1
|
Rodrigues Jardim B, Gambley C, Tran-Nguyen LTT, Webster C, Kehoe M, Kinoti WM, Bond S, Davis R, Jones L, Pathania N, Sharman M, Chapman T, Rodoni BC, Constable FE. A metagenomic investigation of phytoplasma diversity in Australian vegetable growing regions. Microb Genom 2024; 10:001213. [PMID: 38446015 PMCID: PMC10999746 DOI: 10.1099/mgen.0.001213] [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: 10/26/2023] [Accepted: 02/21/2024] [Indexed: 03/07/2024] Open
Abstract
In this study, metagenomic sequence data was used to investigate the phytoplasma taxonomic diversity in vegetable-growing regions across Australia. Metagenomic sequencing was performed on 195 phytoplasma-positive samples, originating either from historic collections (n=46) or during collection efforts between January 2015 and June 2022 (n=149). The sampled hosts were classified as crop (n=155), weed (n=24), ornamental (n=7), native plant (n=6), and insect (n=3) species. Most samples came from Queensland (n=78), followed by Western Australia (n=46), the Northern Territory (n=32), New South Wales (n=17), and Victoria (n=10). Of the 195 draft phytoplasma genomes, 178 met our genome criteria for comparison using an average nucleotide identity approach. Ten distinct phytoplasma species were identified and could be classified within the 16SrII, 16SrXII (PCR only), 16SrXXV, and 16SrXXXVIII phytoplasma groups, which have all previously been recorded in Australia. The most commonly detected phytoplasma taxa in this study were species and subspecies classified within the 16SrII group (n=153), followed by strains within the 16SrXXXVIII group ('Ca. Phytoplasma stylosanthis'; n=6). Several geographic- and host-range expansions were reported, as well as mixed phytoplasma infections of 16SrII taxa and 'Ca. Phytoplasma stylosanthis'. Additionally, six previously unrecorded 16SrII taxa were identified, including five putative subspecies of 'Ca. Phytoplasma australasiaticum' and a new putative 16SrII species. PCR and sequencing of the 16S rRNA gene was a suitable triage tool for preliminary phytoplasma detection. Metagenomic sequencing, however, allowed for higher-resolution identification of the phytoplasmas, including mixed infections, than was afforded by only direct Sanger sequencing of the 16S rRNA gene. Since the metagenomic approach theoretically obtains sequences of all organisms in a sample, this approach was useful to confirm the host family, genus, and/or species. In addition to improving our understanding of the phytoplasma species that affect crop production in Australia, the study also significantly expands the genomic sequence data available in public sequence repositories to contribute to phytoplasma molecular epidemiology studies, revision of taxonomy, and improved diagnostics.
Collapse
Affiliation(s)
- Bianca Rodrigues Jardim
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
- Agriculture Victoria Research, Department of Energy, Environment and Climate Action, AgriBio, Bundoora, Victoria, Australia
| | - Cherie Gambley
- Horticulture and Forestry Science, Department of Agriculture and Fisheries Maroochy Research Facility, Nambour, Queensland, Australia
| | | | - Craig Webster
- Diagnostic Laboratory Services, Department of Primary Industries and Regional Development, South Perth, Western Australia, Australia
| | - Monica Kehoe
- Diagnostic Laboratory Services, Department of Primary Industries and Regional Development, South Perth, Western Australia, Australia
| | - Wycliff M. Kinoti
- Agriculture Victoria Research, Department of Energy, Environment and Climate Action, AgriBio, Bundoora, Victoria, Australia
| | - Samantha Bond
- Biosecurity and Animal Welfare, Department of Industry, Tourism and Trade, Darwin, Northern Territory, Australia
| | - Richard Davis
- Northern Australia Quarantine Strategy, Department of Agriculture, Fisheries and Forestry, Canberra, Australian Capital Territory, 2601, Australia
| | - Lynne Jones
- Northern Australia Quarantine Strategy, Department of Agriculture, Fisheries and Forestry, Canberra, Australian Capital Territory, 2601, Australia
| | - Nandita Pathania
- Department of Agriculture and Fisheries, Mareeba, Queensland, Australia
| | - Murray Sharman
- Department of Agriculture and Fisheries, Ecosciences Precinct, Dutton Park, Queensland 4102, Australia
| | - Toni Chapman
- Biosecurity and Food Safety, New South Wales Department of Primary Industries, Elizabeth Macarthur Agricultural Institute (EMAI), Menangle, New South Wales, 2567, Australia
| | - Brendan C. Rodoni
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
- Agriculture Victoria Research, Department of Energy, Environment and Climate Action, AgriBio, Bundoora, Victoria, Australia
| | - Fiona E. Constable
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
- Agriculture Victoria Research, Department of Energy, Environment and Climate Action, AgriBio, Bundoora, Victoria, Australia
| |
Collapse
|
2
|
Rodriguez-R LM, Conrad RE, Viver T, Feistel DJ, Lindner BG, Venter SN, Orellana LH, Amann R, Rossello-Mora R, Konstantinidis KT. An ANI gap within bacterial species that advances the definitions of intra-species units. mBio 2024; 15:e0269623. [PMID: 38085031 PMCID: PMC10790751 DOI: 10.1128/mbio.02696-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 10/05/2023] [Accepted: 11/03/2023] [Indexed: 01/17/2024] Open
Abstract
IMPORTANCE Bacterial strains and clonal complexes are two cornerstone concepts for microbiology that remain loosely defined, which confuses communication and research. Here we identify a natural gap in genome sequence comparisons among isolate genomes of all well-sequenced species that has gone unnoticed so far and could be used to more accurately and precisely define these and related concepts compared to current methods. These findings advance the molecular toolbox for accurately delineating and following the important units of diversity within prokaryotic species and thus should greatly facilitate future epidemiological and micro-diversity studies across clinical and environmental settings.
Collapse
Affiliation(s)
- Luis M. Rodriguez-R
- Department of Microbiology, and Digital Science Center (DiSC), University of Innsbruck, Innsbruck, Austria
| | - Roth E. Conrad
- School of Civil and Environmental Engineering, and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Tomeu Viver
- Department of Animal and Microbial Biodiversity, Marine Microbiology Group, Mediterranean Institutes for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Dorian J. Feistel
- School of Civil and Environmental Engineering, and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Blake G. Lindner
- School of Civil and Environmental Engineering, and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Stephanus N. Venter
- Department of Biochemistry, Genetics and Microbiology, and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Luis H. Orellana
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Ramon Rossello-Mora
- Department of Animal and Microbial Biodiversity, Marine Microbiology Group, Mediterranean Institutes for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Konstantinos T. Konstantinidis
- School of Civil and Environmental Engineering, and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| |
Collapse
|
3
|
Chhettri S, Sevigny J, Pesce C, Sarkar I, Thomas W, Nouioui I, Sen G, Tisa LS, Sen A. Whole genome sequencing of Streptomyces antnestii sp. nov. with a potency to become an industrial strain. J Genomics 2024; 12:6-13. [PMID: 38164509 PMCID: PMC10751750 DOI: 10.7150/jgen.87156] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 10/12/2023] [Indexed: 01/03/2024] Open
Abstract
Streptomyces Strain San01 is isolated from the soil of ant-nest found in the tea estate of Darjeeling, India. The morphology, biochemical, as well as the molecular characteristics, proved that San01 belonged to the genus Streptomyces. The average nucleotide identity (ANI) value between the genome sequence of the studied strain and its closest phylogenetic neighbors were very low and also could be distinguished from its closest neighbour with broad range of phenotypic data. The draft genome sequence of isolate San01 (NZ_RZYA00000000.1) was estimated to be 9.12 Mbp in size with 71.2% of GC content and it encompasses 39 biosynthetic gene clusters that emphasize the biotechnological potential of this isolate.Based on the phenotypic, genetic and genomic data, isolate San01 (=JCM 34633 = NCTC 14543) merits to be recognized as a type strain of a novel species and hereby propose the name Streptomyces antnestii sp. nov. Incidentally, this is the first report on Streptomyces genomes from Darjeeling, India.
Collapse
Affiliation(s)
- Saroja Chhettri
- Department of Botany, University of North Bengal, Raja Rammohanpur, Siliguri-734013, India
- Midnapore College, Midnapore, West Bengal 721101, India
| | - Joseph Sevigny
- Dept. of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
- Hubbard Center for Genomic Studies, University of New Hampshire, Durham, NH 03824 USA
| | - Céline Pesce
- Dept. of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
- Present address: HM Clause, Davis, California, USA
| | - Indrani Sarkar
- Bioinformatics Facility, University of North Bengal, Raja Rammohanpur, Siliguri-734013, India
| | - W.Kelley Thomas
- Dept. of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
- Hubbard Center for Genomic Studies, University of New Hampshire, Durham, NH 03824 USA
| | - Imen Nouioui
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures: Braunschweig, Germany
| | - Gargi Sen
- Bioinformatics Facility, University of North Bengal, Raja Rammohanpur, Siliguri-734013, India
| | - Louis S. Tisa
- Dept. of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Arnab Sen
- Department of Botany, University of North Bengal, Raja Rammohanpur, Siliguri-734013, India
- Bioinformatics Facility, University of North Bengal, Raja Rammohanpur, Siliguri-734013, India
- Biswa Bangla Genome Center, University of North Bengal, Raja Rammohanpur, Siliguri-734013, India
| |
Collapse
|
4
|
Lindsey RL, Gladney LM, Huang AD, Griswold T, Katz LS, Dinsmore BA, Im MS, Kucerova Z, Smith PA, Lane C, Carleton HA. Rapid identification of enteric bacteria from whole genome sequences using average nucleotide identity metrics. Front Microbiol 2023; 14:1225207. [PMID: 38156000 PMCID: PMC10752928 DOI: 10.3389/fmicb.2023.1225207] [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: 08/08/2023] [Accepted: 11/14/2023] [Indexed: 12/30/2023] Open
Abstract
Identification of enteric bacteria species by whole genome sequence (WGS) analysis requires a rapid and an easily standardized approach. We leveraged the principles of average nucleotide identity using MUMmer (ANIm) software, which calculates the percent bases aligned between two bacterial genomes and their corresponding ANI values, to set threshold values for determining species consistent with the conventional identification methods of known species. The performance of species identification was evaluated using two datasets: the Reference Genome Dataset v2 (RGDv2), consisting of 43 enteric genome assemblies representing 32 species, and the Test Genome Dataset (TGDv1), comprising 454 genome assemblies which is designed to represent all species needed to query for identification, as well as rare and closely related species. The RGDv2 contains six Campylobacter spp., three Escherichia/Shigella spp., one Grimontia hollisae, six Listeria spp., one Photobacterium damselae, two Salmonella spp., and thirteen Vibrio spp., while the TGDv1 contains 454 enteric bacterial genomes representing 42 different species. The analysis showed that, when a standard minimum of 70% genome bases alignment existed, the ANI threshold values determined for these species were ≥95 for Escherichia/Shigella and Vibrio species, ≥93% for Salmonella species, and ≥92% for Campylobacter and Listeria species. Using these metrics, the RGDv2 accurately classified all validation strains in TGDv1 at the species level, which is consistent with the classification based on previous gold standard methods.
Collapse
Affiliation(s)
- Rebecca L. Lindsey
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, GA, United States
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
5
|
Bouznada K, Belaouni HA, Meklat A. Genome-based reclassification of Kitasatospora niigatensis as a later heterotypic synonym of Kitasatospora cineracea Tajima et al. (2001). Antonie Van Leeuwenhoek 2023; 116:1327-1335. [PMID: 37804413 DOI: 10.1007/s10482-023-01884-3] [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: 03/10/2023] [Accepted: 09/12/2023] [Indexed: 10/09/2023]
Abstract
The present study used genome-based approaches to investigate the taxonomic relationship between Kitasatospora cineracea DSM 44780T and Kitasatospora niigatensis DSM 44781T, two species that were previously described by Tajima et al. (Int J Syst Evol Microbiol 51:1765-1771, 2001). The digital DNA-DNA hybridization (dDDH), average amino acid identity (AAI), and average nucleotide identity (ANI) values between the genomes of the two type strains were 90.3, 98.7, and 99.1%, respectively. These values exceeded the established thresholds of 70% (dDDH) and 95-96% (ANI and AAI) for bacterial species delineation, suggesting that K. cineracea and K. niigatensis should share the same taxonomic position. Furthermore, our analysis using the 'Bacterial Pan Genome Analysis' (BPGA) pipeline and the Maximum Likelihood core-genes tree inferred using FastTree2 consistently demonstrated that K. cineracea DSM 44780T and K. niigatensis DSM 44781T are closely related, as indicated by the clustering of these strains in the core-genes phylogenomic tree. Based on these findings, we propose that K. niigatensis should be considered a later heterotypic synonym of K. cineracea.
Collapse
Affiliation(s)
- Khaoula Bouznada
- Laboratoire de Biologie des Systèmes Microbiens (LBSM), Ecole Normale Supérieure Cheikh Mohamed El Bachir El Ibrahimi, BP 92, Kouba, Algiers, Algeria.
| | - Hadj Ahmed Belaouni
- Laboratoire de Biologie des Systèmes Microbiens (LBSM), Ecole Normale Supérieure Cheikh Mohamed El Bachir El Ibrahimi, BP 92, Kouba, Algiers, Algeria
| | - Atika Meklat
- Laboratoire de Biologie des Systèmes Microbiens (LBSM), Ecole Normale Supérieure Cheikh Mohamed El Bachir El Ibrahimi, BP 92, Kouba, Algiers, Algeria
| |
Collapse
|
6
|
Ebu SM, Ray L, Panda AN, Gouda SK. De novo assembly and comparative genome analysis for polyhydroxyalkanoates-producing Bacillus sp. BNPI-92 strain. J Genet Eng Biotechnol 2023; 21:132. [PMID: 37991636 PMCID: PMC10665291 DOI: 10.1186/s43141-023-00578-7] [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: 10/13/2022] [Accepted: 10/26/2023] [Indexed: 11/23/2023]
Abstract
BACKGROUND Certain Bacillus species play a vital role in polyhydroxyalkanoate (PHA) production. However, most of these isolates did not properly identify to species level when scientifically had been reported. RESULTS From NGS analysis, 5719 genes were predicted in the de novo genome assembly. Based on genome annotation using RAST server, 5,527,513 bp sequences were predicted with 5679 bp number of protein-coding sequence. Its genome sequence contains 35.1% and 156 GC content and contigs, respectively. In RAST server analysis, subsystem (43%) and non-subsystem coverage (57%) were generated. Ortho Venn comparative genome analysis indicated that Bacillus sp. BNPI-92 shared 2930 gene cluster (core gene) with B. cereus ATCC 14579 T (AE016877), B. paranthracis Mn5T (MACE01000012), B. thuringiensis ATCC 10792 T (ACNF01000156), and B. antrics Amen T (AE016879) strains. For our strain, the maximum gene cluster (190) was shared with B. cereus ATCC 14579 T (AE016877). For Ortho Venn pair wise analysis, the maximum overlapping gene clusters thresholds have been detected between Bacillus s p.BNPI-92 and Ba. cereus ATCC 14579 T (5414). Average nucleotide identity (ANI) such as OriginalANI and OrthoANI, in silicon digital DND-DNA hybridization (isDDH), Type (Strain) Genome Server (TYGS), and Genome-Genome Distance Calculator (GGDC) were more essentially related Bacillus sp. BNPI-92 with B. cereus ATCC 14579 T strain. Therefore, based on the combination of RAST annotation, OrthoVenn server, ANI and isDDH result Bacillus sp.BNPI-92 strain was strongly confirmed to be a B. cereus type strain. It was designated as B. cereus BNPI-92 strain. In B. cereus BNPI-92 strain whole genome sequence, PHA biosynthesis encoding genes such as phaP, phaQ, phaR (PHA synthesis repressor phaR gene sequence), phaB/phbB, and phaC were predicted on the same operon. These gene clusters were designated as phaPQRBC. However, phaA was located on other operons. CONCLUSIONS This newly obtained isolate was found to be new a strain based on comparative genomic analysis and it was also observed as a potential candidate for PHA biosynthesis.
