoria, IL, 61604, USA
| | - Martín Espariz
- Laboratorio de Biotecnología e Inocuidad de los Alimentos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Municipalidad de Granadero Baigorria, Sede Suipacha 590, Rosario, Santa Fe, Argentina.
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR - CONICET), sede FCByF - UNR, Rosario, Santa Fe, Argentina.
- Área Estadística y Procesamiento de Datos, Departamento de Matemática y Estadística, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina.
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Mavima L, Beukes CW, Palmer M, De Meyer SE, James EK, Maluk M, Gross E, Dos Reis Junior FB, Avontuur JR, Chan WY, Venter SN, Steenkamp ET. Paraburkholderia youngii sp. nov. and 'Paraburkholderia atlantica' - Brazilian and Mexican Mimosa-associated rhizobia that were previously known as Paraburkholderia tuberum sv. mimosae. Syst Appl Microbiol 2020; 44:126152. [PMID: 33276286 DOI: 10.1016/j.syapm.2020.126152] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/11/2020] [Accepted: 10/16/2020] [Indexed: 12/12/2022]
Abstract
Previous studies have recognized South and Central/Latin American mimosoid legumes in the genera Mimosa, Piptadenia and Calliandra as hosts for various nodulating Paraburkholderia species. Several of these species have been validly named in the last two decades, e.g., P. nodosa, P. phymatum, P. diazotrophica, P. piptadeniae, P. ribeironis, P. sabiae and P. mimosarum. There are still, however, a number of diverse Paraburkholderia strains associated with these legumes that have an unclear taxonomic status. In this study, we focus on 30 of these strains which originate from the root nodules of Brazilian and Mexican Mimosa species. They were initially identified as P. tuberum and subsequently placed into a symbiovar (sv. mimosae) based on their host preferences. A polyphasic approach for the delineation of these strains was used, consisting of genealogical concordance analysis (using atpD, gyrB, acnA, pab and 16S rRNA gene sequences), together with comparisons of Average Nucleotide Identity (ANI), DNA G+C content ratios and phenotypic characteristics with those of the type strains of validly named Paraburkholderia species. Accordingly, these 30 strains were delineated into two distinct groups, of which one is conspecific with 'P. atlantica' CNPSo 3155T and the other new to Science. We propose the name Paraburkholderia youngii sp. nov. with type strain JPY169T (= LMG 31411T; SARCC751T) for this novel species.
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Affiliation(s)
- Lazarus Mavima
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Chrizelle W Beukes
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Marike Palmer
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa; School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, United States of America
| | - Sofie E De Meyer
- MALDIID Pty Ltd, Murdoch, Western Australia, Australia; Laboratory of Microbiology, Department Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Euan K James
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Marta Maluk
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Eduardo Gross
- Universidade Estadual de Santa Cruz, km 16 Rodovia Ilhéus - Itabuna, CEP 45662-900 Ilhéus, BA, Brazil
| | | | - Juanita R Avontuur
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Wai Y Chan
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa; Biotechnology Platform, Agricultural Research Council Onderstepoort Veterinary Institute (ARC-OVI), Onderstepoort, South Africa
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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Bian DR, Xue H, Piao CG, Li Y. Stenotrophomonas cyclobalanopsidis sp. nov., isolated from the leaf spot disease of Cyclobalanopsis patelliformis. Antonie Van Leeuwenhoek 2020; 113:1447-1454. [PMID: 32748076 DOI: 10.1007/s10482-020-01453-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/22/2020] [Indexed: 10/23/2022]
Abstract
A Gram-negative, facultatively anaerobic, motile bacterial strain, TPQG1-4T, was isolated from the leaf of Cyclobalanopsis patelliformis with spot disease. The isolate was investigated using the polyphasic taxonomic approach. 16S rRNA gene sequencing and analyzing revealed that the novel strain shares the highest sequence similarity with Stenotrophomonas lactitubi M15T (99.6%), Stenotrophomonas indicatrix WS40T (99.4%), Stenotrophomonas maltophilia IAM 12423T (99.2%) and Stenotrophomonas pavanii LMG 25348T (99.0%). In phylogenetic trees based on 16S rRNA gene sequences, the novel strain branched independently from other species of Stenotrophomonas. Average nucleotide identity values between the novel isolate and S. lactitubi M15T, S. indicatrix WS40T, S. maltophilia IAM 12423T, S. pavanii LMG 25348T, and Pseudomonas geniculata ATCC 19374T were 87.2%, 87.3%, 86.3%, 88.0%, and 81.3%, respectively, suggesting the isolate was a novel species of the genus Stenotrophomonas. The DNA G + C content of TPQG1-4T is 67.1 mol%. The major fatty acids were iso-C15:0 (25.4%) and anteiso-C15:0 (17.0%). The polar lipids of TPQG1-4T included phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, amino phospholipid and phospholipid. Based on phenotypic and genotypic characteristics, the strain represents a novel species in the genus Stenotrophomonas, for which the name Stenotrophomonas cyclobalanopsidis sp. nov. is proposed. The type strain is TPQG1-4T (= CFCC 15341T = LMG 31208T).
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Affiliation(s)
- Dan-Ran Bian
- The Key Laboratory of National Forestry and Grassland Administration on Forest Protection, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Han Xue
- The Key Laboratory of National Forestry and Grassland Administration on Forest Protection, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Chun-Gen Piao
- The Key Laboratory of National Forestry and Grassland Administration on Forest Protection, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Yong Li
- The Key Laboratory of National Forestry and Grassland Administration on Forest Protection, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China.
