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Woo H, Chhetri G, Kim I, So Y, Park S, Jung Y, Seo T. Pedobacter rhodius sp. nov. and Pedobacter punctiformis sp. nov., isolated from soil. Antonie Van Leeuwenhoek 2024; 117:72. [PMID: 38671237 DOI: 10.1007/s10482-024-01963-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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 04/01/2024] [Indexed: 04/28/2024]
Abstract
Two Gram-staining negative, catalase- and oxidase-positive, pinkish-colored and rod-shaped strains, designated SJ11T and HCMS5-2 T, were isolated from soil in South Korea. The growth of strain SJ11T was observed from 15℃ to 35℃ (optimum, 30℃), from pH 6.0 to 11.0 (optimum, pH 6.0-7.0) and with NaCl 0-1% (w/v) (optimum, 0%) and that of strain HCMS5-2 T was observed from 4℃ to 40℃ (optimum, 25℃), from pH 6.0 to pH 8.0 (optimum, pH 7.0) and with NaCl 0-5% (w/v) (optimum, 0-1%). Phylogenetic analysis based on 16S rRNA gene sequences showed that both strains belonged to the genus Pedobacter. Strain SJ11T had the highest 16S rRNA similarities with Pedobacter jejuensis THG-DR3T (98.5%) and strain HCMS5-2 T had the highest similarities with Pedobacter nototheniae 36B243T (98.7%). The digital DNA-DNA hybridization value of strain SJ11T with Pedobacter jejuensis THG-DR3T was 23.6%, with an average nucleotide identity value of 79.6%, and that of strain HCMS5-2 T with Pedobacter nototheniae 36B243T was 26.4%, with an average nucleotide identity value of 83.1%. The predominant cellular fatty acids (> 10%) of SJ11T and HCMS5-2 T were iso-C15:0, summed feature 3 (comprising C16:1ω7c and/or C16:1ω6c) and iso-C17:0 3-OH. The genome size of strain SJ11T was approximately 4.7 Mb with a G + C content of 37.7% and that of strain HCMS5-2 T was approximately 4.1 Mb with a G + C content of 36.4%. The major polar lipid and respiratory quinone of SJ11T and HCMS5-2 T were phosphatidylethanolamine and menaquinone NK-7, respectively. Results of this study showed that strains SJ11T and HCMS5-2 T belonged to the genus Pedobacter as novel species, of which the name Pedobacter rhodius sp. nov., with the type strain SJ11T (= KACC 22884 T = TBRC 16597 T) and Pedobacter punctiformis sp. nov., with the type strain HCMS5-2 T (= KACC 22863 T = TBRC 16598 T) were respectively proposed.
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Affiliation(s)
- Haejin Woo
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Yoonseop So
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Sunho Park
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Yonghee Jung
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea.
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Chhetri G, Kim MJ, Kim I, Tran DVH, Kim YW, Kim HW, Seo T. Streptomyces tagetis sp. nov., a chromomycin producing bacteria isolated from the roots of Tagetes patula. Front Microbiol 2024; 15:1361583. [PMID: 38495511 PMCID: PMC10940327 DOI: 10.3389/fmicb.2024.1361583] [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: 12/26/2023] [Accepted: 02/08/2024] [Indexed: 03/19/2024] Open
Abstract
A novel halotolerant actinobacterium, designated as RG38T, capable of producing black extracellular melanin pigment on SP2 agar, was isolated from the roots of Tagetes patula. Comparative analysis of the 16S rRNA gene sequence revealed the highest similarity to Streptomyces collinus NBRC 12759T (99.3%). Phylogenetic analysis showed that strain RG38T clustered within the genus Streptomyces forming a monophyletic cluster with its close relatives. The average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and amino-acid identity (AAI) values between strain RG38T and related species within the genus Streptomyces were below the standard threshold for prokaryotic species delineation. The DNA G + C content of the strain RG38T was determined to be 73.3%. The genome size measured 7,150,598 bp comprising 17 contigs and encompassed 6,053 protein coding genes. AntiSMASH analysis of the whole genome revealed 35 putative biosynthetic gene clusters (BGCs) responsible for various secondary metabolites. Among these clusters, two gene clusters exhibited 100% similarity to the chromomycin A3, albaflavenone, and anthracimycin, respectively. These compounds were reported to possess significant anticancer and antibacterial activities. LC-MS-based analysis, coupled with further isolation studies, confirmed the production of chromomycins A2 (1), A3 (2), and their derivatives, along with their antibiotic activities. These findings underscore the potential of this novel strain as a novel resource for the discovery of diverse antimicrobial compounds. This study is the first to report an antimicrobial compound producing Streptomyces species isolated from medicinal plant T. patula. Based on a polyphasic study, the strain RG38T isolated from an unexplored habitat with a high potential for new natural products represents a novel species within the genus Streptomyces. Accordingly, we propose the name Streptomyces tagetis sp. nov. for this novel species, with the type strain is RG38T (=KCTC 49624T = TBRC 15113T).