Collapse
Affiliation(s)
- Seid Mohammed Ebu
- Department of Applied Biology, SoANS, Adama Science and Technology University, Oromia, Ethiopia.
| | - Lopamudra Ray
- School of Law, Campus -16 Adjunct Faculty, School of Biotech, Campus-11 KIIT University, Bhubaneswar, Odisha, 751024, India
| | - Ananta N Panda
- School of Biotechnology, Campus-11 KIIT University, Bhubaneswar, Odisha, 751024, India
| | - Sudhansu K Gouda
- School of Biotechnology, Campus-11 KIIT University, Bhubaneswar, Odisha, 751024, India
| |
Collapse
|
7
|
Zhang G, Cheng Y, Li W, Chen Y, Yang J, Jin D, Lu S, Xu J. Arthrobacter zhaoxinii sp. nov. and Arthrobacter jinronghuae sp. nov., isolated from Marmota himalayana. Int J Syst Evol Microbiol 2023; 73. [PMID: 38018813 DOI: 10.1099/ijsem.0.006168] [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] [Indexed: 11/30/2023] Open
Abstract
Four yellow-coloured strains (zg-Y815T/zg-Y108 and zg-Y859T/zg-Y826) were isolated from the intestinal contents of Marmota himalayana and assigned to the 'Arthrobacter citreus group'. The four strains grew optimally on brain heart infusion agar with 5 % defibrinated sheep blood plate at 30 °C, pH 7.0 and with 0.5 % NaCl (w/v). Comparative analysis of their 16S rRNA genes indicated that the two strain pairs belong to the genus Arthrobacter, showing the highest similarity to Arthrobacter yangruifuii 785T (99.52 %), which was further confirmed by the 16S rRNA gene and genome-based phylogenetic analysis. The comparative genomic analysis [digital DNA-DNA hybridization, (dDDH) and average nucleotide identity (ANI)] proved that the four strains are two different species (zg-Y815T/zg-Y108, 71.7 %/96.8 %; zg-Y859T/zg-Y826, 87.3 %/98.5 %) and differ from other known species within the genus Arthrobacter (zg-Y815T, 19.6-32.3 %/77.2-88.0 %; zg-Y859T, 19.5-29.3 %/77.4-86.3 %). Strain pairs zg-Y815T/zg-Y108 and zg-Y859T/zg-Y826 had the same major cellular fatty acids (iso-C16 : 0 and anteiso-C15 : 0), with MK-8(H2) as their dominant respiratory quinone (70.6 and 61.7 %, respectively). The leading polar lipids were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylinositol. The detected amino acids and cell-wall sugars of the two new species were identical (amino acids: alanine, glutamic acid, and lysine; sugars: rhamnose, galactose, mannose, glucose, and ribose). According to the phylogenetic, phenotypic, and chemotaxonomic analyses, we concluded that the four new strains represented two different novel species in the genus Arthrobacter, for which the names Arthrobacter zhaoxinii sp. nov. (zg-Y815T= GDMCC 1.3494T = JCM 35821T) and Arthrobacter jinronghuae sp. nov. (zg-Y859T = GDMCC 1.3493T = JCM 35822T) are proposed.
Collapse
Affiliation(s)
- Gui Zhang
- Department of Infection Control, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, PR China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Yanpeng Cheng
- Shenzhen Center for Disease Control and Prevention, Shenzhen 518073, PR China
| | - Weiguang Li
- Department of Infection Control, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, PR China
| | - Yulu Chen
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Jing Yang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
| | - Dong Jin
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
| | - Shan Lu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
| | - Jianguo Xu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
- Institute of Public Health, Nankai University, Tianjin 300071, PR China
| |
Collapse
|
8
|
Ruan L, Liu L, Jiang X, Mao D, Shao J, He J, Shen Q. Empedobacter sedimenti sp. nov., isolated from sediment of East Taihu Lake. Int J Syst Evol Microbiol 2023; 73. [PMID: 38015206 DOI: 10.1099/ijsem.0.006182] [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] [Indexed: 11/29/2023] Open
Abstract
A Gram-reaction-negative, strictly aerobic, pale yellow, non-gliding, rod-shaped bacterium, designated DT-LB-19T, was isolated from the sediment of East Taihu Lake in Jiangsu Province, PR China. Strain DT-LB-19T showed the highest 16S rRNA gene sequence similarities to members of the genera Algoriella, Chishuiella and Empedobacter (94.84-95.77 %) in the family Weeksellaceae. In phylogenetic trees based on genomes, strain DT-LB-19T clustered within the genus Empedobacter but formed a separate subclade with a high bootstrap value. The average nucleotide identity and digital DNA-DNA hybridization values between DT-LB-19T and the closely related type strains were in the range of 82.5-86.9 % and 25.8-32.3 %, respectively. The major cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 1 ω5c, C16 : 0, summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B), summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and iso-C15 : 03-OH. The predominant menaquinone was menaquinone-6. The polar lipid profile consisted of phosphatidylethanolamine, one glycolipid, two aminophospholipids and five unidentified lipids. The DNA G+C content was 31.8 mol%. Based on the phenotypic, chemotaxonomic, phylogenetic and genomic results, we propose that strain DT-LB-19T represents a novel species of the genus Empedobacter, for which the name Empedobacter sedimenti sp. nov. is proposed, with strain DT-LB-19T (=KCTC 82330T=CCTCC AB 2023026T= JSACC 11448T) as the type strain.
Collapse
Affiliation(s)
- Luyao Ruan
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Le Liu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
- Agricultural Microbial Resources Protection and Germplasm Innovation and Utilization Center of Jiangsu Province, Nanjing, Jiangsu 210095, PR China
| | - Xueting Jiang
- Biological Experiment Center, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Dongmei Mao
- Biological Experiment Center, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Jiahui Shao
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
- Agricultural Microbial Resources Protection and Germplasm Innovation and Utilization Center of Jiangsu Province, Nanjing, Jiangsu 210095, PR China
| | - Jian He
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
- Agricultural Microbial Resources Protection and Germplasm Innovation and Utilization Center of Jiangsu Province, Nanjing, Jiangsu 210095, PR China
| | - Qirong Shen
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
- Agricultural Microbial Resources Protection and Germplasm Innovation and Utilization Center of Jiangsu Province, Nanjing, Jiangsu 210095, PR China
| |
Collapse
|
9
|
Long Y, Li Y, Wang G, Jin J, Mao M, Gao L, Liu G, Fan G, Yu Z. Paenibacillus polygoni sp. nov., an endophytic bacterium isolated from Polygonum lapathifolium L. in wetland. Int J Syst Evol Microbiol 2023; 73. [PMID: 38015052 DOI: 10.1099/ijsem.0.006185] [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] [Indexed: 11/29/2023] Open
Abstract
A Gram-stain-positive, aerobic, rod-shaped, non-motile, yellowish and glossy strain, C31T, was isolated from a wetland plant Polygonum lapathifolium L. located south of Poyang Lake, Jiangxi Province, PR China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain C31T showed similarity values of lower than 97.0 % to other type species belonging to the genus Paenibacillus. The genomic average nucleotide identity values between strain C31T and its reference type species ranged from 68.9-70.9 % and the digital DNA-DNA hybridization values were lower than 27.8 %. The genomic DNA G+C content of strain C31T was 41.9 mol%. The optimal growth temperature, pH and NaCl concentration were 37 °C, pH 7 and 0.5 %, respectively. The major cellular fatty acids (>5.0 %) of strain C31T were anteiso-C15 : 0 (73.7 %), anteiso-C17 : 0 (8.4 %) and iso-C15 : 0 (5.2 %). The polar lipids of strain C31T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and unidentified phospholipids. The respiratory quinone was MK-7. Based on these phylogenetic and phenotypic characterizations, strain C31T represents a novel species within the genus Paenibacillus. Therefore, the proposed name for this newly identified species is Paenibacillus polygoni sp. nov. and the type strain is C31T (=CCTCC AB 2022349T=KCTC 43565T).
Collapse
Affiliation(s)
- Yong Long
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 138 Haping Road, Harbin 150081, PR China
| | - Yansheng Li
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 138 Haping Road, Harbin 150081, PR China
| | - Guanghua Wang
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 138 Haping Road, Harbin 150081, PR China
| | - Jian Jin
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 138 Haping Road, Harbin 150081, PR China
| | - Mengfan Mao
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 138 Haping Road, Harbin 150081, PR China
| | - Lizheng Gao
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 138 Haping Road, Harbin 150081, PR China
| | - Guihua Liu
- Key Laboratory of Poyang Lake Wetland and Watershed Research (Jiangxi Normal University), Ministry of Education, Nanchang 330022, PR China
| | - Guoquan Fan
- Industrial Crops Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang Province 150086, PR China
| | - Zhenhua Yu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 138 Haping Road, Harbin 150081, PR China
| |
Collapse
|
10
|
Zhao M, Gitaitis R, Dutta B. Characterization of Pseudomonas capsici strains from pepper and tomato. Front Microbiol 2023; 14:1267395. [PMID: 37886076 PMCID: PMC10599140 DOI: 10.3389/fmicb.2023.1267395] [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: 07/26/2023] [Accepted: 09/27/2023] [Indexed: 10/28/2023] Open
Abstract
Disease outbreaks of bacterial leaf spot and blight of pepper and tomato often occur in both transplant- and field-production systems worldwide. In some cases, the outbreaks are caused by novel bacterial species. Characterization of these novel bacterial species are critical in developing diagnostic assays and identifying management options for pathogen monitoring and sustainable production, respectively. We characterized strains belonging to novel Pseudomonas species that are responsible for outbreaks in pepper and tomato both in transplant-houses and in production fields in Georgia, USA. Phylogenomic analyses and whole genome sequence indices demonstrated that the pepper and tomato strains belonged to P. capsici. The whole-genome comparison revealed that 13 Pseudomonas strains from diverse isolation sources that were curated in NCBI were indeed P. capsici indicating a potential wide-host range for this bacterial species. Our greenhouse-based host-range assay also indicated that P. capsici strains were pathogenic on pepper, tomato, eggplant, cabbage, lettuce, and watermelon corroborating a wide-host-range. A phylogenetic tree inferred from the whole genome sequence data showed that the P. capsici strains from Georgia (pepper and tomato) were genetically diverse, and were closely related to tomato P. capsici strains from Florida. Genomic presence of traditional bacterial virulence factors in P. capsici strains was also determined. Pseudomonascapsici strains encode one set of type I secretion system, two sets of type II secretion systems, one set of type III secretion system, two sets of type V secretion systems, three sets of type VI secretion systems, and various secondary metabolite gene clusters including lipopeptides. In in-vitro assays, it was demonstrated that six out of seven P. capsici strains (pepper and tomato strains from Georgia) were not sensitive to 0.8 mM CuSO4. When the genomes of copper-tolerant strains were compared with the copper-sensitive strains, it was observed that the former strains encode a cluster of genes related to copper tolerance, which were absent in the genomes of copper-sensitive strains. Considering the ability of P. capsici strains to infect a range of vegetable hosts and possession of a wide range of bacterial virulence factors, secondary metabolites, and copper-tolerance genes, we envision that the management of this pathogen might potentially be a challenge.
Collapse
Affiliation(s)
- Mei Zhao
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
- Department of Plant Pathology, University of Georgia, Tifton, GA, United States
| | - Ron Gitaitis
- Department of Plant Pathology, University of Georgia, Tifton, GA, United States
| | - Bhabesh Dutta
- Department of Plant Pathology, University of Georgia, Tifton, GA, United States
| |
Collapse
|
11
|
Zhou G, Gu Y, Wang H, Chen X, Zhang X, Shao Z, Yan X, Zhang J, Zhang M. Genomic diversity and taxonomic marker for Arcobacter species. Front Microbiol 2023; 14:1278268. [PMID: 37881248 PMCID: PMC10594997 DOI: 10.3389/fmicb.2023.1278268] [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: 08/16/2023] [Accepted: 09/27/2023] [Indexed: 10/27/2023] Open
Abstract
Arcobacter was recognized as an emerging enteropathogen and controversies regarding its classification persisted. This study aimed to reevaluate the taxonomy of Arcobacter utilizing the 16S rRNA gene, 23S rRNA gene, single-copy orthologous genes, as well as genomic indices such as Average Nucleotide Identity (ANI) and in silico DNA-DNA hybridization (isDDH). The taxonomy of this genus was reevaluated in this study using multiple indices with a dataset of 371 genomes comprising 34 known species and 14 potentially new species. Good discrimination could be achieved only in some species but not for the species with higher sequence similarity using the comparisons of the 16S rRNA gene and 23S rRNA gene sequences. A high-accuracy phylogenomic approach for Arcobacter was established using 84 single-copy orthologous genes obtained through various bioinformatics methods. One marker gene (gene711), which was found to possess the same distinguishing ability as ANI, isDDH, and single-copy orthologous methods, was identified as a reliable locus for inferring the phylogeny of the genus. The effective species classification was achieved by employing gene711 with a sequence similarity exceeding 96%, even for species like A. cloacae, A. lanthieri, and A. skirrowii, which exhibited ambiguous classification using ANI and isDDH. Additionally, excellent subspecies categorizing among A. cryaerophilus could be distinguished using gene711. In conclusion, this framework strategy had the potential advantage of developing rapid species identification, particularly for highly variable species, providing a novel insight into the behavior and characteristics of Arcobacter.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Maojun Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| |
Collapse
|
12
|
Ravin NV, Smolyakov DD, Markov ND, Beletsky AV, Mardanov AV, Rudenko TS, Grabovich MY. tilS and rpoB: New Molecular Markers for Phylogenetic and Biodiversity Studies of the Genus Thiothrix. Microorganisms 2023; 11:2521. [PMID: 37894178 PMCID: PMC10609254 DOI: 10.3390/microorganisms11102521] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/01/2023] [Accepted: 10/05/2023] [Indexed: 10/29/2023] Open
Abstract
Currently, the phylogeny of the genus Thiothrix is based on comparative whole genome analysis because of the high homology of the 16S ribosomal RNA gene sequences within the genus. We analyzed the possibility of using various conservative genes as phylogenetic markers for the genus Thiothrix. We found that the levels of similarity of the nucleotide sequences of the tRNA(Ile)-lysidine synthase (tilS) and the β subunit of RNA polymerase (rpoB) genes are in good agreement with the average nucleotide identity (ANI) values between the genomes of various representatives of the genus Thiothrix. The genomes of Thiothrix strains MK1, WS, DNT52, DNT53, and H33 were sequenced. Taxonomic analysis using both whole genomes and the tilS gene consistently showed that MK1 and WS belong to Thiothrix lacustris, while DNT52, DNT53, and H33 belong to Thiothrix subterranea. The tilS gene fragments were subjected to high-throughput sequencing to profile the Thiothrix mat of a sulfidic spring, which revealed the presence of known species of Thiothrix and new species-level phylotypes. Thus, the use of tilS and rpoB as phylogenetic markers will allow for rapid analyses of pure cultures and natural communities for the purpose of phylogenetic identification of representatives of the genus Thiothrix.
