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Update on Novel Taxa and Revised Taxonomic Status of Bacteria Isolated from Nondomestic Animals Described in 2018 to 2021. J Clin Microbiol 2023; 61:e0142522. [PMID: 36533958 PMCID: PMC9945507 DOI: 10.1128/jcm.01425-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Revisions and new additions to bacterial taxonomy can have a significant widespread impact on clinical practice, infectious disease epidemiology, veterinary microbiology laboratory operations, and wildlife conservation efforts. The expansion of genome sequencing technologies has revolutionized our knowledge of the microbiota of humans, animals, and insects. Here, we address novel taxonomy and nomenclature revisions of veterinary significance that impact bacteria isolated from nondomestic wildlife, with emphasis being placed on bacteria that are associated with disease in their hosts or were isolated from host animal species that are culturally significant, are a target of conservation efforts, or serve as reservoirs for human pathogens.
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2
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Rudra B, Gupta RS. Phylogenomic and comparative genomic analyses of species of the family Pseudomonadaceae: Proposals for the genera Halopseudomonas gen. nov. and Atopomonas gen. nov., merger of the genus Oblitimonas with the genus Thiopseudomonas, and transfer of some misclassified species of the genus Pseudomonas into other genera. Int J Syst Evol Microbiol 2021; 71. [PMID: 34546867 DOI: 10.1099/ijsem.0.005011] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The evolutionary relationships among species of the family Pseudomonadaceae were examined based on 255 available genomes representing >85 % of the species from this family. In a phylogenetic tree based on concatenated sequences of 118 core proteins, most species of the genus Pseudomonas grouped within one large cluster which also included members of the genera Azotobacter and Azomonas. Within this large cluster 18-30 clades/subclades of species of the genus Pseudomonas consisting of between 1 and 36 species, were observed. However, a number of species of the genus Pseudomonas branched outside of this main cluster and were interspersed among other genera of the family Pseudomonadaceae. This included a strongly supported clade (Pertucinogena clade) consisting of 19 mainly halotolerant species. The distinctness of this clade from all other members of the family Pseudomonadaceae is strongly supported by 24 conserved signature indels (CSIs) in diverse proteins that are exclusively found in all members of this clade. Nine uncharacterized members of the genus Pseudomonas also shared these CSIs and they branched within the Pertucinogena clade, indicating their affiliation to this clade. On the basis of the strong evidence supporting the distinctness of the Pertucinogena clade, we are proposing transfer of species from this clade into a novel genus Halopseudomonas gen. nov. Pseudomonas caeni also branches outside of the main cluster and groups reliably with Oblitimonas alkaliphila and Thiopseudomonas denitrificans. Six identified CSIs are uniquely shared by these three species and we are proposing their integration into the emended genus Thiopseudomonas, which has priority over the name Oblitimonas. We are also proposing transfer of the deep-branching Pseudomonas hussainii, for which 22 exclusive CSIs have been identified, into the genus Atopomonas gen. nov. Lastly, we present strong evidence that the species Pseudomonas cissicola and Pseudomonas geniculata are misclassified into the genus Pseudomonas and that they are specifically related to the genera Xanthomonas and Stenotrophomonas, respectively. In addition, we are also reclassifying 'Pseudomonas acidophila' as Paraburkholderia acidicola sp. nov. (Type strain: G-6302=ATCC 31363=BCRC 13035).
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Affiliation(s)
- Bashudev Rudra
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
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Saati-Santamaría Z, Peral-Aranega E, Velázquez E, Rivas R, García-Fraile P. Phylogenomic Analyses of the Genus Pseudomonas Lead to the Rearrangement of Several Species and the Definition of New Genera. BIOLOGY 2021; 10:782. [PMID: 34440014 PMCID: PMC8389581 DOI: 10.3390/biology10080782] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 08/03/2021] [Accepted: 08/11/2021] [Indexed: 11/17/2022]
Abstract
Pseudomonas is a large and diverse genus broadly distributed in nature. Its species play relevant roles in the biology of earth and living beings. Because of its ubiquity, the number of new species is continuously increasing although its taxonomic organization remains quite difficult to unravel. Nowadays the use of genomics is routinely employed for the analysis of bacterial systematics. In this work, we aimed to investigate the classification of species of the genus Pseudomonas on the basis of the analyses of the type strains whose genomes are currently available. Based on these analyses, we propose the creation of three new genera (Denitrificimonas gen nov. comb. nov., Neopseudomonas gen nov. comb. nov. and Parapseudomonas gen nov. comb. nov) to encompass several species currently included within the genus Pseudomonas and the reclassification of several species of this genus in already described taxa.