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Taparia T, Krijger M, Haynes E, Elphinstone JG, Noble R, van der Wolf J. Molecular characterization of Pseudomonas from Agaricus bisporus caps reveal novel blotch pathogens in Western Europe. BMC Genomics 2020; 21:505. [PMID: 32698767 PMCID: PMC7374911 DOI: 10.1186/s12864-020-06905-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/10/2020] [Indexed: 12/04/2022] Open
Abstract
Background Bacterial blotch is a group of economically important diseases affecting the cultivation of common button mushroom, Agaricus bisporus. Despite being studied for more than a century, the identity and nomenclature of blotch-causing Pseudomonas species is still unclear. This study aims to molecularly characterize the phylogenetic and phenotypic diversity of blotch pathogens in Western Europe. Methods In this study, blotched mushrooms were sampled from farms across the Netherlands, United Kingdom and Belgium. Bacteria were isolated from symptomatic cap tissue and tested in pathogenicity assays on fresh caps and in pots. Whole genome sequences of pathogenic and non-pathogenic isolates were used to establish phylogeny via multi-locus sequence alignment (MLSA), average nucleotide identity (ANI) and in-silico DNA:DNA hybridization (DDH) analyses. Results The known pathogens “Pseudomonas gingeri”, P. tolaasii, “P. reactans” and P. costantinii were recovered from blotched mushroom caps. Seven novel pathogens were also identified, namely, P. yamanorum, P. edaphica, P. salomonii and strains that clustered with Pseudomonas sp. NC02 in one genomic species, and three non-pseudomonads, i.e. Serratia liquefaciens, S. proteamaculans and a Pantoea sp. Insights on the pathogenicity and symptom severity of these blotch pathogens were also generated. Conclusion A detailed overview of genetic and regional diversity and the virulence of blotch pathogens in Western Europe, was obtained via the phylogenetic and phenotypic analyses. This information has implications in the study of symptomatic disease expression, development of diagnostic tools and design of localized strategies for disease management.
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Affiliation(s)
- Tanvi Taparia
- Biointeractions and Plant Health, Wageningen University and Research, Wageningen, Netherlands. .,Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands.
| | - Marjon Krijger
- Biointeractions and Plant Health, Wageningen University and Research, Wageningen, Netherlands
| | - Edward Haynes
- Department of Plant Protection, Fera Science Limited, York, UK
| | | | - Ralph Noble
- Pershore College, Warwickshire College Group, Worcestershire, UK
| | - Jan van der Wolf
- Biointeractions and Plant Health, Wageningen University and Research, Wageningen, Netherlands.
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Motyka-Pomagruk A, Zoledowska S, Misztak AE, Sledz W, Mengoni A, Lojkowska E. Comparative genomics and pangenome-oriented studies reveal high homogeneity of the agronomically relevant enterobacterial plant pathogen Dickeya solani. BMC Genomics 2020; 21:449. [PMID: 32600255 DOI: 10.1186/s12864-020-06863-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/22/2020] [Indexed: 11/11/2022] Open
Abstract
Background Dickeya solani is an important plant pathogenic bacterium causing severe losses in European potato production. This species draws a lot of attention due to its remarkable virulence, great devastating potential and easier spread in contrast to other Dickeya spp. In view of a high need for extensive studies on economically important soft rot Pectobacteriaceae, we performed a comparative genomics analysis on D. solani strains to search for genetic foundations that would explain the differences in the observed virulence levels within the D. solani population. Results High quality assemblies of 8 de novo sequenced D. solani genomes have been obtained. Whole-sequence comparison, ANIb, ANIm, Tetra and pangenome-oriented analyses performed on these genomes and the sequences of 14 additional strains revealed an exceptionally high level of homogeneity among the studied genetic material of D. solani strains. With the use of 22 genomes, the pangenome of D. solani, comprising 84.7% core, 7.2% accessory and 8.1% unique genes, has been almost completely determined, suggesting the presence of a nearly closed pangenome structure. Attribution of the genes included in the D. solani pangenome fractions to functional COG categories showed that higher percentages of accessory and unique pangenome parts in contrast to the core section are encountered in phage/mobile elements- and transcription- associated groups with the genome of RNS 05.1.2A strain having the most significant impact. Also, the first D. solani large-scale genome-wide phylogeny computed on concatenated core gene alignments is herein reported. Conclusions The almost closed status of D. solani pangenome achieved in this work points to the fact that the unique gene pool of this species should no longer expand. Such a feature is characteristic of taxa whose representatives either occupy isolated ecological niches or lack efficient mechanisms for gene exchange and recombination, which seems rational concerning a strictly pathogenic species with clonal population structure. Finally, no obvious correlations between the geographical origin of D. solani strains and their phylogeny were found, which might reflect the specificity of the international seed potato market.
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Gohil K, Rajput V, Dharne M. Pan-genomics of Ochrobactrum species from clinical and environmental origins reveals distinct populations and possible links. Genomics 2020; 112:3003-3012. [PMID: 32428556 DOI: 10.1016/j.ygeno.2020.04.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 04/19/2020] [Accepted: 04/22/2020] [Indexed: 11/26/2022]
Abstract
Ochrobactrum genus is comprised of soil-dwelling Gram-negative bacteria mainly reported for bioremediation of toxic compounds. Since last few years, mainly two species of this genus, O. intermedium and O. anthropi were documented for causing infections mostly in the immunocompromised patients. Despite such ubiquitous presence, study of adaptation in various niches is still lacking. Thus, to gain insights into the niche adaptation strategies, pan-genome analysis was carried out by comparing 67 genome sequences belonging to Ochrobactrum species. Pan-genome analysis revealed it is an open pan-genome indicative of the continuously evolving nature of the genus. The presence/absence of gene clusters also illustrated the unique presence of antibiotic efflux transporter genes and type IV secretion system genes in the clinical strains while the genes of solvent resistance and exporter pumps in the environmental strains. A phylogenomic investigation based on 75 core genes depicted better and robust phylogenetic resolution and topology than the 16S rRNA gene. To support the pan-genome analysis, individual genomes were also investigated for the mobile genetic elements (MGE), antibiotic resistance genes (ARG), metal resistance genes (MRG) and virulence factors (VF). The analysis revealed the presence of MGE, ARG, and MRG in all the strains which play an important role in the species evolution which is in agreement with the pan-genome analysis. The average nucleotide identity (ANI) based on the genetic relatedness between the Ochrobactrum species indicated a distinction between individual species. Interestingly, the ANI tool was able to classify the Ochrobactrum genomes to the species level which were assigned till the genus level on the NCBI database.
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Affiliation(s)
- Kushal Gohil
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India; National Collection of Industrial Microorganisms (NCIM), CSIR-National Chemical Laboratory, Pune, India
| | - Vinay Rajput
- National Collection of Industrial Microorganisms (NCIM), CSIR-National Chemical Laboratory, Pune, India
| | - Mahesh Dharne
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India; National Collection of Industrial Microorganisms (NCIM), CSIR-National Chemical Laboratory, Pune, India.