Collapse
Affiliation(s)
- Nikolai V. Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (N.V.R.); (A.V.B.); (A.V.M.)
| | - Dmitry D. Smolyakov
- Department of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, 394018 Voronezh, Russia; (D.D.S.); (N.D.M.); (T.S.R.)
| | - Nikita D. Markov
- Department of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, 394018 Voronezh, Russia; (D.D.S.); (N.D.M.); (T.S.R.)
| | - Alexey V. Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (N.V.R.); (A.V.B.); (A.V.M.)
| | - Andrey V. Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (N.V.R.); (A.V.B.); (A.V.M.)
| | - Tatyana S. Rudenko
- Department of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, 394018 Voronezh, Russia; (D.D.S.); (N.D.M.); (T.S.R.)
| | - Margarita Yu. Grabovich
- Department of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, 394018 Voronezh, Russia; (D.D.S.); (N.D.M.); (T.S.R.)
| |
Collapse
|
13
|
Choksket S, Kaur M, Pinnaka AK, Korpole S. An antimicrobial thiopeptide producing novel actinomycetes Streptomyces terrae sp. nov., isolated from subsurface soil of arable land. FEMS Microbes 2023; 4:xtad014. [PMID: 37701422 PMCID: PMC10495126 DOI: 10.1093/femsmc/xtad014] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/22/2023] [Accepted: 08/09/2023] [Indexed: 09/14/2023] Open
Abstract
An antimicrobial producing Gram-positive, aerobic, nonmotile, and filamentous actinobacterial strain SKN60T was isolated from soil The isolate exhibited 99.3% and 99.0% identity with Streptomyces laurentii ATCC 31255T and S. roseicoloratus TRM 44457T, respectively, in 16S rRNA gene sequence analysis. However, the genome sequence displayed maximum ANI (88.45%) and AAI (85.61%) with S. roseicoloratus TRM 44457T. Similarly, the dDDH showed 33.7% identity with S. roseicoloratus TRM 44457T. It formed a cluster with S. roseicoloratus TRM 44457T and S. laurentii ATCC 31255T in phylogenomic tree. Cell wall analysis revealed the presence of diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylcholine as major polar lipids and diaminopimelic acid as diagnostic diamino acid. Major fatty acids were iso-C15:0, anteiso-C15:0, and iso-C16:0. The G+C content was found to be 72.3 mol%. Genome sequence analysis using antiSMASH database showed occurrence of a thiopeptide biosynthesis gene cluster with 94% similarity to berninamycin from S. bernensis UC5144. The mass of 1146 Da is identical with berninamycin. But subtle differences observed in leader peptide sequence of thiopeptide and berninamycin. Notably, S. bernensis is not validly reported and thus SKN60T is the only strain containing berninamycin BGC as no other phylogenetic relative had it. Additionally, strain SKN60T differed in phenotypic and genetic characteristics with all phylogenetic relatives of the genus Streptomyces. Therefore, it is proposed as a novel species with the name Streptomyces terrae sp. nov. strain SKN60T (=MTCC 13163T; = JCM 35768T).
Collapse
Affiliation(s)
- Stanzin Choksket
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh-160036, India
| | - Mahaldeep Kaur
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh-160036, India
| | - Anil Kumar Pinnaka
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh-160036, India
| | - Suresh Korpole
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh-160036, India
| |
Collapse
|
14
|
Rodrigues Jardim B, Tran-Nguyen LTT, Gambley C, Al-Sadi AM, Al-Subhi AM, Foissac X, Salar P, Cai H, Yang JY, Davis R, Jones L, Rodoni B, Constable FE. The observation of taxonomic boundaries for the 16SrII and 16SrXXV phytoplasmas using genome-based delimitation. Int J Syst Evol Microbiol 2023; 73. [PMID: 37486824 DOI: 10.1099/ijsem.0.005977] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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] [Indexed: 07/26/2023] Open
Abstract
Within the 16SrII phytoplasma group, subgroups A-X have been classified based on restriction fragment length polymorphism of their 16S rRNA gene, and two species have been described, namely 'Candidatus Phytoplasma aurantifolia' and 'Ca. Phytoplasma australasia'. Strains of 16SrII phytoplasmas are detected across a broad geographic range within Africa, Asia, Australia, Europe and North and South America. Historically, all members of the 16SrII group share ≥97.5 % nucleotide sequence identity of their 16S rRNA gene. In this study, we used whole genome sequences to identify the species boundaries within the 16SrII group. Whole genome analyses were done using 42 phytoplasma strains classified into seven 16SrII subgroups, five 16SrII taxa without official 16Sr subgroup classifications, and one 16SrXXV-A phytoplasma strain used as an outgroup taxon. Based on phylogenomic analyses as well as whole genome average nucleotide and average amino acid identity (ANI and AAI), eight distinct 16SrII taxa equivalent to species were identified, six of which are novel descriptions. Strains within the same species had ANI and AAI values of >97 %, and shared ≥80 % of their genomic segments based on the ANI analysis. Species also had distinct biological and/or ecological features. A 16SrII subgroup often represented a distinct species, e.g., the 16SrII-B subgroup members. Members classified within the 16SrII-A, 16SrII-D, and 16SrII-V subgroups as well as strains classified as sweet potato little leaf phytoplasmas fulfilled criteria to be included as members of a single species, but with subspecies-level relationships with each other. The 16SrXXV-A taxon was also described as a novel phytoplasma species and, based on criteria used for other bacterial families, provided evidence that it could be classified as a distinct genus from the 16SrII phytoplasmas. As more phytoplasma genome sequences become available, the classification system of these bacteria can be further refined at the genus, species, and subspecies taxonomic ranks.
Collapse
Affiliation(s)
- Bianca Rodrigues Jardim
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
- Agriculture Victoria Research, Department of Energy, Environment and Climate Action, AgriBio, Bundoora, Victoria, Australia
| | | | - Cherie Gambley
- Horticulture and Forestry Science, Department of Agriculture and Fisheries Maroochy Research Facility, Nambour, Queensland, Australia
| | - Abdullah M Al-Sadi
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Muscat, Oman
| | - Ali M Al-Subhi
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Muscat, Oman
| | - Xavier Foissac
- University of Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, 33140, Bordeaux, Villenave d'Ornon, France
| | - Pascal Salar
- University of Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, 33140, Bordeaux, Villenave d'Ornon, France
| | - Hong Cai
- The Key Laboratory for Plant Pathology, Yunnan Agricultural University, Kunming 650201, PR China
| | - Jun-Yi Yang
- Institute of Biochemistry, National Chung Hsing University, Taichung 402, Taiwan, ROC
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan, ROC
| | - Richard Davis
- Northern Australia Quarantine Strategy, Department of Agriculture, Fisheries and Forestry, Canberra, Australian Capital Territory 2601, Australia
| | - Lynne Jones
- Northern Australia Quarantine Strategy, Department of Agriculture, Fisheries and Forestry, Canberra, Australian Capital Territory 2601, Australia
| | - Brendan Rodoni
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
- Agriculture Victoria Research, Department of Energy, Environment and Climate Action, AgriBio, Bundoora, Victoria, Australia
| | - Fiona E Constable
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
- Agriculture Victoria Research, Department of Energy, Environment and Climate Action, AgriBio, Bundoora, Victoria, Australia
| |
Collapse
|
15
|
Sakaguchi M, Urbanczyk Y, Kikuchi T, Urbanczyk H. Grimontia kaedaensis sp. nov., isolated from the estuary of Kaeda river in Miyazaki, Japan. Int J Syst Evol Microbiol 2023; 73. [PMID: 37358383 DOI: 10.1099/ijsem.0.005946] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2023] Open
Abstract
Strain 020920NT was isolated from the estuary of the Kaeda river in the Miyazaki prefecture in Japan. Phylogenetic analysis based on the 16S rRNA gene showed the strain's close evolutionary relationship with bacteria from the genus Grimontia, in the family Vibrionaceae. Phenotypic and chemotaxonomic features of the strain were investigated. Whole genome sequencing revealed that the strain 020920NT genome consists of two chromosomes and a plasmid, for a total of 5.52 Mbp. Calculations of whole genome average nucleotide identity and phylogenetic analysis based on the whole genome sequence showed that the strain represents a new species in the genus Grimontia, for which we propose the name Grimontia kaedaensis sp. nov. with the type strain 020920NT (=LMG 32507T=JCM 34978T).
Collapse
Affiliation(s)
- Masahiro Sakaguchi
- Department of Marine Biology and Environmental Sciences, University of Miyazaki, Faculty of Agriculture, Miyazaki
| | - Yoshiko Urbanczyk
- Department of Marine Biology and Environmental Sciences, University of Miyazaki, Faculty of Agriculture, Miyazaki
| | - Taisei Kikuchi
- Department of Infectious Diseases., University of Miyazaki, Faculty of Medicine, Division of Parasitology, Miyazaki
- Department of Integrated Biosciences, The University of Tokyo, Graduate School of Frontier Sciences, Tokyo, Japan
| | - Henryk Urbanczyk
- Department of Marine Biology and Environmental Sciences, University of Miyazaki, Faculty of Agriculture, Miyazaki
| |
Collapse
|
16
|
Enciso-Ibarra J, Roque A, Bolán-Mejia C, Enciso-Ibarra K, González-Castillo A, Gomez-Gil B. Vibrio eleionomae sp. nov., isolated from shrimp ( Penaeus vannamei) pond water. Int J Syst Evol Microbiol 2023; 73. [PMID: 37167075 DOI: 10.1099/ijsem.0.005866] [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] [Indexed: 05/13/2023] Open
Abstract
A novel Vibrio strain (CAIM 722T=SW9T=DSM 24596T) was isolated in 2003 from water of a shrimp (Penaeus vannamei) culture pond located in Los Mochis, Sinaloa, Mexico, and taxonomically characterized using a polyphasic approach. The 16S rRNA gene sequence clustered within those of the genus Vibrio, showing high similarity to the type strains of the Porteresiae clade. Multilocus sequence analysis using eight housekeeping genes (ftsZ, gapA, gyrB, mreB, pyrH, recA, rpoA, topA and 16S rRNA) and phylogenetic analysis with 139 single-copy genes showed that the strain forms an independent branch. Whole genome sequencing and genomic analyses (average nucleotide identity, OrthoANI, average amino acid identity and in silico DNA-DNA hybridization) produced values well below the thresholds for species delineation with all methods tested. In addition, a phenotypic characterization was performed to support the description and differentiation of the novel strain from related taxa. The results obtained demonstrate that the strain represent a novel species, for which the name Vibrio eleionomae sp. nov. is proposed.
Collapse
Affiliation(s)
| | - Ana Roque
- Institut de Recerca i Tecnologia Agroalimentaries, Centre d'Aquicultura, Crta: Poble Nou, Km 5,5. La Ràpita, 43540, Spain
| | - Carmen Bolán-Mejia
- CIAD, A.C., Mazatlán Unit for Aquaculture, AP. 711 Mazatlán, Sinaloa 82000, Mexico
| | - Karen Enciso-Ibarra
- CIAD, A.C., Mazatlán Unit for Aquaculture, AP. 711 Mazatlán, Sinaloa 82000, Mexico
| | - Adrián González-Castillo
- Universidad Politécnica de Sinaloa, Programa Académico de Ingeniería en Biotecnología, Carretera Municipal Libre Km.3 Mazatlán-Higueras, Mazatlán, Sinaloa 82199, Mexico
| | - Bruno Gomez-Gil
- CIAD, A.C., Mazatlán Unit for Aquaculture, AP. 711 Mazatlán, Sinaloa 82000, Mexico
| |
Collapse
|
17
|
Ling C, Zhao JY, Li LL, Ding ZG, Zhang MY, Tang J, Liang SG, Li JY, Liu XD, Feng LY, Yang PW, Lu Y, Shi ZF, Kong CS, Li MG, Tang SK. Pseudomonas subflava sp. nov., a new Gram-negative bacterium isolated from Guishan in Yunnan province, south-west China. Antonie Van Leeuwenhoek 2023; 116:557-564. [PMID: 37097385 DOI: 10.1007/s10482-023-01826-z] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/22/2023] [Indexed: 04/26/2023]
Abstract
A new Gram-negative, rod-shaped, flagellated bacterium was isolated from soil in the Guishan, Xinping County, Yuxi City, Yunnan Province, China, and named YIM B01952T. Growth occurred at 10-40 °C (optimum, 30 °C), pH 6.0-9.0 (optimum, pH 7.5) and with up to ≤ 5.0% (w/v) NaCl on Tryptic Soy Broth Agar (TSA) plates. Phylogenetic analysis based on the 16S rRNA gene and draft-genome sequence showed that strain YIM B01952T belonged to the genus Pseudomonas, and was closely related to the type strain of Pseudomonas alcaligenes (sequence similarity was 98.8%). The digital DNA-DNA hybridization (dDDH) value between strain YIM B01952T and the parallel strain P. alcaligenes ATCC 14909T was 49.0% based on the draft genome sequence. The predominant menaquinone was Q-9. The major fatty acids were summed feature 8 (C18:1 ω6c and/or C18:1 ω7c), summed feature 3 (C16:1 ω6c and/or C16:1 ω7c) and C16:0. The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, and phosphatidylglycerol. The genome size of strain YIM B01952T was 4.341 Mb, comprising 4156 predicted genes with a DNA G + C content of 66.4 mol%. In addition, we detected that strain YIM B01952T had some traditional functional genes (plant growth promotion and multidrug resistance), unique genes through genome comparison and analysis with similar strains. Based on genetic analyses and biochemical characterization, the strain YIM B01952T was identified as a novel species in the genus Pseudomonas, for which the name Pseudomonas subflava sp. nov. is proposed. The type strain is YIM B01952T (=CCTCC AB 2021498T = KCTC 92073T).
Collapse
Affiliation(s)
- Cheng Ling
- Key Laboratory for Microbial Resources of the Ministry of Education and School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Jiang-Yuan Zhao
- Key Laboratory for Microbial Resources of the Ministry of Education and School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Le-Le Li
- Key Laboratory for Microbial Resources of the Ministry of Education and School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
- Department of Medicine, Qujing Vocational and Technical College, Qujing, 655000, People's Republic of China
| | - Zhang-Gui Ding
- Key Laboratory for Microbial Resources of the Ministry of Education and School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Meng-Yu Zhang
- Key Laboratory for Microbial Resources of the Ministry of Education and School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Jing Tang
- Key Laboratory for Microbial Resources of the Ministry of Education and School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Song-Guo Liang
- Key Laboratory for Microbial Resources of the Ministry of Education and School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Jian-Yu Li
- Key Laboratory for Microbial Resources of the Ministry of Education and School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Xiao-Di Liu
- Key Laboratory for Microbial Resources of the Ministry of Education and School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Lu-Yao Feng
- Key Laboratory for Microbial Resources of the Ministry of Education and School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
- Institute of Agricultural Environmental Resources, Yunnan Academy of Agricultural Sciences, Kunming, 650205, People's Republic of China
| | - Pei-Wen Yang
- Institute of Agricultural Environmental Resources, Yunnan Academy of Agricultural Sciences, Kunming, 650205, People's Republic of China
| | - Yao Lu
- Institute of Agricultural Environmental Resources, Yunnan Academy of Agricultural Sciences, Kunming, 650205, People's Republic of China
| | - Zhu-Feng Shi
- Institute of Agricultural Environmental Resources, Yunnan Academy of Agricultural Sciences, Kunming, 650205, People's Republic of China
| | - Chui-Si Kong
- Institute of Agricultural Environmental Resources, Yunnan Academy of Agricultural Sciences, Kunming, 650205, People's Republic of China.
| | - Ming-Gang Li
- Key Laboratory for Microbial Resources of the Ministry of Education and School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China.
| | - Shu-Kun Tang
- Key Laboratory for Microbial Resources of the Ministry of Education and School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China.
| |
Collapse
|
18
|
Shelomi M, Han CJ, Chen WM, Chen HK, Liaw SJ, Mühle E, Clermont D. Chryseobacterium oryctis sp. nov., isolated from the gut of the beetle Oryctes rhinoceros, and Chryseobacterium kimseyorum sp. nov., isolated from a stick insect rearing cage. Int J Syst Evol Microbiol 2023; 73. [PMID: 37074162 DOI: 10.1099/ijsem.0.005813] [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] [Indexed: 04/20/2023] Open
Abstract
Two strains of Chryseobacterium identified from different experiments are proposed to represent new species. Strain WLa1L2M3T was isolated from the digestive tract of an Oryctes rhinoceros beetle larva. Strain 09-1422T was isolated from a cage housing the stick insect Eurycantha calcarata. Sequence analysis of the 16S rRNA and rpoB genes found both strains to be similar but not identical to other Chryseobacterium species. Whole-genome sequencing suggested the isolates represent new species, with average nucleotide identity values ranging from 74.6 to 80.5 %. Genome-to-genome distance calculations produced values below 25.3 %, and digital DNA-DNA hybridization values were 13.7-29.9 %, all suggesting they are distinct species. The genomic DNA G+C content of WLa1L2M3T is approximately 32.53 %, and of 09-1422T is approximately 35.89 %. The predominant cellular fatty acids of strain WLa1L2M3T are C15 : 0 iso, summed feature 9 (C16 : 0 10OH or C17 : 1 iso ω6c), C17 : 0 iso 3OH, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C15 : 0 iso 3OH, C15 : 0 anteiso and C13 : 0 iso, and those of strain 09-1422T are C15 : 0 iso, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C17 : 0 iso 3OH, C15 : 0 anteiso, C15 : 0 iso 3OH, C16 : 1 ω7c, C17 : 0 2OH and C18 : 0. In addition, physiological and biochemical tests revealed phenotypic differences from related Chryseobacterium type strains. These cumulative data indicate that the two strains represent novel species of the genus Chryseobacterium for which the names Chryseobacterium oryctis sp. nov. and Chryseobacterium kimseyorum sp. nov. are proposed with WLa1L2M3T (=BCRC 81350T=JCM 35215T=CIP 112035T) and 09-1422T (=UCDFST 09-1422T=BCRC 81359T=CIP 112165T), as type strains, respectively.