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Affiliation(s)
- Zaki Saati-Santamaría
- Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain; (E.P.-A.); (E.V.); (R.R.); (P.G.-F.)
- Institute for Agribiotechnology Research (CIALE), 37185 Salamanca, Spain
| | - Ezequiel Peral-Aranega
- Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain; (E.P.-A.); (E.V.); (R.R.); (P.G.-F.)
- Institute for Agribiotechnology Research (CIALE), 37185 Salamanca, Spain
| | - Encarna Velázquez
- Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain; (E.P.-A.); (E.V.); (R.R.); (P.G.-F.)
- Institute for Agribiotechnology Research (CIALE), 37185 Salamanca, Spain
- Associated Research Unit of Plant-Microorganism Interaction, University of Salamanca-IRNASA-CSIC, 37008 Salamanca, Spain
| | - Raúl Rivas
- Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain; (E.P.-A.); (E.V.); (R.R.); (P.G.-F.)
- Institute for Agribiotechnology Research (CIALE), 37185 Salamanca, Spain
- Associated Research Unit of Plant-Microorganism Interaction, University of Salamanca-IRNASA-CSIC, 37008 Salamanca, Spain
| | - Paula García-Fraile
- Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain; (E.P.-A.); (E.V.); (R.R.); (P.G.-F.)
- Institute for Agribiotechnology Research (CIALE), 37185 Salamanca, Spain
- Associated Research Unit of Plant-Microorganism Interaction, University of Salamanca-IRNASA-CSIC, 37008 Salamanca, Spain
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Philippon T, Tian J, Bureau C, Chaumont C, Midoux C, Tournebize J, Bouchez T, Barrière F. Denitrifying bio-cathodes developed from constructed wetland sediments exhibit electroactive nitrate reducing biofilms dominated by the genera Azoarcus and Pontibacter. Bioelectrochemistry 2021; 140:107819. [PMID: 33894567 DOI: 10.1016/j.bioelechem.2021.107819] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/24/2021] [Accepted: 04/01/2021] [Indexed: 10/21/2022]
Abstract
To limit the nitrate contamination of ground and surface water, stimulation of denitrification by electrochemical approach is an innovative way to be explored. Two nitrate reducing bio-cathodes were developed under constant polarization (-0.5 V vs SCE) using sediments and water from a constructed wetland (Rampillon, Seine-et-Marne, France). The bio-cathodes responded to nitrate addition on chronoamperometry through an increase of the reductive current. The denitrification efficiency of the pilots increased by 47% compared to the negative controls without electrodes after polarization. 16S rRNA gene sequencing of the biofilms and sediments evidenced the significant and discriminating presence of the Azoarcus and Pontibacter genera in the biofilms from biocathodes active for nitrate reduction. Our study shows the possibility to promote the development of efficient Azoarcus-dominated biocathodes from freshwater sediment to enhance nitrate removal from surface waters.
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Affiliation(s)
- Timothé Philippon
- Univ Rennes, CNRS, Institut des Sciences Chimiques de Rennes, 35042 Rennes, France.
| | - Jianghao Tian
- Université Paris-Saclay, INRAE, UR PROSE, 92160 Antony, France
| | | | - Cédric Chaumont
- Université Paris-Saclay, INRAE, UR HYCAR, 92160 Anthony, France
| | - Cédric Midoux
- Université Paris-Saclay, INRAE, UR PROSE, 92160 Antony, France
| | | | | | - Frédéric Barrière
- Univ Rennes, CNRS, Institut des Sciences Chimiques de Rennes, 35042 Rennes, France.
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Maity JP, Huang YH, Lin HF, Chen CY. Variation of Microbial Diversity in Catastrophic Oil Spill Area in Marine Ecosystem and Hydrocarbon Degradation of UCMs (Unresolved Complex Mixtures) by Marine Indigenous Bacteria. Appl Biochem Biotechnol 2020; 193:1266-1283. [PMID: 32445124 DOI: 10.1007/s12010-020-03335-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 04/23/2020] [Indexed: 11/29/2022]
Abstract
The study targeted an assessment of microbial diversity during oil spill in the marine ecosystem (Kaohsiung port, Taiwan) and screened dominant indigenous bacteria for oil degradation, as well as UCM weathering. DO was detected lower and TDS/conductivity was observed higher in oil-spilled area, compared to the control, where a significant correlation (R2 = 1; P < 0.0001) was noticed between DO and TDS. The relative abundance (RA) of microbial taxa and diversities (> 90% similarity by NGS) were found higher in the boundary region of spilled-oily-water (site B) compared to the control (site C) and center of the oil spill area (site A) (BRA/diversity > CRA/diversity > ARA/diversity). The isolated indigenous bacteria, such as Staphylococcus saprophyticus (CYCTW1), Staphylococcus saprophyticus (CYCTW2), and Bacillus megaterium (CYCTW3) degraded the C10-C30 including UCM of oil, where Bacillus sp. are exhibited more efficient, which are applicable for environmental cleanup of the oil spill area. Thus, the marine microbial diversity changes due to oil spill and the marine microbial community play an important role to biodegrade the oil, besides restoring the catastrophic disorders through changing their diversity by ecological selection and adaptation process.