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Zhou Y, Zheng J, Wu Y, Zhang W, Jin J. A completeness-independent method for pre-selection of closely related genomes for species delineation in prokaryotes. BMC Genomics 2020; 21:183. [PMID: 32102653 PMCID: PMC7045542 DOI: 10.1186/s12864-020-6597-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 02/19/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Whole-genome approaches are widely preferred for species delineation in prokaryotes. However, these methods require pairwise alignments and calculations at the whole-genome level and thus are computationally intensive. To address this problem, a strategy consisting of sieving (pre-selecting closely related genomes) followed by alignment and calculation has been proposed. RESULTS Here, we initially test a published approach called "genome-wide tetranucleotide frequency correlation coefficient" (TETRA), which is specially tailored for sieving. Our results show that sieving by TETRA requires > 40% completeness for both genomes of a pair to yield > 95% sensitivity, indicating that TETRA is completeness-dependent. Accordingly, we develop a novel algorithm called "fragment tetranucleotide frequency correlation coefficient" (FRAGTE), which uses fragments rather than whole genomes for sieving. Our results show that FRAGTE achieves ~ 100% sensitivity and high specificity on simulated genomes, real genomes and metagenome-assembled genomes, demonstrating that FRAGTE is completeness-independent. Additionally, FRAGTE sieved a reduced number of total genomes for subsequent alignment and calculation to greatly improve computational efficiency for the process after sieving. Aside from this computational improvement, FRAGTE also reduces the computational cost for the sieving process. Consequently, FRAGTE extremely improves run efficiency for both the processes of sieving and after sieving (subsequent alignment and calculation) to together accelerate genome-wide species delineation. CONCLUSIONS FRAGTE is a completeness-independent algorithm for sieving. Due to its high sensitivity, high specificity, highly reduced number of sieved genomes and highly improved runtime, FRAGTE will be helpful for whole-genome approaches to facilitate taxonomic studies in prokaryotes.
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Affiliation(s)
- Yizhuang Zhou
- Laboratory of Hepatobiliary and Pancreatic Surgery, The Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, 541001, People's Republic of China. .,Peking-Tsinghua Center for Life Science, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, People's Republic of China.
| | - Jifang Zheng
- Guangxi Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin, Guangxi, 541001, People's Republic of China
| | - Yepeng Wu
- China-USA Lipids in Health and Disease Research Center, Guilin Medical University, Guilin, Guangxi, 541001, People's Republic of China.,Guangxi Key Laboratory of Molecular Medicine in Liver Injury and Repair, Guilin Medical University, Guilin, Guangxi, 541001, People's Republic of China
| | - Wenting Zhang
- Guangxi Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin, Guangxi, 541001, People's Republic of China
| | - Junfei Jin
- Laboratory of Hepatobiliary and Pancreatic Surgery, The Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, 541001, People's Republic of China. .,China-USA Lipids in Health and Disease Research Center, Guilin Medical University, Guilin, Guangxi, 541001, People's Republic of China. .,Guangxi Key Laboratory of Molecular Medicine in Liver Injury and Repair, Guilin Medical University, Guilin, Guangxi, 541001, People's Republic of China.
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Das L, Deb S, Das SK. Glutamicibacter mishrai sp. nov., isolated from the coral Favia veroni from Andaman Sea. Arch Microbiol 2020; 202:733-45. [PMID: 31796989 DOI: 10.1007/s00203-019-01783-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 10/21/2019] [Accepted: 11/25/2019] [Indexed: 10/25/2022]
Abstract
A novel aerobic marine actinobacterium (strain S5-52T) belonging to the genus Glutamicibacter was isolated from the coral Favia veroni sampled from the Andaman Sea, India. Cells are Gram stain positive and rod shaped. The DNA G+C content was 58.7 mol%. The major quinones were MK-8 and MK-9. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, glycolipid, trimannosyldiacylglycerol, phospholipid and dimannosylglyceride. The peptidoglycan type was A4α. Strain S5-52T showed a maximum 16S rRNA similarity of 99.36% with Glutamicibacter halophytocola DSM 101718T. The genome of strain S5-52T was 3.57 Mb that contains 3274 protein coding sequences (CDS). DNA-DNA similarity and ANI values between S5-52T and the reference strains were below 70% and 95-96%, respectively. Analysis of genomic reduction events in the evolutionary path from the LUCA (last universal common ancestor) to G. mishrai LMG 29155T and G. halophytocola DSM 101718T exhibit a number of genes involved in amino acid metabolism, cell wall biogenesis and replication, recombination and repair mechanism that reduced in both the species. Based on phenotypic, chemotaxonomic properties and comparative genomic studies, the strain S5-52T is considered a novel species of the genus Glutamicibacter, for which the name Glutamicibacter mishrai sp. nov. is proposed. The type strain is S5-52T (= KCTC 39846T = LMG 29155T).
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Valenzuela-Ruiz V, Robles-Montoya RI, Parra-Cota FI, Santoyo G, Del Carmen Orozco-Mosqueda M, Rodríguez-Ramírez R, de Los Santos-Villalobos S. Draft genome sequence of Bacillus paralicheniformis TRQ65, a biological control agent and plant growth-promoting bacterium isolated from wheat ( Triticum turgidum subsp. durum) rhizosphere in the Yaqui Valley, Mexico. 3 Biotech 2019; 9:436. [PMID: 31696041 DOI: 10.1007/s13205-019-1972-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 10/23/2019] [Indexed: 01/25/2023] Open
Abstract
The strain denominated TRQ65 was isolated from wheat (Triticum turgidum subsp. durum) commercial fields in the Yaqui Valley, Mexico. Here, we report its draft genome sequence, which presented ~ 4.5 million bp and 45.5% G + C content. Based on the cutoff values on species delimitation established for average nucleotide identity (> 95 to 96%), genome-to-genome distance calculator (> 70%), and the reference sequence alignment-based phylogeny builder method, TRQ65 was strongly affiliated to Bacillus paralicheniformis. The rapid annotation using subsystem technology server revealed that TRQ65 contains genes related to osmotic, and oxidative stress response, as well as auxin biosynthesis (plant growth promotion traits). In addition, antiSMASH and BAGEL revealed the presence of genes involved in lipopeptides and antibiotic biosynthesis. The function of those annotated genes was validated at a metabolic level, observing that strain TRQ65 was able to tolerate saline (91.0%), and water (155.0%) stress conditions, besides producing 28.8 ± 0.9 µg/mL indoles. In addition, strain TRQ65 showed growth inhibition (1.6 ± 0.4 cm inhibition zone) against the causal agent of wheat spot blotch, Bipolaris sorokiniana. Finally, plant-microbe interactions assays confirm the ability of strain TRQ65 to regulate wheat growth, showing a significant increment in shoot height (26%), root length (40%), shoot dry weight (48%), stem diameter (55%), and biovolume index (246%). These findings provide insights for future agricultural studies of this strain.