Collapse
Affiliation(s)
- Matan Shelomi
- Department of Entomology, National Taiwan University, Taipei, Taiwan, ROC
| | - Chiao-Jung Han
- Department of Entomology, National Taiwan University, Taipei, Taiwan, ROC
| | - Wen-Ming Chen
- Department of Marine Biotechnology, National Kaohsiung University of Science and Technology, Kaohsiung, Taiwan, ROC
| | - Hsin-Kuang Chen
- Center for Biotechnology, National Taiwan University, Taipei, Taiwan, ROC
| | - Shwu-Jen Liaw
- Department and Graduate Institute of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan, ROC
| | - Estelle Mühle
- Institut Pasteur, Université Paris Cité, Collection of Institut Pasteur, F-75015 Paris, France
| | - Dominique Clermont
- Institut Pasteur, Université Paris Cité, Collection of Institut Pasteur, F-75015 Paris, France
| |
Collapse
|
19
|
Granados-Casas AO, Sastoque AP, Stchigel AM, Fernández-Bravo A, Cano-Lira JF. Hybrid De Novo Whole-Genome Assembly, Annotation, and Identification of Secondary Metabolite Gene Clusters in the Ex-Type Strain of Chrysosporium keratinophilum. J Fungi (Basel) 2023; 9:jof9040389. [PMID: 37108844 PMCID: PMC10145314 DOI: 10.3390/jof9040389] [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: 02/23/2023] [Revised: 03/18/2023] [Accepted: 03/21/2023] [Indexed: 04/29/2023] Open
Abstract
Chrysosporium is a polyphyletic genus belonging (mostly) to different families of the order Onygenales (Eurotiomycetes, Ascomycota). Certain species, such as Chrysosporium keratinophilum, are pathogenic for animals, including humans, but are also a source of proteolytic enzymes (mainly keratinases) potentially useful in bioremediation. However, only a few studies have been published regarding bioactive compounds, of which the production is mostly unpredictable due to the absence of high-quality genomic sequences. During the development of our study, the genome of the ex-type strain of Chrysosporium keratinophilum, CBS 104.66, was sequenced and assembled using a hybrid method. The results showed a high-quality genome of 25.4 Mbp in size spread across 25 contigs, with an N50 of 2.0 Mb, 34,824 coding sequences, 8002 protein sequences, 166 tRNAs, and 24 rRNAs. The functional annotation of the predicted proteins was performed using InterProScan, and the KEGG pathway mapping using BlastKOALA. The results identified a total of 3529 protein families and 856 superfamilies, which were classified into six levels and 23 KEGG categories. Subsequently, using DIAMOND, we identified 83 pathogen-host interactions (PHI) and 421 carbohydrate-active enzymes (CAZymes). Finally, the analysis using AntiSMASH showed that this strain has a total of 27 biosynthesis gene clusters (BGCs), suggesting that it has a great potential to produce a wide variety of secondary metabolites. This genomic information provides new knowledge that allows for a deeper understanding of the biology of C. keratinophilum, and offers valuable new information for further investigations of the Chrysosporium species and the order Onygenales.
Collapse
Affiliation(s)
- Alan Omar Granados-Casas
- Mycology Unit, Medical School, Universitat Rovira i Virgili, C/Sant Llorenç 21, 43201 Reus, Spain
| | - Angie Paola Sastoque
- Mycology Unit, Medical School, Universitat Rovira i Virgili, C/Sant Llorenç 21, 43201 Reus, Spain
| | - Alberto Miguel Stchigel
- Mycology Unit, Medical School, Universitat Rovira i Virgili, C/Sant Llorenç 21, 43201 Reus, Spain
| | - Ana Fernández-Bravo
- Mycology Unit, Medical School, Universitat Rovira i Virgili, C/Sant Llorenç 21, 43201 Reus, Spain
| | - José Francisco Cano-Lira
- Mycology Unit, Medical School, Universitat Rovira i Virgili, C/Sant Llorenç 21, 43201 Reus, Spain
| |
Collapse
|
20
|
Kovács ÁB, Wehmann E, Grózner D, Bali K, Nemesházi E, Hrivnák V, Morrow CJ, Bányai K, Kreizinger Z, Gyuranecz M. Characterization of atypical Mycoplasma anserisalpingitidis strains. Vet Microbiol 2023; 280:109722. [PMID: 36940525 DOI: 10.1016/j.vetmic.2023.109722] [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: 12/20/2022] [Revised: 02/22/2023] [Accepted: 03/09/2023] [Indexed: 03/13/2023]
Abstract
Mycoplasma anserisalpingitidis is a waterfowl colonizing mycoplasma, mainly found in geese. In this study, we compared the whole genomes of five atypical M. anserisalpingitidis strains originating from China, Vietnam and Hungary, with the rest of the collection. Common methods used in the description of species are genomic analyses like the analysis of 16 S - intergenic transcribed spacer (ITS) - 23 S rRNA, of housekeeping genes, of the average nucleotide identity (ANI) and average amino acid identity (AAI) and phenotypic analyses like testing the growth inhibition and the growth parameters of the strains. The atypical strains showed notable genomic differences in all of the genetic analyses: on average ANI and AAI 95% (M. anserisalpingitidis ANI Minimum: 92.45, Maximum: 95.10; AAI Minimum: 93.34, Maximum: 96.37). The atypical strains formed a separate branch among the M. anserisalpingitidis strains in all phylogenetic studies. The small genome size and possibly higher mutation rate of the M. anserisalpingitidis species likely contributed to the observed genetic difference. Based on genetic analyses, the studied strains clearly represent a new genotype of M. anserisalpingitidis. The atypical strains showed slower growth in the medium containing fructose and three of the atypical strains showed diminished growth in the inhibition test. However, no definitive geno-phenotype associations were found regarding the fructose metabolism pathway in the atypical strains. The atypical strains are potentially at an early stage of speciation.
Collapse
Affiliation(s)
- Áron B Kovács
- Veterinary Medical Research Institute, Budapest, Hungary; National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Veterinary Medical Research Institute, Budapest, Hungary
| | - Enikő Wehmann
- Veterinary Medical Research Institute, Budapest, Hungary; National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Veterinary Medical Research Institute, Budapest, Hungary
| | - Dénes Grózner
- Veterinary Medical Research Institute, Budapest, Hungary
| | - Krisztina Bali
- Veterinary Medical Research Institute, Budapest, Hungary
| | | | | | - Chris J Morrow
- Asia Pacific Centre for Animal Health, Melbourne Veterinary School, The University of Melbourne, Victoria, Australia; Bioproperties Pty Ltd., Victoria, Australia
| | - Krisztián Bányai
- Veterinary Medical Research Institute, Budapest, Hungary; National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Veterinary Medical Research Institute, Budapest, Hungary; Department of Pharmacology and Toxicology, University of Veterinary Medicine, Budapest, Hungary
| | - Zsuzsa Kreizinger
- Veterinary Medical Research Institute, Budapest, Hungary; MolliScience Kft., Biatorbágy, Hungary
| | - Miklós Gyuranecz
- Veterinary Medical Research Institute, Budapest, Hungary; National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Veterinary Medical Research Institute, Budapest, Hungary; MolliScience Kft., Biatorbágy, Hungary.
| |
Collapse
|
21
|
Kannan S, Sharma S, Ciufo S, Clark K, Turner S, Kitts PA, Schoch CL, DiCuccio M, Kimchi A. Collection and curation of prokaryotic genome assemblies from type strains at NCBI. Int J Syst Evol Microbiol 2023; 73. [PMID: 36748495 DOI: 10.1099/ijsem.0.005707] [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] [Indexed: 01/20/2023] Open
Abstract
The public sequence databases are entrusted with the dual responsibility of providing an accessible archive to all submitters and supporting data reliability and its re-use to all users. Genomes from type materials can act as an unambiguous reference for a taxonomic name and play an important role in comparative genomics, especially for taxon verification or reclassification. The National Center for Biotechnology Information (NCBI) collects and curates information on prokaryotic type strains and genomes from type strains. The average nucleotide identity (ANI)-based quality control processes introduced at NCBI to verify the genomes from type strains and improve related sequence records are detailed here. Using the curated genomes from type strains as reference, the taxonomy of over 1.1 million GenBank genomes were verified and the taxonomy of over 7000 new submissions before acceptance to GenBank and over 1800 existing genomes in GenBank were reclassified.
Collapse
Affiliation(s)
- Sivakumar Kannan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD, 20892, USA
| | - Shobha Sharma
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD, 20892, USA
| | - Stacy Ciufo
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD, 20892, USA
| | - Karen Clark
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD, 20892, USA
| | - Seán Turner
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD, 20892, USA
| | - Paul A Kitts
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD, 20892, USA
| | - Conrad L Schoch
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD, 20892, USA
| | - Michael DiCuccio
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD, 20892, USA
| | - Avi Kimchi
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD, 20892, USA
| |
Collapse
|
22
|
Bertolizio G, Garbin M, Ingelmo PM. Evaluation of Nociception during Pediatric Surgery: A Topical Review. J Pers Med 2023; 13:260. [PMID: 36836492 PMCID: PMC9964458 DOI: 10.3390/jpm13020260] [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: 01/02/2023] [Revised: 01/26/2023] [Accepted: 01/26/2023] [Indexed: 02/03/2023] Open
Abstract
The association between intraoperative nociception and increased patient's morbidity is well established. However, hemodynamic parameters, such as heart rate and blood pressure, may result in an inadequate monitor of nociception during surgery. Over the last two decades, different devices have been marketed to "reliably" detect intraoperative nociception. Since the direct measure of nociception is impractical during surgery, these monitors measures nociception surrogates such as sympathetic and parasympathetic nervous systems responses (heart rate variability, pupillometry, skin conductance), electroencephalographic changes, and muscular reflex arc. Each monitor carries its own advantages and disadvantages. The manuscript aims to give an overview of the most up-to-date information available in the literature on current nociceptor monitors available in clinical practice, with particular focus on their applications in pediatrics.
Collapse
Affiliation(s)
- Gianluca Bertolizio
- Department of Pediatric Anesthesiology, Montreal Children’s Hospital, Montreal, QC H4A 3J1, Canada
- Department of Anesthesia, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC H4A 3J1, Canada
- Research Institute, McGill University Health Center, Montreal, QC H4A 3J1, Canada
| | - Marta Garbin
- Department of Clinical Sciences, Université de Montréal, St-Hyacinthe, QC J2S 2M2, Canada
| | - Pablo M. Ingelmo
- Department of Pediatric Anesthesiology, Montreal Children’s Hospital, Montreal, QC H4A 3J1, Canada
- Department of Anesthesia, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC H4A 3J1, Canada
- Research Institute, McGill University Health Center, Montreal, QC H4A 3J1, Canada
- Edwards Family Interdisciplinary Center for Complex Pain, Montreal Children’s Hospital, Montreal, QC H4A 3J1, Canada
- Alan Edwards Center for Research on Pain, McGill University, Montreal, QC H3A 2B4, Canada
| |
Collapse
|
23
|
Jähne J, Le Thi TT, Blumenscheit C, Schneider A, Pham TL, Le Thi PT, Blom J, Vater J, Schweder T, Lasch P, Borriss R. Novel Plant-Associated Brevibacillus and Lysinibacillus Genomospecies Harbor a Rich Biosynthetic Potential of Antimicrobial Compounds. Microorganisms 2023; 11. [PMID: 36677460 DOI: 10.3390/microorganisms11010168] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 01/03/2023] [Accepted: 01/06/2023] [Indexed: 01/12/2023] Open
Abstract
We have previously reported the draft genome sequences of 59 endospore-forming Gram-positive bacterial strains isolated from Vietnamese crop plants due to their ability to suppress plant pathogens. Based on their draft genome sequence, eleven of them were assigned to the Brevibacillus and one to the Lysinibacillus genus. Further analysis including full genome sequencing revealed that several of these strains represent novel genomospecies. In vitro and in vivo assays demonstrated their ability to promote plant growth, as well as the strong biocontrol potential of Brevibacilli directed against phytopathogenic bacteria, fungi, and nematodes. Genome mining identified 157 natural product biosynthesis gene clusters (BGCs), including 36 novel BGCs not present in the MIBiG data bank. Our findings indicate that plant-associated Brevibacilli are a rich source of putative antimicrobial compounds and might serve as a valuable starting point for the development of novel biocontrol agents.
Collapse
|
24
|
Deng Y, Han XF, Jiang ZM, Yu LY, Li Y, Zhang YQ. Characterization of three Stenotrophomonas strains isolated from different ecosystems and proposal of Stenotrophomonas mori sp. nov. and Stenotrophomonas lacuserhaii sp. nov. Front Microbiol 2022; 13:1056762. [PMID: 36590414 PMCID: PMC9797726 DOI: 10.3389/fmicb.2022.1056762] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 09/29/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
Stenotrophomonas spp. have primarily been reported as non-pathogenic, plant-probiotic bacteria, despite the presence of some opportunistic human pathogens in the genus. Here, three Gram-stain negative, rod-shaped, non-spore-forming bacteria, designated as strains CPCC 101365T, CPCC 101269T, and CPCC 101426 were isolated from surface-sterilized medicinal plant roots of a mulberry plant in Chuxiong of the Yunnan Province, freshwater from Erhai Lake in the Yunnan Province, and sandy soils in the Badain Jaran desert in Inner Mongolia Autonomous Region, China, respectively. The 16S rRNA gene sequences analysis of these isolates in comparison with sequences from the GenBank database indicated that they belong to the genus Stenotrophomonas, with nucleotide similarities of 96.52-99.92% to identified Stenotrophomonas members. Phylogenetic analysis based on 16S rRNA gene and genome sequences confirmed that the isolates are members of the genus Stenotrophomonas. Values for genomic average nucleotide identity (ANI; <95%) and digital DNA-DNA hybridization (dDDH; < 70%) indicated that strains CPCC 101365T and CPCC 101269T were well-differentiated from validly described Stenotrophomonas species, while strain CPCC 101426 shared high ANI (97.7%) and dDDH (78.3%) identity with its closest phylogenetic neighbor, Stenotrophomonas koreensis JCM 13256T. The three genomes were approximately 3.1-4.0 Mbp in size and their G + C content ranged in 66.2-70.2%, with values slightly differing between CPCC 101365T (3.4 Mbp; 70.2%), CPCC 101269T (4.0 Mbp; 66.4%), and CPCC 101426 (3.1 Mbp; 66.2%). Genes encoding enzymes involved in the biosynthesis of indole-3-acetic acid (IAA) and siderophores were identified in the genomes of the three isolates, suggesting that these strains might serve roles as plant-growth promoting microorganisms. The polar lipid fractions of the three isolates primarily comprised diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), and phosphatidylethanolamine (PE). The predominant cellular fatty acid was iso-C15: 0, with moderate amounts of antesio-C15: 0, iso-C11: 0, iso C17: 1 ɷ9c/C16: 0 10-methyl, iso-C14: 0, and C16: 1 ɷ7c/C16: 1 ɷ6c. These results indicated that polyphasic characteristics of strains CPCC 101365T and CPCC 101269T differed from other identified Stenotrophomonas species and that strain CPCC 101426 was affiliated with the species Stenotrophomonas koreensis. Accordingly, two novel species of the genus Stenotrophomonas were consequently proposed, corresponding to Stenotrophomonas mori sp. nov. (type strain CPCC 101365T = DY006T = KCTC 82900T) and Stenotrophomonas lacuserhaii sp. nov. (type strain CPCC 101269T = K32T = KCTC 82901T). Highlights Members of the genus Stenotrophomonas, and particularly Stenotrophomonas maltophilia, are opportunistic human pathogens, but not enough research has evaluated the identification of environmental Stenotrophomonas spp. However, most Stenotrophomonas spp. serves as plant-probiotic bacteria.In this study, we obtained and characterized three Stenotrophomonas strains from different ecosystems. Based on phenotypic differences, chemotaxonomic properties, ANI and dDDH identity values, and phylogenetic analyses, two novel Stenotrophomonas species are proposed for the strains identified here. The encoding genes related to plant-growth promotion in the genomes of the newly recovered Stenotrophomonas spp. were retrieved. Follow-on experiments confirmed that these strains produced the important plant hormone IAA. Thus, these Stenotrophomonas spp. could considerably contribute to shaping and maintaining ecological stability in plant-associated environments, particularly while acting as plant-probiotic microorganisms.