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Affiliation(s)
- Jyoti Prakash Maity
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Ming-Shung, Chiayi County, 62102, Taiwan.,School of Civil Engineering and Surveying and International Centre for Applied Climate Science, University of Southern Queensland, Toowoomba, Australia
| | - Yi-Hsun Huang
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Ming-Shung, Chiayi County, 62102, Taiwan
| | - Hsien-Feng Lin
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Ming-Shung, Chiayi County, 62102, Taiwan
| | - Chien-Yen Chen
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Ming-Shung, Chiayi County, 62102, Taiwan. .,Center for Innovative Research on Aging Society, AIM-HI, National Chung Cheng University, 168, University Rd., Min-Hsiung, Chiayi, 62102, Taiwan.
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Ye Y, Chen C, Ren Y, Wang R, Zhang C, Han S, Ju Z, Zhao Z, Sun C, Wu M. Pseudomonas mangrovi sp. nov., isolated from mangrove soil. Int J Syst Evol Microbiol 2019; 69:377-383. [PMID: 30601113 DOI: 10.1099/ijsem.0.003141] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, non-motile, short-rod-shaped bacterium, designated as strain TC11T, was isolated from rhizosphere soil of mangrove forest (Kandeliaobovata) in Fugong village, Zhangzhou, Fujian, China. Strain TC11T grew at 15-45 °C (optimum, 35 °C), 0-8 % (w/v) NaCl (optimum, 1 %, w/v) and pH 5.5-9.5 (optimum, pH 7.5). Phylogenetic analyses revealed that strain TC11T belonged to a clade of the genus Pseudomonas and showed the highest sequence similarity of 98.4 % to Pseudomonas fluvialis ASS-1T, followed by Pseudomonas oleovorans subsp.oleovorans DSM 1045T (97.9 %), Pseudomonas indoloxydans JCM 14246T (97.7 %), Pseudomonas guguanensis JCM 18416T(97.6 %) and Pseudomonas alcaliphila JCM 10630T (97.5 %) on the basis of their 16S rRNA gene sequences. The DNA G+C content was 64.3 mol%. In silico DNA-DNA hybridization and average nucleotide identity values between strain TC11T and the reference strains were 19-22 % and 72-78 %, respectively. Studies based on the three housekeeping genes, rpoB, gyrB and rpoD, further confirmed that strain TC11T is a novel member of the genus Pseudomonas. The major fatty acids of strain TC11Twere C16 : 0, summed feature 8 (C18 : 1ω6c/C18 : 1ω7c) and summed feature 3 (C16 : 1ω7c/C16 : 1ω6c). The sole isoprenoid quinone was Q-9. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Based on the phenotypic, chemotaxonomic and phylogenetic properties, strain TC11T represents a novel species of the genus Pseudomonas, for which the name Pseudomonasmangrovi sp. nov., is proposed. The type strain is TC11T (=KCTC 62159=MCCC 1K03499).