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Wang X, Zhu J, Feng J, Sardar A, Hu Z, Wang H. Tropicibacter alexandrii sp. nov., a novel marine bacterium isolated from the phycosphere of a dinoflagellate, Alexandrium minutum. Antonie Van Leeuwenhoek 2019; 113:311-320. [PMID: 31595364 DOI: 10.1007/s10482-019-01339-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 09/26/2019] [Indexed: 01/31/2023]
Abstract
An aerobic, Gram-negative, rod-shaped, non-motile bacterium was isolated from a liquid culture of the dinoflagellate Alexandrium minutum and designated as strain LMIT003T. Analyses of 16S rRNA gene sequences revealed that this strain is affiliated with the genus Tropicibacter in the family Rhodobacteraceae of the class Alphaproteobacteria and shows high similarity (97.3%) with the type species Tropicibacter naphthalenivorans C02T. Phylogenetic analysis based on core genes showed that the isolate groups with members of the genus Tropicibacter. The G + C content of strain LMIT003T was determined to be 61.9 mol%. The major fatty acids identified included summed feature 8 (C18:1 ω7c/C18:1 ω6c), C18:0, C12:1 3-OH and C16:0. The sole respiratory lipoquinone was found to be ubiquinone-10. The major polar lipids were found to be phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, two unidentified aminolipids and four unidentified phospholipids. The draft genome size of strain LMIT003T was determined to be 4.8 Mbp. The average nucleotide identity values between strain LMIT003T and reference Tropicibacter species were determined to be 78.7% (T. naphthalenivorans) and 74.2% (Tropicibacter phthalicicus). Based on physiological, chemotaxonomic and phylogenetic analysis, strain LMIT003T is concluded to represent a novel species in the genus Tropicibacter, for which the name Tropicibacter alexandrii sp. nov., is proposed. The type strain is LMIT003T (= CICC 24660T = KCTC 62895T).
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Affiliation(s)
- Xiaoli Wang
- Biology Department, College of Science, Shantou University, Shantou, 515063, China
| | - Jianming Zhu
- Biology Department, College of Science, Shantou University, Shantou, 515063, China
| | - Jiarong Feng
- Biology Department, College of Science, Shantou University, Shantou, 515063, China
| | - Ali Sardar
- Biology Department, College of Science, Shantou University, Shantou, 515063, China
| | - Zhong Hu
- Biology Department, College of Science, Shantou University, Shantou, 515063, China
| | - Hui Wang
- Biology Department, College of Science, Shantou University, Shantou, 515063, China.
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Tortoli E, Meehan CJ, Grottola A, Fregni Serpini G, Fabio A, Trovato A, Pecorari M, Cirillo DM. Genome-based taxonomic revision detects a number of synonymous taxa in the genus Mycobacterium. Infect Genet Evol 2019; 75:103983. [PMID: 31352146 DOI: 10.1016/j.meegid.2019.103983] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 07/21/2019] [Accepted: 07/25/2019] [Indexed: 12/16/2022]
Abstract
The aim of this study was to clarify the taxonomic status of named species within the genus Mycobacterium. The analysis of genomes belonging to 174 taxa (species or subspecies) of the genus Mycobacterium was conducted using both the Average Nucleotide Identity and the Genome to Genome Distance. A number of synonymous taxa were detected. The list of synonyms includes: two subspecies of M. chelonae (M. chelonae subsp. bovis and M. chelonae subsp. gwanakae), two subspecies of M. fortuitum (M. fortuitum subsp. fortuitum and M. fortuitum subsp. acetamidolyticum), four subspecies of M. avium (M. avium subsp. avium, M. avium subsp. silvaticum, M. avium subsp. paratuberculosis and "M. avium subsp. hominissuis"), two couples of subspecies of M. intracellulare (M. intracellulare subsp. intracellulare/M. intracellulare subsp. paraintracellulare and M. intracellulare subsp. chimaera/M. intracellulare subsp. yongonense), the species M. austroafricanum and M. vanbaalenii, the species M. senegalense and M. conceptionense, the species M. talmoniae and M. eburneum and the species M. marinum, M. ulcerans and M. pseudoshottsii. Furthermore one species were reclassified as subspecies of another mycobacterium: M. lepraemurium was reclassified as a subspecies of M. avium (M. avium subsp. lepraemurium). The updates to nomenclature are proposed basing on the priority of names according the Code of nomenclature of prokaryotes. For two species (M. bouchedurhonense and M. marseillense) the loss of standing in nomenclature is proposed because of unavailability of respective type strains in culture collections.
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Affiliation(s)
- Enrico Tortoli
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milano, Italy.
| | - Conor J Meehan
- BCCM/ITM Mycobacterial Culture Collection, Department of Biomedical Science, Institute of Tropical Medicine, Antwerp, Belgium
| | - Antonella Grottola
- Microbiology and Virology Unit, University Hospital Polyclinic, Modena, Italy
| | | | - Anna Fabio
- Microbiology and Virology Unit, University Hospital Polyclinic, Modena, Italy
| | - Alberto Trovato
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Monica Pecorari
- Microbiology and Virology Unit, University Hospital Polyclinic, Modena, Italy
| | - Daniela M Cirillo
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milano, Italy
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Desmet S, De Keyser E, Van Vaerenbergh J, Baeyen S, Van Huylenbroeck J, Geelen D, Dhooghe E. Differential efficiency of wild type rhizogenic strains for rol gene transformation of plants. Appl Microbiol Biotechnol 2019; 103:6657-6672. [PMID: 31273398 DOI: 10.1007/s00253-019-10003-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 06/21/2019] [Accepted: 06/27/2019] [Indexed: 10/26/2022]
Abstract
Rhizogenic agrobacteria induce extensive root proliferation, in several economically valuable, dicotyledonous plant species, a phenomenon referred to as "hairy roots." Besides their pathogenic nature, agrobacteria have proven to be a valuable asset in biotechnology and molecular plant breeding. To assess the potential of frequently used rhizogenic strains, growth in yeast extract glucose broth and antibiotic resistance was analyzed. Growth curves were established for Arqua1, NCPPB2659, LMG150, LMG152, and ATCC15834; and regression analysis of the exponential growth phase resulted in a reliable and standardized method for preparation of a bacterial suspension for inoculation. Cell density did not correlate with the timing of hairy root emergence. The highest number of hairy roots was obtained with an inoculum of 1 × 108 CFU ml-1 for Arqua1, NCPPB2659, and LMG152. Cell density of ATCC15834 did not affect the number of hairy roots formed. The identity of the rhizogenic strains for plant transformation was verified in phylogenetic analysis using average nucleotide identity (ANI), which also provided insight in their genetic diversity within the Rhizobium taxon.