Collapse
Affiliation(s)
- Yang Deng
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China,State Key Laboratory of Dao-di Herb, Beijing, China
| | - Xue-Fei Han
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China,State Key Laboratory of Dao-di Herb, Beijing, China
| | - Zhu-Ming Jiang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China,State Key Laboratory of Dao-di Herb, Beijing, China
| | - Li-Yan Yu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yong Li
- Faculty of Geosciences and Environmental Engineering, Southwest Jiaotong University, Chengdu, China
| | - Yu-Qin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China,State Key Laboratory of Dao-di Herb, Beijing, China,*Correspondence: Yu-Qin Zhang,
| |
Collapse
|
25
|
Gašić K, Zlatković N, Kuzmanović N. Polyphasic study of phytopathogenic bacterial strains associated with deep bark canker of walnut in Serbia revealed a new species, Brenneria izbisi sp. nov. Front Plant Sci 2022; 13:1055186. [PMID: 36507448 PMCID: PMC9730526 DOI: 10.3389/fpls.2022.1055186] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 10/24/2022] [Indexed: 06/17/2023]
Abstract
Serious outbreaks of walnut deep bark canker were observed on young walnut trees (Juglans regia L.) in two localities in the northern part of Serbia during 2020. From the symptomatic walnut tissues, two types of bacterial colonies were isolated, predominantly, light cream, circular and smooth colonies, as well as small, yellowish, mucoid and convex ones. PCR analysis and phenotypic assays suggested that the former group belongs to Brenneria spp., while the latter isolates were identified as Xanthomonas arboricola pv. juglandis. Within the Brenneria group, two strains were identified as Brenneria nigrifluens, while other 15 strains did not belong to any Brenneria species described so far. Therefore, we selected four representative strains of the unknown Brenneria sp. and subjected them to polyphasic analysis. As expected, in a phylogenetic tree based on partial 16S rDNA sequences, four novel strains grouped with other Brenneria representatives, and showed close phylogenetic relationship to Brenneria salicis. Furthermore, multilocus sequence analysis (MLSA) based on the partial sequences of atpD, gyrB, infB and rpoB housekeeping genes and core-genome phylogeny indicated that the studied strains form a novel and a clearly separate Brenneria lineage. Overall genome relatedness indices showed that they represent a new Brenneria species. The new species can be differentiated from the other Brenneria spp. infecting walnut and closely related B. salicis strains based on phenotypic characteristics, as well. Moreover, the pathogenicity tests on two-year-old walnut plants proved the ability of strains to cause necrosis and longitudinal black lesions and cracks on the trunk and branches of walnut trees. Overall, polyphasic characterization showed that the studied strains isolated from walnut with symptoms of deep bark canker represent a novel species of the genus Brenneria for which the name Brenneria izbisi sp. nov. is proposed. The type strain of B. izbisi is KBI 423T (= CFBP 9035T = LMG 32479T). To facilitate rapid identification of newly described species, a conventional PCR protocol and primers targeting the putative gene hrpP, were developed. Further study should reveal the potential role of each pathogen isolated from symptomatic walnut in disease development as well as possible interaction between them.
Collapse
Affiliation(s)
- Katarina Gašić
- Department of Plant Diseases, Institute for Plant Protection and Environment (IPPE), Belgrade, Serbia
| | - Nevena Zlatković
- Department of Plant Diseases, Institute for Plant Protection and Environment (IPPE), Belgrade, Serbia
| | - Nemanja Kuzmanović
- Julius Kühn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Horticulture and Urban Green, Braunschweig, Germany
| |
Collapse
|
26
|
Kong L, Bryce RA. Modeling pyranose ring pucker in carbohydrates using machine learning and semi-empirical quantum chemical methods. J Comput Chem 2022; 43:2009-2022. [PMID: 36165294 PMCID: PMC9828179 DOI: 10.1002/jcc.27000] [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: 06/09/2022] [Revised: 08/17/2022] [Accepted: 08/22/2022] [Indexed: 01/12/2023]
Abstract
Pyranose ring pucker is a key coordinate governing the structure, interactions and reactivity of carbohydrates. We assess the ability of the machine learning potentials, ANI-1ccx and ANI-2x, and the GFN2-xTB semiempirical quantum chemical method, to model ring pucker conformers of five monosaccharides and oxane in the gas phase. Relative to coupled-cluster quantum mechanical calculations, we find that ANI-1ccx most accurately reproduces the ring pucker energy landscape for these molecules, with a correlation coefficient r2 of 0.83. This correlation in relative energies lowers to values of 0.70 for ANI-2x and 0.60 for GFN2-xTB. The ANI-1ccx also provides the most accurate estimate of the energetics of the 4 C1 -to-1 C4 minimum energy pathway for the six molecules. All three models reproduce chair more accurately than non-chair geometries. Analysis of small model molecules suggests that the ANI-1ccx model favors puckers with equatorial hydrogen bonding substituents; that ANI-2x and GFN2-xTB models overstabilize conformers with axially oriented groups; and that the endo-anomeric effect is overestimated by the machine learning models and underestimated via the GFN2-xTB method. While the pucker conformers considered in this study correspond to a gas phase environment, the accuracy and computational efficiency of the ANI-1ccx approach in modeling ring pucker in vacuo provides a promising basis for future evaluation and application to condensed phase environments.
Collapse
Affiliation(s)
- Linghan Kong
- Division of Pharmacy and Optometry, School of Health Sciences, Manchester Academic Health Sciences CentreUniversity of ManchesterManchesterUK
| | - Richard A. Bryce
- Division of Pharmacy and Optometry, School of Health Sciences, Manchester Academic Health Sciences CentreUniversity of ManchesterManchesterUK
| |
Collapse
|
27
|
Gtari M. Taxogenomic status of phylogenetically distant Frankia clusters warrants their elevation to the rank of genus: A description of Protofrankia gen. nov., Parafrankia gen. nov., and Pseudofrankia gen. nov. as three novel genera within the family Frankiaceae. Front Microbiol 2022; 13:1041425. [PMID: 36425027 PMCID: PMC9680954 DOI: 10.3389/fmicb.2022.1041425] [Citation(s) in RCA: 2] [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: 09/10/2022] [Accepted: 10/12/2022] [Indexed: 11/10/2022] Open
Abstract
The genus Frankia is at present the sole genus in the family Frankiaceae and encompasses filamentous, sporangia-forming actinomycetes principally isolated from root nodules of taxonomically disparate dicotyledonous hosts named actinorhizal plants. Multiple independent phylogenetic analyses agree with the division of the genus Frankia into four well-supported clusters. Within these clusters, Frankia strains are well defined based on host infectivity range, mode of infection, morphology, and their behaviour in culture. In this study, phylogenomics, overall genome related indices (OGRI), together with available data sets for phenotypic and host-plant ranges available for the type strains of Frankia species, were considered. The robustness and the deep radiation observed in Frankia at the subgeneric level, fulfilling the primary principle of phylogenetic systematics, were strengthened by establishing genome criteria for new genus demarcation boundaries. Therefore, the taxonomic elevation of the Frankia clusters to the rank of the genus is proposed. The genus Frankia should be revised to encompass cluster 1 species only and three novel genera, Protofrankia gen. nov., Parafrankia gen. nov., and Pseudofrankia gen. nov., are proposed to accommodate clusters 2, 3, and 4 species, respectively. New combinations for validly named species are also provided.
Collapse
Affiliation(s)
- Maher Gtari
- USCR Bactériologie Moléculaire & Génomique, Institut National des Sciences Appliquées et de Technologie, Université de Carthage, Tunis, Tunisia
| |
Collapse
|
28
|
Deng Z, Xia X, Deng Y, Zhao M, Gu C, Geng Y, Wang J, Yang Q, He M, Xiao Q, Xiao W, He L, Liang S, Xu H, Lü M, Yu Z. ANI analysis of poxvirus genomes reveals its potential application to viral species rank demarcation. Virus Evol 2022; 8:veac031. [PMID: 35646390 PMCID: PMC9071573 DOI: 10.1093/ve/veac031] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/25/2022] [Accepted: 04/28/2022] [Indexed: 11/12/2022] Open
Abstract
Average nucleotide identity (ANI) is a prominent approach for rapidly classifying archaea and bacteria by recruiting both whole genomic sequences and draft assemblies. To evaluate the feasibility of ANI in virus taxon demarcation, 685 poxviruses were assessed. Prior to the analysis, the fragment length and threshold of the ANI value were optimized as 200 bp and 98 per cent, respectively. After ANI analysis and network visualization, the resulting sixty-one species (ANI species rank) were clustered and largely consistent with the groupings found in National Center for Biotechnology Information Virus [within the International Committee on Taxonomy of Viruses (ICTV) Master Species List]. The species identities of thirty-four other poxviruses (excluded by the ICTV Master Species List) were also identified. Subsequent phylogenetic analysis and Guanine-Cytosine (GC) content comparison done were found to support the ANI analysis. Finally, the BLAST identity of concatenated sequences from previously identified core genes showed 91.8 per cent congruence with ANI analysis at the species rank, thus showing potential as a marker gene for poxviruses classification. Collectively, our results reveal that the ANI analysis may serve as a novel and efficient method for poxviruses demarcation.
Collapse
Affiliation(s)
| | - Xuyang Xia
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, No. 8 Linyin Street, Wuhou District, Chengdu 610000, P. R. China
| | - Yiqi Deng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, No. 8 Linyin Street, Wuhou District, Chengdu 610000, P. R. China
| | - Mingde Zhao
- Laboratory Animal Center, Southwest Medical University, No. 1, Section 1, Xianglin Road, Longmatan District, Luzhou 64600, P. R. China
| | - Congwei Gu
- Laboratory Animal Center, Southwest Medical University, No. 1, Section 1, Xianglin Road, Longmatan District, Luzhou 64600, P. R. China
| | - Yi Geng
- College of Veterinary Medicine, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang District, Chengdu 610000, P. R. China
| | - Jun Wang
- Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, No. 1124 Dongtong Road, Neijiang 641100, P. R. China
| | - Qian Yang
- Laboratory Animal Center, Southwest Medical University, No. 1, Section 1, Xianglin Road, Longmatan District, Luzhou 64600, P. R. China
| | - Manli He
- Laboratory Animal Center, Southwest Medical University, No. 1, Section 1, Xianglin Road, Longmatan District, Luzhou 64600, P. R. China
| | - Qihai Xiao
- Laboratory Animal Center, Southwest Medical University, No. 1, Section 1, Xianglin Road, Longmatan District, Luzhou 64600, P. R. China
| | - Wudian Xiao
- Laboratory Animal Center, Southwest Medical University, No. 1, Section 1, Xianglin Road, Longmatan District, Luzhou 64600, P. R. China
| | - Lvqin He
- Laboratory Animal Center, Southwest Medical University, No. 1, Section 1, Xianglin Road, Longmatan District, Luzhou 64600, P. R. China
| | - Sicheng Liang
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, No. 25 Taiping Street, Jiangyang District, Luzhou 646000, P. R. China
| | - Heng Xu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, No. 8 Linyin Street, Wuhou District, Chengdu 610000, P. R. China
| | - Muhan Lü
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, No. 25 Taiping Street, Jiangyang District, Luzhou 646000, P. R. China
- Laboratory Animal Center, Southwest Medical University, No. 1, Section 1, Xianglin Road, Longmatan District, Luzhou 64600, P. R. China
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
- School of Comprehensive Human Sciences, Doctoral Program in Biomedical Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Zehui Yu
- Laboratory Animal Center, Southwest Medical University, No. 1, Section 1, Xianglin Road, Longmatan District, Luzhou 64600, P. R. China
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, No. 25 Taiping Street, Jiangyang District, Luzhou 646000, P. R. China
- School of Basic Medical Sciences, Zhejiang University, No. 866 Yuhangtang Road, Xihu District, Hangzhou 310000, P. R. China
| |
Collapse
|
29
|
Ullmann L, Wibberg D, Busche T, Rückert C, Müsgens A, Kalinowski J, Blank LM. Seventeen Ustilaginaceae High-Quality Genome Sequences Allow Phylogenomic Analysis and Provide Insights into Secondary Metabolite Synthesis. J Fungi (Basel) 2022; 8. [PMID: 35330271 DOI: 10.3390/jof8030269] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 02/09/2022] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 02/04/2023] Open
Abstract
The family of Ustilaginaceae belongs to the order of Basidiomycetes. Despite their plant pathogenicity causing, e.g., corn smut disease, they are also known as natural producers of value-added chemicals such as extracellular glycolipids, organic acids, and polyols. Here, we present 17 high-quality draft genome sequences (N50 > 1 Mb) combining third-generation nanopore and second-generation Illumina sequencing. The data were analyzed with taxonomical genome-based bioinformatics methods such as Percentage of Conserved Proteins (POCP), Average Nucleotide Identity (ANI), and Average Amino Acid Identity (AAI) analyses indicating that a reclassification of the Ustilaginaceae family might be required. Further, conserved core genes were determined to calculate a phylogenomic core genome tree of the Ustilaginaceae that also supported the results of the other phylogenomic analysis. In addition, to genomic comparisons, secondary metabolite clusters (e.g., itaconic acid, mannosylerythritol lipids, and ustilagic acid) of biotechnological interest were analyzed, whereas the sheer number of clusters did not differ much between species.
Collapse
|
30
|
Sabourdin N, Burey J, Tuffet S, Thomin A, Rousseau A, Al-Hawari M, Taconet C, Louvet N, Constant I. Analgesia Nociception Index-Guided Remifent anil versus Standard Care during Propofol Anesthesia: A Randomized Controlled Trial. J Clin Med 2022; 11:jcm11020333. [PMID: 35054027 PMCID: PMC8778406 DOI: 10.3390/jcm11020333] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 12/15/2021] [Revised: 12/31/2021] [Accepted: 01/06/2022] [Indexed: 12/30/2022] Open
Abstract
The clinical benefits to be expected from intraoperative nociception monitors are currently under investigation. Among these devices, the Analgesia Nociception-Index (ANI) has shown promising results under sevoflurane anesthesia. Our study investigated ANI-guided remifentanil administration under propofol anesthesia. We hypothesized that ANI guidance would result in reduced remifentanil consumption compared with standard management. This prospective, randomized, controlled, single-blinded, bi-centric study included women undergoing elective gynecologic surgery under target-controlled infusion of propofol and remifentanil. Patients were randomly assigned to an ANI or Standard group. In the ANI group, remifentanil target concentration was adjusted by 0.5 ng mL−1 steps every 5 min according to the ANI value. In the Standard group, remifentanil was managed according to standard practice. Our primary objective was to compare remifentanil consumption between the groups. Our secondary objectives were to compare the quality of anesthesia, postoperative analgesia and the incidence of chronic pain. Eighty patients were included. Remifentanil consumption was lower in the ANI group: 4.4 (3.3; 5.7) vs. 5.8 (4.9; 7.1) µg kg−1 h−1 (difference = −1.4 (95% CI, −2.6 to −0.2), p = 0.0026). Propofol consumption was not different between the groups. Postoperative pain scores were low in both groups. There was no difference in morphine consumption 24 h after surgery. The proportion of patients reporting pain 3 months after surgery was 18.8% in the ANI group and 30.8% in the Standard group (difference = −12.0 (95% CI, −32.2 to 9.2)). ANI guidance resulted in lower remifentanil consumption compared with standard practice under propofol anesthesia. There was no difference in short- or long-term postoperative analgesia.