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Affiliation(s)
- Yanghui Ye
- 1Ocean College, Zhejiang University, Zhoushan 316000, PR China
| | - Can Chen
- 1Ocean College, Zhejiang University, Zhoushan 316000, PR China
| | - Yanhu Ren
- 1Ocean College, Zhejiang University, Zhoushan 316000, PR China
| | - Ruijun Wang
- 1Ocean College, Zhejiang University, Zhoushan 316000, PR China
| | - Chongya Zhang
- 1Ocean College, Zhejiang University, Zhoushan 316000, PR China
| | - Shuaibo Han
- 2College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Zhao Ju
- 2College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Zhu Zhao
- 2College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Cong Sun
- 3College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Min Wu
- 1Ocean College, Zhejiang University, Zhoushan 316000, PR China
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Solaiman DK, Ashby RD, Aneja KK, Crocker NV, Liu Y. Galacto-oligosaccharide hydrolysis by genetically-engineered alpha-galactosidase-producing Pseudomonas chlororaphis strains. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2018. [DOI: 10.1016/j.bcab.2017.12.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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8
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The current status on the taxonomy of Pseudomonas revisited: An update. INFECTION GENETICS AND EVOLUTION 2017; 57:106-116. [PMID: 29104095 DOI: 10.1016/j.meegid.2017.10.026] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 10/28/2017] [Accepted: 10/30/2017] [Indexed: 12/20/2022]
Abstract
The genus Pseudomonas described in 1894 is one of the most diverse and ubiquitous bacterial genera which encompass species isolated worldwide. In the last years more than 70 new species have been described, which were isolated from different environments, including soil, water, sediments, air, animals, plants, fungi, algae, compost, human and animal related sources. Some of these species have been isolated in extreme environments, such as Antarctica or Atacama desert, and from contaminated water or soil. Also, some species recently described are plant or animal pathogens. In this review, we revised the current status of the taxonomy of genus Pseudomonas and the methodologies currently used for the description of novel species which includes, in addition to the classic ones, new methodologies such as MALDI-TOF MS, MLSA and genome analyses. The novel Pseudomonas species described in the last years are listed, together with the available genome sequences of the type strains of Pseudomonas species present in different databases.
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Draft Genome Sequence of Pseudomonas hussainii Strain MB3, a Denitrifying Aerobic Bacterium Isolated from the Rhizospheric Region of Mangrove Trees in the Andaman Islands, India. GENOME ANNOUNCEMENTS 2017; 5:5/5/e01527-16. [PMID: 28153890 PMCID: PMC5289676 DOI: 10.1128/genomea.01527-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The genome sequence of Pseudomonas hussainii MB3, isolated from the rhizospheric region of mangroves in the Andaman Islands, is comprised of 3,644,788 bp and 3,159 protein coding genes. Draft genome analysis indicates that MB3 is an aerobic bacterium capable of performing assimilatory sulfate reduction, dissimilatory nitrate reduction, and denitrification.
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10
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Lin SY, Hameed A, Hung MH, Liu YC, Hsu YH, Young LS, Young CC. Pseudomonas matsuisoli sp. nov., isolated from a soil sample. Int J Syst Evol Microbiol 2015; 65:902-909. [DOI: 10.1099/ijs.0.000035] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An aerobic, Gram-stain-negative, rod-shaped and polar-flagellated bacterium, designated strain CC-MHH0089T, was isolated from a soil sample taken on Matsu Island (Taiwan). Strain CC-MHH0089T grew at 15–30 °C and pH 5.0–10.0 and tolerated ≤8 % (w/v) NaCl. 16S rRNA gene sequence analysis showed high pairwise sequence similarity to
Pseudomonas azotifigens
6H33bT (97.3 %) and
Pseudomonas balearica
SP1402T (96.7 %) and lower sequence similarity to other strains (<96.0 %). In DNA–DNA reassociation experiments, the relatedness of strain CC-MHH0089T to
P. azotifigens
JCM 12708T was 38.3 % (reciprocal value 19.5 %). Evolutionary trees reconstructed on the basis of 16S rRNA, gyrB and rpoB gene sequences revealed a varying phylogenetic neighbourhood of strain CC-MHH0089T with regard to the most closely related type strains. The predominant quinone system was ubiquinone 9 (Q-9) and the DNA G+C content was 63.6 mol%. The major fatty acids were C12 : 0, C16 : 0, C17 : 0, C19 : 0 cyclo ω8c and summed features 2 (C14 : 0 3-OH/iso-C16 : 1 I), 3 (C16 : 1ω7c/C16 : 1ω6c) and 8 (C18 : 1ω7c/C18 : 1ω6c). The major polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and diphosphatidylglycerol. According to its distinct phylogenetic, phenotypic and chemotaxonomic features, strain CC-MHH0089T is proposed to represent a novel species within the genus
Pseudomonas
, for which the name Pseudomonas matsuisoli sp. nov. is proposed. The type strain is CC-MHH0089T ( = BCRC 80771T = JCM 30078T).
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Affiliation(s)
- Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
| | - Asif Hameed
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
| | - Mei-Hua Hung
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
| | - You-Cheng Liu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
| | - Yi-Han Hsu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
| | - Li-Sen Young
- Department of Biotechnology, College of Applied Arts and Sciences, National Formosa University, Yunlin, Taiwan
| | - Chiu-Chung Young
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
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