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Affiliation(s)
- Siel Desmet
- Flanders Research Institute for Agricultural, Fisheries and Food (ILVO), Plant Sciences Unit, Caritasstraat 39, 9090, Melle, Belgium. .,Department Plant and Crop, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
| | - Ellen De Keyser
- Flanders Research Institute for Agricultural, Fisheries and Food (ILVO), Plant Sciences Unit, Caritasstraat 39, 9090, Melle, Belgium
| | - Johan Van Vaerenbergh
- Flanders Research Institute for Agricultural, Fisheries and Food (ILVO), Plant Sciences Unit, Caritasstraat 39, 9090, Melle, Belgium
| | - Steve Baeyen
- Flanders Research Institute for Agricultural, Fisheries and Food (ILVO), Plant Sciences Unit, Caritasstraat 39, 9090, Melle, Belgium
| | - Johan Van Huylenbroeck
- Flanders Research Institute for Agricultural, Fisheries and Food (ILVO), Plant Sciences Unit, Caritasstraat 39, 9090, Melle, Belgium
| | - Danny Geelen
- Department Plant and Crop, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Emmy Dhooghe
- Flanders Research Institute for Agricultural, Fisheries and Food (ILVO), Plant Sciences Unit, Caritasstraat 39, 9090, Melle, Belgium
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Zhang G, Yang J, Lai XH, Lu S, Jin D, Pu J, Bai X, Luo X, Xiong Y, Huang Y, Chen C, Xu J. Neisseria chenwenguii sp. nov. isolated from the rectal contents of a plateau pika (Ochotona curzoniae). Antonie Van Leeuwenhoek 2019; 112:1001-10. [PMID: 30798492 DOI: 10.1007/s10482-019-01234-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 01/18/2019] [Indexed: 01/27/2023]
Abstract
Two Gram-stain negative, catalase positive, coccus shaped bacteria, designated 10023T and 10010, were isolated from the rectal contents of a plateau pika (Ochotona curzoniae) in Qinghai–Tibet Plateau, China. Based on 16S rRNA gene sequence analysis, phylogenetic trees showed that these two isolates (10023T, 10010) group with members of the genus Neisseria. Additionally, these two isolates exhibited high 16S rRNA gene sequence similarity with Neisseria zalophi CSL 7565T (96.98%), Neisseria wadsworthii WC 05-9715T (96.92%) and Neisseria canis ATCC 14687T (96.79%). Further phylogenetic analysis based on the rplF gene showed that these two novel strains can be easily discriminated from phylogenetically closely related species. Optimal growth was found to occur on BHI agar with 5% defibrinated sheep blood at 37 °C and growth was also observed on nutrient agar, Columbia blood agar and chocolate agar plates; however, growth was not observed on MacConkey agar after 7 days. The major cellular fatty acids of these strains were identified as C16:0 and C16:1ω7c/C16:1ω6c. The complete genome size of the type strain 10023T is 2,496,444 bp, with DNA G+C content of 54.0 mol %. The average nucleotide identity values were 73.5–79.3% between isolate 10023T and reference Neisseria spp. Based on polyphasic analysis, these isolates (10023T and 10010) are considered to represent a novel species in the genus Neisseria, for which the name Neisseria chenwenguii sp. nov. is proposed. The type strain is 10023T (= DSM 103440T = CGMCC 1.15736T).
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Martins da Costa E, Soares de Carvalho T, Azarias Guimarães A, Ribas Leão AC, Magalhães Cruz L, de Baura VA, Lebbe L, Willems A, de Souza Moreira FM. Classification of the inoculant strain of cowpea UFLA03-84 and of other strains from soils of the Amazon region as Bradyrhizobium viridifuturi (symbiovar tropici). Braz J Microbiol 2019; 50:335-345. [PMID: 30759310 DOI: 10.1007/s42770-019-00045-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 11/20/2018] [Indexed: 12/20/2022] Open
Abstract
Cowpea (Vigna unguiculata L.) is a legume species that considerably benefits from inoculation with nitrogen fixing bacteria of the genus Bradyrhizobium. One of the strains recommended for inoculation in cowpea in Brazil is UFLA03-84 (Bradyrhizobium sp.). The aim of our study was to define the taxonomic position of the UFLA03-84 strain and of two other strains of Bradyrhizobium (UFLA03-144 and INPA237B), all belonging to the same phylogenetic group and isolated from soils of the Brazilian Amazon. Multilocus sequence analysis (MLSA) of the housekeeping genes atpD, gyrB, recA, and rpoB grouped (with similarity higher than 99%) the three strains with Bradyrhizobium viridifuturi SEMIA 690T. The analyses of average nucleotide identity and digital DNA-DNA hybridization supported classification of the group as Bradyrhizobium viridifuturi. The three strains exhibited similar behavior in relation to the most of the phenotypic characteristics evaluated. However, some characteristics exhibited variation, indicating phenotypic diversity within the species. Phylogenetic analysis of the nodC and nifH genes showed that the three strains are members of the same symbiovar (tropici) that contains type strains of Bradyrhizobium species coming from tropical soils (SEMIA 690TB. viridifuturi, CNPSo 1112TB. tropiciagri, CNPSo 2833TB. embrapense, and B. brasilense UFLA03-321T).