Collapse
Affiliation(s)
- Nada Sabourdin
- Département d’Anesthésie-Réanimation, Hopital Trousseau, GRC 29, DMU DREAM, Sorbonne Université, AP-HP, 75012 Paris, France; (M.A.-H.); (N.L.); (I.C.)
- EA 7323: Pharmacologie et Evaluation des Thérapeutiques chez L’enfant et la Femme Enceinte, Université de Paris, 75006 Paris, France
- Correspondence:
| | - Julien Burey
- Département d’Anesthésie-Réanimation, Hopital Tenon, GRC 29, DMU DREAM, Sorbonne Université, AP-HP, 75020 Paris, France; (J.B.); (C.T.)
| | - Sophie Tuffet
- Department of Clinical Pharmacology and Clinical Research Platform of the East of Paris (URC-CRC-CRB), Hôpital St Antoine, AP-HP, 75012 Paris, France; (S.T.); (A.R.)
| | - Anne Thomin
- Département de Gynécologie et Obstétrique, Hopital Trousseau, FHU PREMA, Sorbonne Université, AP-HP, 75012 Paris, France;
| | - Alexandra Rousseau
- Department of Clinical Pharmacology and Clinical Research Platform of the East of Paris (URC-CRC-CRB), Hôpital St Antoine, AP-HP, 75012 Paris, France; (S.T.); (A.R.)
| | - Mossab Al-Hawari
- Département d’Anesthésie-Réanimation, Hopital Trousseau, GRC 29, DMU DREAM, Sorbonne Université, AP-HP, 75012 Paris, France; (M.A.-H.); (N.L.); (I.C.)
| | - Clementine Taconet
- Département d’Anesthésie-Réanimation, Hopital Tenon, GRC 29, DMU DREAM, Sorbonne Université, AP-HP, 75020 Paris, France; (J.B.); (C.T.)
| | - Nicolas Louvet
- Département d’Anesthésie-Réanimation, Hopital Trousseau, GRC 29, DMU DREAM, Sorbonne Université, AP-HP, 75012 Paris, France; (M.A.-H.); (N.L.); (I.C.)
| | - Isabelle Constant
- Département d’Anesthésie-Réanimation, Hopital Trousseau, GRC 29, DMU DREAM, Sorbonne Université, AP-HP, 75012 Paris, France; (M.A.-H.); (N.L.); (I.C.)
- EA 7323: Pharmacologie et Evaluation des Thérapeutiques chez L’enfant et la Femme Enceinte, Université de Paris, 75006 Paris, France
| |
Collapse
|
31
|
Soutar CD, Stavrinides J. Phylogenomic analysis of the Erwiniaceae supports reclassification of Kalamiella piersonii to Pantoea piersonii comb. nov. and Erwinia gerundensis to the new genus Duffyella gen. nov. as Duffyella gerundensis comb. nov. Mol Genet Genomics 2022. [PMID: 34988605 DOI: 10.1007/s00438-021-01829-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 10/27/2021] [Indexed: 01/20/2023]
Abstract
To better understand the taxonomy of Erwinia in the context of the Erwiniaceae family, we carried out a taxogenomic analysis of the Erwiniaceae, a family that was created following the taxonomic revision of the family, Enterobacteriaceae. There has been no systematic analysis of this family, including the agriculturally relevant genus, Erwinia. Our analyses focused on 80 strains of Erwinia along with 37 strains representing 7 other genera in the family. We identified 308 common proteins, generated a genome-level phylogeny and carried out Average Nucleotide Identity, Average Amino Acid Identity and Percentage of Conserved Protein analyses. We show that multiple strains of Erwinia cannot be assigned to established species groups and that both Erwinia gerundensis and "Erwinia mediterraneensis" are not members of Erwinia. We propose the creation of the genus Duffyella gen. nov. and the reclassification of Erwinia gerundensis to this genus as the type species, Duffyella gerundensis comb. nov. Furthermore, divergence between other species within Erwinia as measured by Average Amino Acid Identity is greater than the divergence between Erwinia and other genera, supporting the possible subdivision of the genus Erwinia into at least two genera. Our analyses also suggest that there is no basis for the establishment of the genus Kalamiella within the Erwiniaceae or the taxonomic revision of the Pantoea septica lineage. Therefore, we propose reclassifying Kalamiella piersonii as Pantoea piersonii comb. nov. Our study provides new insight into the diversity of the Erwiniaceae and provides a solid foundation for advancing taxonomic revision of this broadly relevant family.
Collapse
|
32
|
Zhou H, Zhang J, Shao Y, Wang J, Xu W, Liu Y, Yu S, Ye Q, Pang R, Wu S, Gu Q, Xue L, Zhang J, Li H, Wu Q, Ding Y. Development of a high resolution melting method based on a novel molecular target for discrimination between Bacillus cereus and Bacillus thuringiensis. Food Res Int 2022; 151:110845. [PMID: 34980383 DOI: 10.1016/j.foodres.2021.110845] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 05/10/2021] [Revised: 11/03/2021] [Accepted: 11/27/2021] [Indexed: 11/04/2022]
Abstract
Delimitation within the Bacillus cereus group is confusing due to the highly similar genetic background of its constituent bacteria. This study aimed to develop a rapid and efficient method for the identification of Bacillus cereus and Bacillus thuringiensis, two closely related species within the B. cereus group. Using average nucleotide identity analysis (ANI) and ribosomal multilocus sequence typing (rMLST), the authenticity of the genomes of B. cereus and B. thuringiensis was determined. Emetic B. cereus and Bacillus bombysepticus were also included to provide novel genomic insights into the boundaries within the B. cereus group. Using pan-genome analysis, ispD, a novel core and single-copy molecular target, was identified for the differentiation between B. cereus and B. thuringiensis. Based on the single nucleotide polymorphism within ispD, a high resolution melting (HRM) method for the determination of B. cereus and B. thuringiensis was developed. This method can not only distinguish B. cereus and B. thuringiensis, but can also separate B. cereus from other foodborne pathogenic bacteria. The detection limit of this method could reach 1 pg of pure genomic DNA and 3.7 × 102 cfu/mL of pure culture. Moreover, this new method could effectively differentiate B. cereus and B. thuringiensis in spiked, mixed, and real food samples. Collectively, the established HRM method can provide a new reference paradigm for the sensitive and specific nucleic acid detection of pathogens with identical genomes.
Collapse
Affiliation(s)
- Huan Zhou
- College of Life Science and Technology, Jinan University, Guangzhou 510632, China; Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Junhui Zhang
- Department of Food Science & Technology, Institute of Food Safety & Nutrition, Jinan University, Guangzhou 510632, China; Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Yanna Shao
- College of Life Science and Technology, Jinan University, Guangzhou 510632, China; Department of Food Science & Technology, Institute of Food Safety & Nutrition, Jinan University, Guangzhou 510632, China; Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Juan Wang
- College of Food Science, South China Agricultural University, Guangzhou 510432, China
| | - Wenxing Xu
- Department of Food Science & Technology, Institute of Food Safety & Nutrition, Jinan University, Guangzhou 510632, China; Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Yang Liu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Shubo Yu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Qinghua Ye
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Rui Pang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Shi Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Qihui Gu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Liang Xue
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Jumei Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Hongye Li
- College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Yu Ding
- College of Life Science and Technology, Jinan University, Guangzhou 510632, China; Department of Food Science & Technology, Institute of Food Safety & Nutrition, Jinan University, Guangzhou 510632, China; Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
| |
Collapse
|
33
|
Zhang G, Yang J, Lai XH, Jin D, Lu S, Ren Z, Qin T, Pu J, Ge Y, Cheng Y, Yang C, Lv X, Jiao Y, Huang Y, Xu J. Corynebacterium zhongnanshanii sp. nov. isolated from trachea of Marmota himalayana, Corynebacterium lujinxingii sp. nov. and Corynebacterium wankanglinii sp. nov. from human faeces. Int J Syst Evol Microbiol 2021; 71. [PMID: 34846289 DOI: 10.1099/ijsem.0.005069] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Six novel facultatively anaerobic, Gram-stain-positive, rod-shaped, non-haemolytic bacteria (zg-320T/zg-336, zg-917T/zg-910 and zg-913T/zg-915) isolated from animal tissues and human faeces were found to belong to the genus Corynebacterium based on the phylogenetic analyses of 16S rRNA gene and 262 core genes set. Based on the greatest degree of 16S rRNA similarity, zg-320T/zg-336 had the highest 16S rRNA gene similarity to Corynebacterium falsenii DSM 44353T (97.51 %), zg-917T/zg-910 to Corynebacterium coyleae DSM 44184T (98.68 %), and zg-913T/zg-915 to Corynebacterium afermentans subsp. lipophilum CIP 103500T (98.79 %). The three novel type strains had a relatively high DNA G+C content (61.2-64.4 mol%), low DNA relatedness and ANI values with their respective neighbours: 23.5/72.7 %, 25.0/72.3%and 22.6/73.1 % (zg-320T vs. Corynebacterium auriscanis CIP 106629T, Corynebacterium resistens DSM 45100T and Corynebacterium suicordis DSM 45110T); 24.4/82.3% and 23.7/81.3 % (zg-917T vs. C. coyleae DSM 44184T and Corynebacterium jeddahense JCBT); 26.8/83.7% and 27.7/84.4 % (zg-913T vs. Corynebacterium mucifaciens ATCC 700355T and C. afermentans subsp. lipophilum CCUG 32105T). The three novel species had C16 : 0, C18 : 0, C18 : 1 ω9c and C18 : 0 ante/C18 : 2 ω6,9c as the major cellular fatty acids; MK-8(H2) in strain zg-917T and MK-9(H2) in strains zg-320T and zg-913T were found to be the major respiratory quinones. For the three novel species, the detected major polar lipids included diphosphatidylglycerol, phosphatidyl inositol mannoside, phosphatidylglycerol and phosphatidylinositol, the cell-wall peptidoglycan was based on meso-DAP, and the whole-cell sugars mainly included ribose, arabinose and galactose. The three novel species grew optimally at 35-37 °C, 0.5 % (w/v) NaCl and pH 7.0-8.0; notably, they were tolerant of 10.5 % (w/v) NaCl. Based on the results of these comprehensive analyses, three novel species in the genus Corynebacterium are proposed, aptly named Corynebacterium zhongnanshanii sp. nov. (zg-320T = GDMCC 1.1719T = JCM 34106T), Corynebacterium lujinxingii sp. nov. (zg-917T = GDMCC 1.1707T = JCM 34094T) and Corynebacterium wankanglinii sp. nov. (zg-913T = GDMCC 1.1706T = JCM 34398T).
Collapse
Affiliation(s)
- Gui Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China.,Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, PR China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
| | - Xin-He Lai
- Henan Key Laboratory of Biomolecular Recognition and Sensing, College of Chemistry and Chemical Engineering, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, Shangqiu Normal University, Shangqiu 476000, PR China
| | - Dong Jin
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China.,Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, PR China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
| | - Shan Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China.,Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, PR China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
| | - Zhihong Ren
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Tian Qin
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Yajun Ge
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China.,Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, PR China
| | - Yanpeng Cheng
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China.,Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, PR China
| | - Caixin Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China.,Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, PR China
| | - Xianglian Lv
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China.,Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, PR China
| | - Yifan Jiao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China.,Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, PR China
| | - Ying Huang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Jianguo Xu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China.,Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, PR China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China.,Institute of Public Health, Nankai University, Tianjin 300071, PR China
| |
Collapse
|
34
|
Shahiri TS, Richebé P, Richard-Lalonde M, Gélinas C. Description of the validity of the Analgesia Nociception Index ( ANI) and Nociception Level Index (NOL) for nociception assessment in anesthetized patients undergoing surgery: a systematized review. J Clin Monit Comput 2021; 36:623-635. [PMID: 34783941 DOI: 10.1007/s10877-021-00772-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [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: 01/22/2021] [Accepted: 10/17/2021] [Indexed: 11/29/2022]
Abstract
Maintaining optimum analgesia in anesthetized patients is challenging due to the inability to self-report pain or exhibit pain-related behaviours. The Analgesia Nociception Index (ANI) (based on heart rate variability [HRV]) and the Nociception Level Index (NOL) (based on HRV, photoplethysmography, skin conductance, and temperature) both include HRV and provide continuous index monitoring for nociception assessment. The research question was: "What are the validation strategies of the NOL and ANI for nociception assessment in anesthetized patients?". The objectives were to describe and analyze the validation strategies and results. A systematized review was conducted using a comprehensive search with keywords under three concepts (nociception/pain, ANI/NOL, and validity) in four databases. A quality assessment using an adapted GRADE approach for measurement tools, and a risk of bias assessment using QUADAS-2 tool were performed by two reviewers. Out of 525 results, 15 validation studies were included. Strategies included hypothesis testing, discriminative, and criterion validation. Significant changes in ANI/NOL values were found in response to nociceptive stimuli at different opioid concentrations (hypothesis testing). Higher ANI/NOL values were observed during nociceptive stimuli (discriminative). AUCs ranging from 0.83 to 0.99 were obtained to detect nociceptive stimuli (criterion). Both technologies performed superiorly in detecting nociceptive stimuli compared to individual monitoring of HR and blood pressure. Although the aforementioned validation strategies are deemed appropriate, in the absence of a gold standard, criterion validation findings should be interpreted with caution. Moreover, reliability could be examined using test-retest with consistent ANI/NOL values during a stable time-interval.
Collapse
Affiliation(s)
- T Shiva Shahiri
- Ingram School of Nursing, McGill University, Montréal, Canada.,Centre for Nursing Research and Lady Davis Institute, Jewish General Hospital - CIUSSS West-Central Montréal, Montréal, Canada
| | - Philippe Richebé
- Department of Anesthesiology and Pain Medicine, University of Montréal, Hôpital Maisonneuve-Rosemont - CIUSSS Est-de-lÏle-de-Montréal, Montréal, Canada
| | - Melissa Richard-Lalonde
- Ingram School of Nursing, McGill University, Montréal, Canada.,Centre for Nursing Research and Lady Davis Institute, Jewish General Hospital - CIUSSS West-Central Montréal, Montréal, Canada
| | - Céline Gélinas
- Ingram School of Nursing, McGill University, Montréal, Canada. .,Centre for Nursing Research and Lady Davis Institute, Jewish General Hospital - CIUSSS West-Central Montréal, Montréal, Canada.
| |
Collapse
|
35
|
Zhu L, Ping W, Zhang S, Chen Y, Zhang Y, Zhang J. Description and genome analysis of Microvirga antarctica sp. nov., a novel pink-pigmented psychrotolerant bacterium isolated from Antarctic soil. Antonie Van Leeuwenhoek 2021; 114:2219-28. [PMID: 34697697 DOI: 10.1007/s10482-021-01674-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 10/11/2021] [Indexed: 10/20/2022]
Abstract
A novel pink-pigmented bacterium, designated strain 3D7T, was isolated during an investigation of potential psychrotolerant species from Antarctic soil. Cells of the isolate were observed to be rod-shaped (0.7-0.9 × 1.0-2.2 µm), Gram-stain negative and non-motile. It was able to grow at 4-32 °C, pH 7.0-10.0 and in the presence of 0-3% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 3D7T belongs to the genus Microvirga and was most closely related to 'Microvirga brassicacearum' CDVBN77T (98.3%), Microvirga subterranea DSM 14364 T (96.8%), Microvirga guangxiensis 25BT (96.5%) and Microvirga aerophila DSM 21344 T (96.5%). The predominant quinone was ubiquinone 10 (Q-10), and the major fatty acids were summed feature 8 (C18:1ω7c and/or C18:1ω6c) and C19:0 cyclo ω8c. The predominant polar lipids were phosphatidylcholine and phosphatidylethanolamine. The genomic DNA G + C content of strain 3D7T was 63.5 mol%. Its genome sequence showed genes encoding phosphatases and lipases. Genetic machinery related to carbohydrate-active enzymes and secondary metabolites were also observed. The average nucleotide identity and digital DNA-DNA hybridization values based on whole genome sequences of strain 3D7T and its closely related species were below the threshold range for species determination. Phenotypic, chemotaxonomic, phylogenetic and genomic analyses suggested that strain 3D7T represents a novel species of the genus Microvirga, for which the name Microvirga antarctica sp. nov. is proposed. The type strain is 3D7T (= CGMCC 1.13821T = KCTC 72465T).