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Affiliation(s)
- Elaine Martins da Costa
- Departamento de Ciência do Solo, Universidade Federal de Lavras, Lavras, MG, 37200-000, Brazil.,Universidade Federal do Piauí, Campus Professora Cinobelina Elvas, Bom Jesus, Piauí, 64900-000, Brazil
| | | | | | - Aniele Carolina Ribas Leão
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, Paraná, 81531990, Brazil
| | - Leonardo Magalhães Cruz
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, Paraná, 81531990, Brazil
| | - Valter Antonio de Baura
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, Paraná, 81531990, Brazil
| | - Liesbeth Lebbe
- Department of Biochemistry and Microbiology, Ghent University, B-9000, Ghent, Belgium
| | - Anne Willems
- Department of Biochemistry and Microbiology, Ghent University, B-9000, Ghent, Belgium
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Gan HM, Lee MVL, Savka MA. Improved genome of Agrobacterium radiobacter type strain provides new taxonomic insight into Agrobacterium genomospecies 4. PeerJ 2019; 7:e6366. [PMID: 30775173 PMCID: PMC6369824 DOI: 10.7717/peerj.6366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 12/20/2018] [Indexed: 12/21/2022] Open
Abstract
The reported Agrobacterium radiobacter DSM 30174T genome is highly fragmented, hindering robust comparative genomics and genome-based taxonomic analysis. We re-sequenced the Agrobacterium radiobacter type strain, generating a dramatically improved genome with high contiguity. In addition, we sequenced the genome of Agrobacterium tumefaciens B6T, enabling for the first time, a proper comparative genomics of these contentious Agrobacterium species. We provide concrete evidence that the previously reported Agrobacterium radiobacter type strain genome (Accession Number: ASXY01) is contaminated which explains its abnormally large genome size and fragmented assembly. We propose that Agrobacterium tumefaciens be reclassified as Agrobacterium radiobacter subsp. tumefaciens and that Agrobacterium radiobacter retains it species status with the proposed name of Agrobacterium radiobacter subsp. radiobacter. This proposal is based, first on the high pairwise genome-scale average nucleotide identity supporting the amalgamation of both Agrobacterium radiobacter and Agrobacterium tumefaciens into a single species. Second, maximum likelihood tree construction based on the concatenated alignment of shared genes (core genes) among related strains indicates that Agrobacterium radiobacter NCPPB3001 is sufficiently divergent from Agrobacterium tumefaciens to propose two independent sub-clades. Third, Agrobacterium tumefaciens demonstrates the genomic potential to synthesize the L configuration of fucose in its lipid polysaccharide, fostering its ability to colonize plant cells more effectively than Agrobacterium radiobacter.
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Affiliation(s)
- Han Ming Gan
- Deakin Genomics Centre, Deakin University, Geelong, VIC, Australia.,Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia.,School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia
| | - Melvin V L Lee
- School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia
| | - Michael A Savka
- College of Science, The Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USA
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Braun MS, Wang E, Zimmermann S, Wink M. Corynebacterium heidelbergense sp. nov., isolated from the preen glands of Egyptian geese (Alopochen aegyptiacus). Syst Appl Microbiol 2018; 41:564-9. [PMID: 29958724 DOI: 10.1016/j.syapm.2018.06.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 06/01/2018] [Accepted: 06/04/2018] [Indexed: 11/23/2022]
Abstract
Two strains (pedersoliT and girotti) of a new species of bacteria were isolated from the preen glands of wild Egyptian geese (Alopochen aegyptiacus) from the river Neckar in southern Germany in two subsequent years. The strains were lipophilic, fastidious, Gram-positive rods and belonged to the genus Corynebacterium. Phylogenetically, the isolates were most closely related to Corynebacterium falsenii DSM 44353T which has been found to be associated with birds before. 16S rRNA gene sequence similarity to all known Corynebacterium spp. was significantly <97%. Corresponding values of rpoB showed low levels of similarity <87% and ANIb was <73%. G+C content of the genomic DNA was 65.0mol% for the type strain of the goose isolates, as opposed to 63.2mol% in Corynebacterium falsenii. MALDI-TOF MS analysis of the whole-cell proteins revealed patterns clearly different from the related species, as did biochemical tests, and polar lipid profiles. We therefore conclude that the avian isolates constitute strains of a new species, for which the name Corynebacterium heidelbergense sp. nov. is proposed. The type strain is pedersoliT (=DSM 104638T=LMG 30044T).
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de Matos GF, Zilli JE, de Araújo JLS, Parma MM, Melo IS, Radl V, Baldani JI, Rouws LFM. Bradyrhizobium sacchari sp. nov., a legume nodulating bacterium isolated from sugarcane roots. Arch Microbiol 2017; 199:1251-1258. [PMID: 28601967 DOI: 10.1007/s00203-017-1398-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 05/07/2017] [Accepted: 06/05/2017] [Indexed: 10/19/2022]
Abstract
Members of the genus Bradyrhizobium are well-known as nitrogen-fixing microsymbionts of a wide variety of leguminous species, but they have also been found in different environments, notably as endophytes in non-legumes such as sugarcane. This study presents a detailed polyphasic characterization of four Bradyrhizobium strains (type strain BR 10280T), previously isolated from roots of sugarcane in Brazil. 16S rRNA sequence analysis, multilocus sequence analysis (MLSA) and analysis of the 16S-23S rRNA internal transcribed spacer showed that these strains form a novel clade close to, but different from B. huanghuaihaiense strain CCBAU 23303T. Average nucleotide identity (ANI) analyses confirmed that BR 10280T represents a novel species. Phylogenetic analysis based on nodC gene sequences also placed the strains close to CCBAU 23303T, but different from this latter strain, the sugarcane strains did not nodulate soybean, although they effectively nodulated Vigna unguiculata, Cajanus cajan and Macroptilium atropurpureum. Physiological traits are in agreement with the placement of the strains in the genus Bradyrhizobium as a novel species for which the name Bradyrhizobium sacchari sp. nov. is proposed.
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Affiliation(s)
- Gustavo Feitosa de Matos
- Embrapa Agrobiologia, Rodovia BR 465 km 7, Seropédica, Rio De Janeiro, 23890-000, Brazil
- Universidade Federal Rural do Rio de Janeiro, Curso de Pós-graduação em Fitotecnia, Rodovia BR 465 km 07, Seropédica, Rio De Janeiro, 23890-000, Brazil
| | - Jerri Edson Zilli
- Embrapa Agrobiologia, Rodovia BR 465 km 7, Seropédica, Rio De Janeiro, 23890-000, Brazil
| | | | - Marcia Maria Parma
- Embrapa Meio Ambiente, C.P. 69, Jaguariúna, São Paulo, 13820-000, Brazil
| | - Itamar Soares Melo
- Embrapa Meio Ambiente, C.P. 69, Jaguariúna, São Paulo, 13820-000, Brazil
| | - Viviane Radl
- Helmholtz Zentrum München, Research Unit Comparative Microbiome Analysis, Ingolstädter Landtraße 1, 85764, Oberschleißheim, Germany
| | - José Ivo Baldani
- Embrapa Agrobiologia, Rodovia BR 465 km 7, Seropédica, Rio De Janeiro, 23890-000, Brazil
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Tortoli E, Fedrizzi T, Meehan CJ, Trovato A, Grottola A, Giacobazzi E, Serpini GF, Tagliazucchi S, Fabio A, Bettua C, Bertorelli R, Frascaro F, De Sanctis V, Pecorari M, Jousson O, Segata N, Cirillo DM. The new phylogeny of the genus Mycobacterium: The old and the news. Infect Genet Evol 2017; 56:19-25. [PMID: 29030295 DOI: 10.1016/j.meegid.2017.10.013] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 10/09/2017] [Accepted: 10/10/2017] [Indexed: 10/18/2022]
Abstract
BACKGROUND Phylogenetic studies of bacteria have been based so far either on a single gene (usually the 16S rRNA) or on concatenated housekeeping genes. For what concerns the genus Mycobacterium these approaches support the separation of rapidly and slowly growing species and the clustering of most species in well-defined phylogenetic groups. The advent of high-throughput shotgun sequencing leads us to revise conventional taxonomy of mycobacteria on the light of genomic data. For this purpose we investigated 88 newly sequenced species in addition to 60 retrieved from GenBank and used the Average Nucleotide Identity pairwise scores to reconstruct phylogenetic relationships within this genus. RESULTS Our analysis confirmed the separation of slow and rapid growers and the intermediate position occupied by the M. terrae complex. Among the rapid growers, the species of the M. chelonae-abscessus complex belonged to the most ancestral cluster. Other major clades of rapid growers included the species related to M. fortuitum and M. smegmatis and a large grouping containing mostly environmental species rarely isolated from humans. The members of the M. terrae complex appeared as the most ancestral slow growers. Among slow growers two deep branches led to the clusters of species related to M. celatum and M. xenopi and to a large group harboring most of the species more frequently responsible of disease in humans, including the major pathogenic mycobacteria (M. tuberculosis, M. leprae, M. ulcerans). The species previously grouped in the M. simiae complex were allocated in a number of sub-clades; of them, only the one including the species M. simiae identified the real members of this complex. The other clades included also species previously not considered related to M. simiae. The ANI analysis, in most cases supported by Genome to Genome Distance and by Genomic Signature-Delta Difference, showed that a number of species with standing in literature were indeed synonymous. CONCLUSIONS Genomic data revealed to be much more informative in comparison with phenotype. We believe that the genomic revolution enabled by high-throughput shotgun sequencing should now be considered in order to revise the conservative approaches still informing taxonomic sciences.
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Affiliation(s)
- Enrico Tortoli
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milano, Italy.
| | - Tarcisio Fedrizzi
- Centre for Integrative Biology, University of Trento, Trento, Italy.
| | - Conor J Meehan
- Mycobacteriology unit, Department of Biomedical Science, Institute of Tropical Medicine, Antwerp, Belgium.
| | - Alberto Trovato
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milano, Italy.
| | - Antonella Grottola
- Microbiology and Virology Unit, University Hospital Polyclinic, Modena, Italy.
| | | | | | - Sara Tagliazucchi
- Microbiology and Virology Unit, University Hospital Polyclinic, Modena, Italy.
| | - Anna Fabio
- Microbiology and Virology Unit, University Hospital Polyclinic, Modena, Italy.
| | - Clotilde Bettua
- Centre for Integrative Biology, University of Trento, Trento, Italy.
| | - Roberto Bertorelli
- NGS Facility, Laboratory of Biomolecular Sequence and Structure Analysis for Health, Centre for Integrative Biology, University of Trento, Italy.
| | - Francesca Frascaro
- Microbiology and Virology Unit, University Hospital Polyclinic, Modena, Italy.
| | - Veronica De Sanctis
- NGS Facility, Laboratory of Biomolecular Sequence and Structure Analysis for Health, Centre for Integrative Biology, University of Trento, Italy.
| | - Monica Pecorari
- Microbiology and Virology Unit, University Hospital Polyclinic, Modena, Italy.
| | - Olivier Jousson
- Centre for Integrative Biology, University of Trento, Trento, Italy.
| | - Nicola Segata
- Centre for Integrative Biology, University of Trento, Trento, Italy.
| | - Daniela M Cirillo
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milano, Italy.
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Vinatzer BA, Tian L, Heath LS. A proposal for a portal to make earth's microbial diversity easily accessible and searchable. Antonie Van Leeuwenhoek 2017; 110:1271-9. [PMID: 28281028 DOI: 10.1007/s10482-017-0849-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 02/22/2017] [Indexed: 11/27/2022]
Abstract
Estimates of the number of bacterial species range from 107 to 1012. At the pace at which descriptions of new species are currently being published, the description of all bacterial species on earth will only be completed in thousands of years. However, even if one day all species were named and described, these names and descriptions would still be of little practical value unless they could be easily searched and accessed, so that novel strains could be easily identified as members of any of these species. To complicate the situation further, many of the currently known species contain significant genotypic and phenotypic diversity that would still be missed if description of microbial diversity were limited to species. The solution to this problem could be a database in which every bacterial species and every intra-specific group is anchored to a genome-similarity framework. This ideal database should be searchable using complete or partial genome sequences as well as phenotypes. Moreover, the database should include functions to easily add newly sequenced novel strains, automatically place them into the genome-similarity framework, identify them as members of an already named species, or tag them as members of yet to be described species or new intra-specific groups. Here, we propose the means to develop such a database by taking advantage of the concept of genome sequence similarity-based codes, called Life Identification Numbers or LINs.
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Yoon SH, Ha SM, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 2017; 110:1281-6. [PMID: 28204908 DOI: 10.1007/s10482-017-0844-4] [Citation(s) in RCA: 2095] [Impact Index Per Article: 299.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 02/07/2017] [Indexed: 10/20/2022]
Abstract
Average nucleotide identity (ANI) is a category of computational analysis that can be used to define species boundaries of Archaea and Bacteria. Calculating ANI usually involves the fragmentation of genome sequences, followed by nucleotide sequence search, alignment, and identity calculation. The original algorithm to calculate ANI used the BLAST program as its search engine. An improved ANI algorithm, called OrthoANI, was developed to accommodate the concept of orthology. Here, we compared four algorithms to compute ANI, namely ANIb (ANI algorithm using BLAST), ANIm (ANI using MUMmer), OrthoANIb (OrthoANI using BLAST) and OrthoANIu (OrthoANI using USEARCH) using >100,000 pairs of genomes with various genome sizes. By comparing values to the ANIb that is considered a standard, OrthoANIb and OrthoANIu exhibited good correlation in the whole range of ANI values. ANIm showed poor correlation for ANI of <90%. ANIm and OrthoANIu runs faster than ANIb by an order of magnitude. When genomes that are larger than 7 Mbp were analysed, the run-times of ANIm and OrthoANIu were shorter than that of ANIb by 53- and 22-fold, respectively. In conclusion, ANI calculation can be greatly sped up by the OrthoANIu method without losing accuracy. A web-service that can be used to calculate OrthoANIu between a pair of genome sequences is available at http://www.ezbiocloud.net/tools/ani . For large-scale calculation and integration in bioinformatics pipelines, a standalone JAVA program is available for download at http://www.ezbiocloud.net/tools/orthoaniu .