Collapse
|
36
|
Werinder A, Aspán A, Söderlund R, Backhans A, Sjölund M, Guss B, Jacobson M. Whole-Genome Sequencing Evaluation of MALDI-TOF MS as a Species Identification Tool for Streptococcus suis. J Clin Microbiol 2021; 59:e0129721. [PMID: 34469186 DOI: 10.1128/JCM.01297-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Streptococcus suis is an important bacterial pathogen in pigs that may also cause zoonotic disease in humans. The aim of the study was to evaluate matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) identification of S. suis case isolates from diseased pigs and tonsil isolates from healthy pigs and wild boar using sequence analysis methods. Isolates (n = 348) that had been classified as S. suis by MALDI-TOF MS were whole-genome sequenced and investigated using analyses of (i) the 16S rRNA gene, (ii) the recN gene, and (iii) whole-genome average nucleotide identity (ANI). Analysis of the 16S rRNA gene indicated that 82.8% (288 out of 348) of the isolates were S. suis, while recN gene analysis indicated that 75.6% (263 out of 348) were S. suis. ANI analysis classified 44.3% (154 out of 348) as S. suis. In total, 44% (153 out of 348) of the investigated isolates were classified as S. suis by all of the species identification methods employed. The mean MALDI-TOF MS score was significantly higher for the S. suis case isolates than for the tonsil isolates; however, the difference is of limited practical use. The results show that species confirmation beyond MALDI-TOF MS is needed for S. suis isolates. Since the resolution of 16S rRNA gene analysis is too low for Streptococcus spp., ANI analysis with a slightly lowered cutoff of 94% may be used instead of, or in addition to, recN gene analysis. Supplementation of the MALDI-TOF MS reference library with mass spectra from S. orisratti, S. parasuis, S. ruminantium, and additional S. suis serotypes should be considered in order to produce more accurate classifications.
Collapse
|
37
|
Erratum: Genomic Metrics Applied to Rhizobiales (Hyphomicrobiales): Species Reclassification, Identification of Unauthentic Genomes and False Type Strains. Front Microbiol 2021; 12:734850. [PMID: 34381440 PMCID: PMC8352568 DOI: 10.3389/fmicb.2021.734850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 07/01/2021] [Indexed: 11/17/2022] Open
|
38
|
Wang H, Hou H, Huang J. Citrobacter arsenatis sp. nov., an arsenate-reducing bacterium isolated from freshwater sediment. Antonie Van Leeuwenhoek 2021; 114:1285-92. [PMID: 34117562 DOI: 10.1007/s10482-021-01601-y] [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: 12/11/2020] [Accepted: 05/27/2021] [Indexed: 10/21/2022]
Abstract
A novel arsenate-reducing bacterium, LY-1T, was isolated from freshwater sediment in Huangshi, China. Morphological analysis indicated that the cells were shaped like rods and were gram-negative. The major fatty acids (> 10%) were C16:0, summed feature 3 (C16:1 ω7c, C16:1 ω6c) and summed feature 8 (C18:1 ω7c, C18:1 ω6c). An assessment of the phylogeny based on 16S rRNA gene sequences indicated that the strain LY-1T belonged to the genus Citrobacter, while further analysis based on the recN gene indicated that LY-1T occupies a distinct phylogenetic niche within the Citrobacter genus. Moreover, average nucleotide identity and digital DNA-DNA hybridization between the strain LY-1T and the type strains of closely related species of the genus Citrobacter (C. europaeus, C. brakii, C. portucalensis, C. freundii, C. werkmanii, C. cronae, C. youngae, C. pasteurii, C. tructae, C. gillenii, and C. murliniae) were 85.8-93.8% and 31.2-56.9%, respectively. In addition, the LY-1T strain's capacity to metabolize various compounds and its characteristic G + C content of 51.9% were also distinct from other species of the Citrobacter genus. These discriminatory features cumulatively indicate the LY-1T strain as a new species within the Citrobacter genus. We propose the species name Citrobacter arsenatis for this new species, with LY-1T (= CCTCC AB 2019169T = KCTC 72440T) as the type strain.
Collapse
|
39
|
Nahar A, Baker AL, Nichols DS, Bowman JP, Britz ML. Benchmarking DNA Extraction Methods for Phylogenomic Analysis of Sub-Antarctic Rhodococcus and Williamsia Species. Microorganisms 2021; 9:microorganisms9061253. [PMID: 34207615 PMCID: PMC8227252 DOI: 10.3390/microorganisms9061253] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 04/21/2021] [Revised: 05/25/2021] [Accepted: 06/04/2021] [Indexed: 11/29/2022] Open
Abstract
Bacteria containing mycolic acids in their cell envelope are often recalcitrant to cell lysis, so extracting DNA of sufficient quality for third-generation sequencing and high-fidelity genome assembly requires optimization, even when using commercial kits with protocols for hard-to-lyse bacteria. We benchmarked three spin-column-based kits against a classical DNA extraction method employing lysozyme, proteinase K and SDS for six lysozyme-resistant, sub-Antarctic strains of Corynebaceriales. Prior cultivation in broths containing glycine at highly growth-inhibitory concentrations (4.0–4.5%) improved cell lysis using both classical and kit methods. The classical method produced DNA with average fragment sizes of 27–59 Kbp and tight fragment size ranges, meeting quality standards for genome sequencing, assembly and phylogenomic analyses. By 16S rRNA gene sequencing, we classified two strains as Williamsia and four strains as Rhodococcus species. Pairwise comparison of average nucleotide identity (ANI) and alignment fraction (AF), plus genome clustering analysis, confirmed Rhodococcus sp. 1163 and 1168 and Williamsia sp. 1135 and 1138 as novel species. Phylogenetic, lipidomic and biochemical analyses classified psychrotrophic strains 1139 and 1159 as R. qingshengii and R. erythropolis, respectively, using ANI similarity of >98% and AF >60% for species delineation. On this basis, some members of the R. erythropolis genome cluster groups, including strains currently named as R. enclensis, R. baikonurensis, R. opacus and R. rhodochrous, would be reclassified either as R. erythropolis or R. qingshengii.
Collapse
Affiliation(s)
- Akhikun Nahar
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7005, Australia; (A.L.B.); (J.P.B.)
- Correspondence: (A.N.); (M.L.B.)
| | - Anthony L. Baker
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7005, Australia; (A.L.B.); (J.P.B.)
| | - David S. Nichols
- Central Science Laboratory, Division of Research, University of Tasmania, Hobart, TAS 7005, Australia;
| | - John P. Bowman
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7005, Australia; (A.L.B.); (J.P.B.)
| | - Margaret L. Britz
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7005, Australia; (A.L.B.); (J.P.B.)
- Correspondence: (A.N.); (M.L.B.)
| |
Collapse
|
40
|
Parveen S, Akhtar N, Akram J. Genomic analysis provides insights into the Gordonia sp. W3S5 taxonomy and sulfur metabolism-related genes. 3 Biotech 2021; 11:300. [PMID: 34194893 DOI: 10.1007/s13205-021-02850-4] [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: 10/13/2020] [Accepted: 05/17/2021] [Indexed: 10/21/2022] Open
Abstract
The Gordonia sp. W3S5, isolated from oil-polluted soil samples can remove sulfur from a variety of symmetric and asymmetric thiophenic compounds and diesel oil. Its draft genome sequence was comprised of 49 contigs, total genome size 4.86 Mb, and a G + C content of 67.50%. According to the current bacterial taxonomy procedures (16S rRNA gene sequence and overall genome-related index), the W3S5 was affiliated to Gordonia rubripertincta. Rapid Annotation using Subsystem Technology (ClassicRAST) server revealed that the W3S5 contains 4435 coding sequences, 404 subsystems and 60 sulfur metabolism genes. The RAST comparative genomic analysis showed that the genes connected with organic sulfur metabolism are majorly related to ssu and dszABC operons. Moreover, the comparison of orthologous gene clusters using OrthoVenn2 web server revealed a total of 4869 clusters, 2685 core orthologs, 632 shared orthologs and 112 unique ortholog clusters among the W3S5 and other type strains of Gordonia. This is the first report describing genome-based characterization of a Gordonia rubripertincta strain desulfurizing thiophenic compounds and diesel oil. The desulfurization potential of Gordonia rubripertincta W3S5 and genomic analyses revealed it as a valuable biocatalyst for process development to desulfurize a broad range of thiophenic sulfur-containing compounds, which are a major component of organic sulfur in petroleum oil. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02850-4.
Collapse
|
41
|
Lian FB, Jiang S, Zhu KL, Shang DD, Zhang J, Du ZJ. Salegentibacter maritimus sp. nov., isolated from marine coastal sediment. Syst Appl Microbiol 2021; 44:126209. [PMID: 33992955 DOI: 10.1016/j.syapm.2021.126209] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 04/20/2021] [Accepted: 04/23/2021] [Indexed: 11/22/2022]
Abstract
Two bacterial strains were isolated from a marine sediment sample taken from Jingzi Wharf, Weihai, China. These two strains were characterized at the phenotypic, chemotaxonomic, and genomic level. The two strains possessed almost identical 16S rRNA gene sequences (99.9 %). However, RAPD-PCR fingerprint patterns discriminated that they were not from one clonal origin. The average nucleotide identity (ANI) value and the digital DNA-DNA hybridization (dDDH) value between the two strains were 98.3 % and 85.4 %, respectively, suggestingthat they belonged to the same species. On the basis of the result of phylogenetic analysis of the 16S rRNA gene sequences, the two strains belonged to the genus Salegentibacter and were closely related to S. holothuriorum KCTC 12371T (98.6 %) and S. salegens DSM 5424T (98.2-98.3 %). The ANI and dDDH clearly separated strains F63223T and F60176 from the the most related type strains with values below the thresholds for species. The genome sizes of strains F63223T and F60176 were approximate 3.89 and 3.59 Mbp, respectively. The strain F63223T had 3,335 predicted genes with DNA G + C content of 35.6 %. The major respiratory quinone was MK-6 and the major polar lipids were phosphatidylethanolamine and one unidentified lipid. According to the results of the phenotypic, chemotaxonomic characterization, phylogenetic classification and genome analysis, the two isolates could be considered to represent a novel species of the genus Salegentibacter, for which the name Salegentibacter maritimus sp. nov., is proposed, with F63223T (=MCCC 1H00433T = KCTC 82417T) as the type strain.
Collapse
|
42
|
Carlin CR, Liao J, Weller D, Guo X, Orsi R, Wiedmann M. Listeria cossartiae sp. nov., Listeria farberi sp. nov., Listeria immobilis sp. nov., Listeria portnoyi sp. nov. and Listeria rustica sp. nov., isolated from agricultural water and natural environments. Int J Syst Evol Microbiol 2021; 71:004795. [PMID: 33999788 PMCID: PMC8289207 DOI: 10.1099/ijsem.0.004795] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 04/02/2021] [Indexed: 12/20/2022] Open
Abstract
A total of 27 Listeria isolates that could not be classified to the species level were obtained from soil samples from different locations in the contiguous United States and an agricultural water sample from New York. Whole-genome sequence-based average nucleotide identity blast (ANIb) showed that the 27 isolates form five distinct clusters; for each cluster, all draft genomes showed ANI values of <95 % similarity to each other and any currently described Listeria species, indicating that each cluster represents a novel species. Of the five novel species, three cluster with the Listeria sensu stricto clade and two cluster with sensu lato. One of the novel sensu stricto species, designated L. cossartiae sp. nov., contains two subclusters with an average ANI similarity of 94.9%, which were designated as subspecies. The proposed three novel sensu stricto species (including two subspecies) are Listeria farberi sp. nov. (type strain FSL L7-0091T=CCUG 74668T=LMG 31917T; maximum ANI 91.9 % to L. innocua), Listeria immobilis sp. nov. (type strain FSL L7-1519T=CCUG 74666T=LMG 31920T; maximum ANI 87.4 % to L. ivanovii subsp. londoniensis) and Listeria cossartiae sp. nov. [subsp. cossartiae (type strain FSL L7-1447T=CCUG 74667T=LMG 31919T; maximum ANI 93.4 % to L. marthii) and subsp. cayugensis (type strain FSL L7-0993T=CCUG 74670T=LMG 31918T; maximum ANI 94.7 % to L. marthii). The two proposed novel sensu lato species are Listeria portnoyi sp. nov. (type strain FSL L7-1582T=CCUG 74671T=LMG 31921T; maximum ANI value of 88.9 % to L. cornellensis and 89.2 % to L. newyorkensis) and Listeria rustica sp. nov. (type strain FSL W9-0585T=CCUG 74665T=LMG 31922T; maximum ANI value of 88.7 % to L. cornellensis and 88.9 % to L. newyorkensis). L. immobilis is the first sensu stricto species isolated to date that is non-motile. All five of the novel species are non-haemolytic and negative for phosphatidylinositol-specific phospholipase C activity; the draft genomes lack the virulence genes found in Listeria pathogenicity island 1 (LIPI-1), and the internalin genes inlA and inlB, indicating that they are non-pathogenic.
Collapse
Affiliation(s)
| | - Jingqiu Liao
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
- Present address: Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Dan Weller
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
- Present address: Department of Environmental and Forest Biology, SUNY College of Environmental Science and Forestry, Syracuse NY 13210, USA
| | - Xiaodong Guo
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Renato Orsi
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| |
Collapse
|
43
|
Loeffler JR, Fernández-Quintero ML, Waibl F, Quoika PK, Hofer F, Schauperl M, Liedl KR. Conformational Shifts of Stacked Heteroaromatics: Vacuum vs. Water Studied by Machine Learning. Front Chem 2021; 9:641610. [PMID: 33842433 PMCID: PMC8032969 DOI: 10.3389/fchem.2021.641610] [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: 12/14/2020] [Accepted: 03/08/2021] [Indexed: 11/13/2022] Open
Abstract
Stacking interactions play a crucial role in drug design, as we can find aromatic cores or scaffolds in almost any available small molecule drug. To predict optimal binding geometries and enhance stacking interactions, usually high-level quantum mechanical calculations are performed. These calculations have two major drawbacks: they are very time consuming, and solvation can only be considered using implicit solvation. Therefore, most calculations are performed in vacuum. However, recent studies have revealed a direct correlation between the desolvation penalty, vacuum stacking interactions and binding affinity, making predictions even more difficult. To overcome the drawbacks of quantum mechanical calculations, in this study we use neural networks to perform fast geometry optimizations and molecular dynamics simulations of heteroaromatics stacked with toluene in vacuum and in explicit solvation. We show that the resulting energies in vacuum are in good agreement with high-level quantum mechanical calculations. Furthermore, we show that using explicit solvation substantially influences the favored orientations of heteroaromatic rings thereby emphasizing the necessity to include solvation properties starting from the earliest phases of drug design.