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Davis II EW, Weisberg AJ, Tabima JF, Grunwald NJ, Chang JH. Gall-ID: tools for genotyping gall-causing phytopathogenic bacteria. PeerJ 2016; 4:e2222. [PMID: 27547538 PMCID: PMC4958008 DOI: 10.7717/peerj.2222] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 06/15/2016] [Indexed: 11/20/2022] Open
Abstract
Understanding the population structure and genetic diversity of plant pathogens, as well as the effect of agricultural practices on pathogen evolution, is important for disease management. Developments in molecular methods have contributed to increase the resolution for accurate pathogen identification, but those based on analysis of DNA sequences can be less straightforward to use. To address this, we developed Gall-ID, a web-based platform that uses DNA sequence information from 16S rDNA, multilocus sequence analysis and whole genome sequences to group disease-associated bacteria to their taxonomic units. Gall-ID was developed with a particular focus on gall-forming bacteria belonging to Agrobacterium, Pseudomonas savastanoi, Pantoea agglomerans, and Rhodococcus. Members of these groups of bacteria cause growth deformation of plants, and some are capable of infecting many species of field, orchard, and nursery crops. Gall-ID also enables the use of high-throughput sequencing reads to search for evidence for homologs of characterized virulence genes, and provides downloadable software pipelines for automating multilocus sequence analysis, analyzing genome sequences for average nucleotide identity, and constructing core genome phylogenies. Lastly, additional databases were included in Gall-ID to help determine the identity of other plant pathogenic bacteria that may be in microbial communities associated with galls or causative agents in other diseased tissues of plants. The URL for Gall-ID is http://gall-id.cgrb.oregonstate.edu/.
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Affiliation(s)
- Edward W. Davis II
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
- Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR, United States
| | - Alexandra J. Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Javier F. Tabima
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Niklaus J. Grunwald
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
- Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR, United States
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, United States
- Horticultural Crops Research Laboratory, USDA-ARS, Corvallis, OR, United States
| | - Jeff H. Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
- Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR, United States
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, United States
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Chen M, Li Y, Li S, Tang L, Zheng J, An Q. Genomic identification of nitrogen-fixing Klebsiella variicola, K. pneumoniae and K. quasipneumoniae. J Basic Microbiol 2015; 56:78-84. [PMID: 26471769 DOI: 10.1002/jobm.201500415] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 10/06/2015] [Indexed: 11/09/2022]
Abstract
It was difficult to differentiate Klebsiella pneumoniae, K. quasipneumoniae and K. variicola by biochemical and phenotypic tests. Genomics increase the resolution and credibility of taxonomy for closely-related species. Here, we obtained the complete genome sequence of the K. variicola type strain DSM 15968(T) (=F2R9(T)). The genome of the type strain is a circular chromosome of 5,521,203 bp with 57.56% GC content. From 540 Klebsiella strains whose genomes had been publicly available as at 3 March 2015, we identified 21 strains belonging to K. variicola and 8 strains belonging to K. quasipneumoniae based on the genome average nucleotide identities (ANI). All the K. variicola strains, one K. pneumoniae strain and five K. quasipneumoniae strains contained nitrogen-fixing genes. A phylogenomic analysis showed clear species demarcations for these nitrogen-fixing bacteria. In accordance with the key biochemical characteristics of K. variicola, the idnO gene encoding 5-keto-D-gluconate 5-reductase for utilization of 5-keto-D-gluconate and the sorCDFBAME operon for catabolism of L-sorbose were present whereas the rbtRDKT operon for catabolism of adonitol was absent in the genomes of K. variicola strains. Therefore, the genomic analyses supported the ANI-based species delineation; the genome sequence of the K. variicola type strain provides the reference genome for genomic identification of K. variicola, which is a nitrogen-fixing species.
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Affiliation(s)
- Mingyue Chen
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yuanyuan Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Shuying Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Lie Tang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Jingwu Zheng
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Qianli An
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
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Kim M, Park SC, Baek I, Chun J. Large-scale evaluation of experimentally determined DNA G+C contents with whole genome sequences of prokaryotes. Syst Appl Microbiol 2014; 38:79-83. [PMID: 25564067 DOI: 10.1016/j.syapm.2014.11.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 11/18/2014] [Accepted: 11/24/2014] [Indexed: 11/30/2022]
Abstract
Historically, DNA G+C content has played a critical role in the description of bacterial and archaeal species. Despite its importance in prokaryote taxonomy, its accuracy has been questioned due to methodological heterogeneity and measurement errors of conventional methods. Here we investigated the extent of accuracy of experimentally determined DNA G+C contents by comparing the reference values calculated from whole genome sequences. The large-scale comparison revealed that G+C contents determined by high-performance liquid chromatography and buoyant density centrifugation methods were more similar to the genome-derived reference values than those generated by thermal denaturation method. However, there was a substantial degree of discrepancy in DNA G+C contents between values obtained by conventional methods and genome-derived reference values. The majority of the differences between them fell out of the acceptable range (i.e. 1 mol% G+C content difference) for species delimitation of prokaryotes. In contrast, when average nucleotide identity (ANI) was correlated to G+C difference among genomes, most G+C difference was confined to less than 1% within species. Therefore, erroneous conventional methods are not meaningful in the description of bacterial and archaeal species. For taxonomic purposes, DNA G+C content should be determined by calculating directly from high-quality genome sequences with at least 16× or higher sequencing depth of coverage.
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Affiliation(s)
- Mincheol Kim
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, Republic of Korea
| | - Sang-Cheol Park
- Interdisciplinary Program in Bioinformatics and Bioinformatics Institute, Seoul National University, Seoul 151-742, Republic of Korea
| | - Inwoo Baek
- School of Biological Sciences, Seoul National University, Seoul 151-742, Republic of Korea
| | - Jongsik Chun
- School of Biological Sciences, Seoul National University, Seoul 151-742, Republic of Korea; Interdisciplinary Program in Bioinformatics and Bioinformatics Institute, Seoul National University, Seoul 151-742, Republic of Korea.
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