Collapse
Affiliation(s)
- Johannes R Loeffler
- Center of Molecular Biosciences Innsbruck, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Monica L Fernández-Quintero
- Center of Molecular Biosciences Innsbruck, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Franz Waibl
- Center of Molecular Biosciences Innsbruck, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Patrick K Quoika
- Center of Molecular Biosciences Innsbruck, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Florian Hofer
- Center of Molecular Biosciences Innsbruck, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Michael Schauperl
- Center of Molecular Biosciences Innsbruck, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Klaus R Liedl
- Center of Molecular Biosciences Innsbruck, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| |
Collapse
|
44
|
Lian FB, Jiang S, Ren TY, Zhou BJ, Du ZJ. Thalassotalea algicola sp. nov., an alginate-utilizing bacterium isolated from a red alga. Antonie Van Leeuwenhoek 2021; 114:835-44. [PMID: 33774759 DOI: 10.1007/s10482-021-01562-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 03/15/2021] [Indexed: 10/21/2022]
Abstract
A facultatively anaerobic bacterium, strain M1531T, was isolated from a red alga (Porphyra) at coastal water in Weihai, China. Cells of the novel strain were Gram-stain-negative, rod-shaped, motile by means of a single polar flagellum and around 0.6-0.8 × 2.0-3.0 µm in size. Optimum growth occurred at 30 °C, with 2% (w/v) NaCl and at pH 6.5-7.0. On the basis of the result of phylogenetic analysis of the 16S rRNA gene sequence, stain M1531T had close relative with Thalassotalea euphylliae KCTC 42743T (96.9%). Genome sequencing revealed a genome size of 4,061,950 bp, a G + C content of 39.1 mol% and four protein-coding genes related to the degradation of alginate. According to the data obtained, strain M1531T shared ANI value below 95-96%, dDDH value below 23.8% with the closely related type species. Strain M1531T had Q-8 as the predominant isoprenoid quinone and possessed Summed Features 3 (C16:1 ω7c/C16:1 ω6c), C16:0 and Summed Features 8 (C18:1 ω7c/C18:1 ω6c) as the major fatty acids. The polar lipids of strain M1531T were identified as phosphatidylglycerol, phosphatidylethanolamine, one unidentified phospholipid, one unidentified aminolipid and four unidentified lipids. According to the results of the phenotypic, chemotaxonomic characterization, phylogenetic properties and genome analysis, strain M1531T represents a novel specie of the genus Thalassotalea, for which the name Thalassotalea algicola sp. nov. is proposed. The type strain is M1531T (= MCCC 1H00400T = KCTC 72865T).
Collapse
|
45
|
Volpiano CG, Sant'Anna FH, Ambrosini A, de São José JFB, Beneduzi A, Whitman WB, de Souza EM, Lisboa BB, Vargas LK, Passaglia LMP. Genomic Metrics Applied to Rhizobiales ( Hyphomicrobiales): Species Reclassification, Identification of Unauthentic Genomes and False Type Strains. Front Microbiol 2021; 12:614957. [PMID: 33841347 PMCID: PMC8026895 DOI: 10.3389/fmicb.2021.614957] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [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: 10/07/2020] [Accepted: 03/04/2021] [Indexed: 12/13/2022] Open
Abstract
Taxonomic decisions within the order Rhizobiales have relied heavily on the interpretations of highly conserved 16S rRNA sequences and DNA–DNA hybridizations (DDH). Currently, bacterial species are defined as including strains that present 95–96% of average nucleotide identity (ANI) and 70% of digital DDH (dDDH). Thus, ANI values from 520 genome sequences of type strains from species of Rhizobiales order were computed. From the resulting 270,400 comparisons, a ≥95% cut-off was used to extract high identity genome clusters through enumerating maximal cliques. Coupling this graph-based approach with dDDH from clusters of interest, it was found that: (i) there are synonymy between Aminobacter lissarensis and Aminobacter carboxidus, Aurantimonas manganoxydans and Aurantimonas coralicida, “Bartonella mastomydis,” and Bartonella elizabethae, Chelativorans oligotrophicus, and Chelativorans multitrophicus, Rhizobium azibense, and Rhizobium gallicum, Rhizobium fabae, and Rhizobium pisi, and Rhodoplanes piscinae and Rhodoplanes serenus; (ii) Chelatobacter heintzii is not a synonym of Aminobacter aminovorans; (iii) “Bartonella vinsonii” subsp. arupensis and “B. vinsonii” subsp. berkhoffii represent members of different species; (iv) the genome accessions GCF_003024615.1 (“Mesorhizobium loti LMG 6125T”), GCF_003024595.1 (“Mesorhizobium plurifarium LMG 11892T”), GCF_003096615.1 (“Methylobacterium organophilum DSM 760T”), and GCF_000373025.1 (“R. gallicum R-602 spT”) are not from the genuine type strains used for the respective species descriptions; and v) “Xanthobacter autotrophicus” Py2 and “Aminobacter aminovorans” KCTC 2477T represent cases of misuse of the term “type strain”. Aminobacter heintzii comb. nov. and the reclassification of Aminobacter ciceronei as A. heintzii is also proposed. To facilitate the downstream analysis of large ANI matrices, we introduce here ProKlust (“Prokaryotic Clusters”), an R package that uses a graph-based approach to obtain, filter, and visualize clusters on identity/similarity matrices, with settable cut-off points and the possibility of multiple matrices entries.
Collapse
Affiliation(s)
- Camila Gazolla Volpiano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Fernando Hayashi Sant'Anna
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Adriana Ambrosini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Anelise Beneduzi
- Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria Estadual da Agricultura, Pecuária e Desenvolvimento Rural, Porto Alegre, Brazil
| | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, GA, United States
| | - Emanuel Maltempi de Souza
- Departamento de Bioquímica e Biologia Molecular, Centro Politécnico, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Brazil
| | - Bruno Brito Lisboa
- Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria Estadual da Agricultura, Pecuária e Desenvolvimento Rural, Porto Alegre, Brazil
| | - Luciano Kayser Vargas
- Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria Estadual da Agricultura, Pecuária e Desenvolvimento Rural, Porto Alegre, Brazil
| | | |
Collapse
|
46
|
Lian FB, Chen XY, Jiang S, Li GY, Du ZJ. Marinobacter orientalis sp. nov., a thiosulfate-oxidizing bacterium isolated from a marine solar saltern. Antonie Van Leeuwenhoek 2021; 114:765-775. [PMID: 33751321 DOI: 10.1007/s10482-021-01556-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 10/22/2020] [Accepted: 03/06/2021] [Indexed: 11/25/2022]
Abstract
A facultatively anaerobic bacterium, strain W62T, was isolated from the marine solar saltern in Weihai, China. Cells of the novel strain were Gram-stain negative, non-flagellated, non-gliding, rod-shaped and around 0.3-0.5 × 2.5-3.9 µm in size. Optimum growth occurred at 33-37 °C, with 3-5% (w/v) NaCl and at pH 7.0-7.5. On the basis of phylogenetic analysis of the 16S rRNA gene sequence, strain W62T had close relationship with Marinobacter vulgaris F01T (98.6%), Marinobacter confluentis KCTC 42705T (98.4%) and Marinobacter halotolerans NBRC 110910T (97.7%). Genome sequencing revealed a genome size of 4,050,555 bp, a G+C content of 57.3% and a complete sox system related to thiosulfate oxidization. Strain W62T had ubiquinone-9 as the sole respiratory quinone and possessed Summed Features 3 (C16:1 ω7c/C16:1 ω6c), C16:0 and C18:1 ω9c as the major fatty acids. The major polar lipids of strain W62T were identified as aminophospholipid, phosphatidylglycerol and phosphatidylethanolamine. According to the results of the phenotypic, chemotaxonomic characterization, phylogenetic properties and genome analysis, strain W62T should represent a novel specie of the genus Marinobacter, for which the name Marinobacter orientalis sp. nov. is proposed. The type strain is W62T (= MCCC 1H00317T = KCTC 62593T).
Collapse
Affiliation(s)
- Feng-Bai Lian
- Marine College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - Xu-Yang Chen
- Marine College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - Shan Jiang
- Marine College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - Guang-Yu Li
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, Fujian, People's Republic of China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, 264209, Shandong, People's Republic of China.
| |
Collapse
|
47
|
Graça R, Lobo FA. Analgesia Nociception Index ( ANI) and ephedrine: a dangerous liasion. J Clin Monit Comput 2021; 35:953-4. [PMID: 33730304 DOI: 10.1007/s10877-021-00682-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 10/21/2022]
Abstract
The Analgesia Nociception Index is a dimensionless scale derived from the heart rate variability; by analyzing the heart rate variability oscillations, it reflects the activity of the sympathetic and parasympathetic nervous systems and ultimately helps to evaluate the Nociception-Antinociception balance during anesthesia and surgery. Drugs like ephedrine affect the heart rate variability inducing artifacts in the ANI readings which should be taken into account in the clinical practice and in clinical research.
Collapse
|
48
|
Abstract
A facultatively anaerobic bacterium, strain S0837T, was isolated from the marine sediment of Jingzi Wharf, Weihai, China. Cells of the novel strain were Gram-stain-negative, non-flagellated, non-gliding, non-pigmented and rod-shaped. Cells were around 0.3-0.5×1.0-1.4 µm in size and often appeared singly. Optimum growth occurred at 33 °C, with 2 % (w/v) NaCl and at pH 7.0-7.5. On the basis of the results of 16S rRNA gene sequences, stain S0837T had the closest relative with Sulfitobacter delicatus KCTC 32183T (98.0 %). Genome sequencing revealed a genome size of 3 785 026 bp, a G+C content of 59.8 mol% and several genes related with sulphur oxidation. The strain shared 98.0 % 16S rRNA sequence similarities with closely related type species and shared ANI value below 95-96 %, dDDH value of showed relatedness of 27.4, 25.2 and 25.2 % respectively with the closely related type species. Strain S0837T had ubiquinone-10 as the sole respiratory quinone, and possessed summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c) as the major fatty acid. The major polar lipids were phosphatidylglycerol, phosphatidylcholine and phosphatidylethanolamine. According to the results of the phenotypic, chemotaxonomic characterization, phylogenetic properties and genome analysis, strain S0837T should represent a novel species of the genus Sulfitobacter, for which the name Sulfitobacter maritimus sp. nov. is proposed. The type strain is S0837T (=MCCC 1K04635T=KCTC 72860T).
Collapse
Affiliation(s)
- Feng-Bai Lian
- Marine College, Shandong University, Weihai 264209, Shandong, PR China
| | - Yong-Qin Li
- Life Science and Technology School, Lingnan Normal University, Zhanjiang 524048, Guangdong, PR China
| | - Jing Zhang
- Marine College, Shandong University, Weihai 264209, Shandong, PR China
| | - Shan Jiang
- Marine College, Shandong University, Weihai 264209, Shandong, PR China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai 264209, Shandong, PR China
| |
Collapse
|
49
|
Bijlani S, Singh NK, Eedara VVR, Podile AR, Mason CE, Wang CCC, Venkateswaran K. Methylobacterium ajmalii sp. nov., Isolated From the International Space Station. Front Microbiol 2021; 12:639396. [PMID: 33790880 PMCID: PMC8005752 DOI: 10.3389/fmicb.2021.639396] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [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: 12/08/2020] [Accepted: 02/22/2021] [Indexed: 11/22/2022] Open
Abstract
Four strains belonging to the family of Methylobacteriaceae were isolated from different locations on the International Space Station (ISS) across two consecutive flights. Of these, three were identified as Gram-negative, rod-shaped, catalase-positive, oxidase-positive, motile bacteria, designated as IF7SW-B2T, IIF1SW-B5, and IIF4SW-B5, whereas the fourth was identified as Methylorubrum rhodesianum. The sequence similarity of these three ISS strains, designated as IF7SW-B2T, IIF1SW-B5, and IIF4SW-B5, was <99.4% for 16S rRNA genes and <97.3% for gyrB gene, with the closest being Methylobacterium indicum SE2.11T. Furthermore, the multi-locus sequence analysis placed these three ISS strains in the same clade of M. indicum. The average nucleotide identity (ANI) values of these three ISS strains were <93% and digital DNA-DNA hybridization (dDDH) values were <46.4% with any described Methylobacterium species. Based on the ANI and dDDH analyses, these three ISS strains were considered as novel species belonging to the genus Methylobacterium. The three ISS strains showed 100% ANI similarity and dDDH values with each other, indicating that these three ISS strains, isolated during various flights and from different locations, belong to the same species. These three ISS strains were found to grow optimally at temperatures from 25 to 30°C, pH 6.0 to 8.0, and NaCl 0 to 1%. Phenotypically, these three ISS strains resemble M. aquaticum and M. terrae since they assimilate similar sugars as sole carbon substrate when compared to other Methylobacterium species. Fatty acid analysis showed that the major fatty acid produced by the ISS strains are C18:1−ω7c and C18:1−ω6c. The predominant quinone was ubiquinone 10, and the major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, and an unidentified lipid. Therefore, based on genomic, phylogenetic, biochemical, and fatty acid analyses, strains IF7SW-B2T, IIF1SW-B5, and IIF4SW-B5, are assigned to a novel species within the genus Methylobacterium, and the name Methylobacterium ajmalii sp. nov. is proposed. The type strain is IF7SW-B2T (NRRL B-65601T and LMG 32165T).
Collapse
Affiliation(s)
- Swati Bijlani
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
| | - Nitin K Singh
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - V V Ramprasad Eedara
- Department of Plant Science, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Appa Rao Podile
- Department of Plant Science, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Christopher E Mason
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, United States
| | - Clay C C Wang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
| | - Kasthuri Venkateswaran
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| |
Collapse
|
50
|
Maiti PK, Mandal S. Streptomyces himalayensis sp. nov. including Streptomyces himalayensis subsp. himalayensis subsp. nov. and Streptomyces himalayensis subsp. aureolus subsp. nov. isolated from Western Himalaya. Arch Microbiol 2021; 203:2325-2334. [PMID: 33649903 DOI: 10.1007/s00203-021-02232-7] [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: 08/18/2020] [Revised: 01/25/2021] [Accepted: 02/11/2021] [Indexed: 12/27/2022]
Abstract
Two novel actinobacteria, strain PSKA28T and PSKA54T were isolated from soil sample of Kashmir-Himalaya, India (latitude 34°-01' N; longitude 74°-47' E; altitude 5328 ft). Polyphasic-taxonomic analysis revealed that these strains belong to the genus Streptomyces. The 16S rRNA gene-sequence similarity of these strain were highest (98.6%) with that of the Streptomyces torulosus NRRLB-3889T. They showed 92.1% gyrB gene-sequence similarity but 92.9 and 94.6% rpoB gene-sequence similarity, respectively, with Streptomyces torulosus NRRLB-3889T. The sequence similarities were significantly lower than the recommended threshold value for novel taxonomic position and the 16S rRNA sequence-based phylogenetic analysis indicated that these two isolates are in distinct clade. Phylogenomic analysis with their genome sequences, conferred by Type Strain Genome Server separated them from rest of the Streptomyces type strains. The cell wall contained LL-diaminopimelic acid and the whole-cell hydrolysate contained glucose and ribose. Major fatty acid methyl esters were 15:0 anteiso, 16:0 iso and 17:0 anteiso. Average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization (dDDH) values as well as evolutionary distance based on multilocus sequence analysis, between closely related type strains and either of the strain PSKA28T or PSKA54T, were considerably lower than the recommended threshold value (< 70% dDDH or < 95-96% ANI/AAI or > 0.007 MLSA distance). Therefore, these isolates represent a novel Streptomyces species, for which we proposed the name Streptomyces himalayensis sp. nov. Genotypic and phenotypic analyses clearly split these strains into two closely related sub-clusters. Based on this, two novel subspecies Streptomyces himalayensis subsp. himalayensis subsp. nov. and Streptomyces himalayensis subsp. aureolus subsp. nov. are proposed, with type strains JCM33755T (= MTCC12933T, MCC4145T) and JCM33759T (= MTCC12938, MCC4180), respectively.
Collapse
Affiliation(s)
- Pulak Kumar Maiti
- Department of Microbiology, Laboratory of Molecular Bacteriology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
| | - Sukhendu Mandal
- Department of Microbiology, Laboratory of Molecular Bacteriology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India.
| |
Collapse
|