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Affiliation(s)
- Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang, Republic of Korea
| | - Myeong Ji Kim
- College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Goyang, Republic of Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, Republic of Korea
| | - Duc V. H. Tran
- College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Goyang, Republic of Korea
| | - Young-Woo Kim
- College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Goyang, Republic of Korea
| | - Hyun Woo Kim
- College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Goyang, Republic of Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang, Republic of Korea
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Arnquist IJ, Avignone FT, Barabash AS, Barton CJ, Bhimani KH, Blalock E, Bos B, Busch M, Buuck M, Caldwell TS, Chan YD, Christofferson CD, Chu PH, Clark ML, Cuesta C, Detwiler JA, Efremenko Y, Ejiri H, Elliott SR, Giovanetti GK, Green MP, Gruszko J, Guinn IS, Guiseppe VE, Haufe CR, Henning R, Hervas Aguilar D, Hoppe EW, Hostiuc A, Kidd MF, Kim I, Kouzes RT, Lannen V TE, Li A, Lopez AM, López-Castaño JM, Martin EL, Martin RD, Massarczyk R, Meijer SJ, Mertens S, Oli TK, Othman G, Paudel LS, Pettus W, Poon AWP, Radford DC, Rager J, Reine AL, Rielage K, Ruof NW, Schaper DC, Tedeschi D, Varner RL, Vasilyev S, Wilkerson JF, Wiseman C, Xu W, Yu CH, Zhu BX. Exotic Dark Matter Search with the Majorana Demonstrator. Phys Rev Lett 2024; 132:041001. [PMID: 38335333 DOI: 10.1103/physrevlett.132.041001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/08/2023] [Accepted: 11/09/2023] [Indexed: 02/12/2024]
Abstract
With excellent energy resolution and ultralow-level radiogenic backgrounds, the high-purity germanium detectors in the Majorana Demonstrator enable searches for several classes of exotic dark matter (DM) models. In this work, we report new experimental limits on keV-scale sterile neutrino DM via the transition magnetic moment from conversion to active neutrinos ν_{s}→ν_{a}. We report new limits on fermionic dark matter absorption (χ+A→ν+A) and sub-GeV DM-nucleus 3→2 scattering (χ+χ+A→ϕ+A), and new exclusion limits for bosonic dark matter (axionlike particles and dark photons). These searches utilize the (1-100)-keV low-energy region of a 37.5-kg y exposure collected by the Demonstrator between May 2016 and November 2019 using a set of ^{76}Ge-enriched detectors whose surface exposure time was carefully controlled, resulting in extremely low levels of cosmogenic activation.
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Affiliation(s)
- I J Arnquist
- Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - F T Avignone
- Department of Physics and Astronomy, University of South Carolina, Columbia, South Carolina 29208, USA
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - A S Barabash
- National Research Center "Kurchatov Institute" Institute for Theoretical and Experimental Physics, Moscow 117218, Russia
| | - C J Barton
- Department of Physics, University of South Dakota, Vermillion, South Dakota 57069, USA
| | - K H Bhimani
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - E Blalock
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - B Bos
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - M Busch
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
- Department of Physics, Duke University, Durham, North Carolina 27708, USA
| | - M Buuck
- Center for Experimental Nuclear Physics and Astrophysics, and Department of Physics, University of Washington, Seattle, Washington 98195, USA
| | - T S Caldwell
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
| | - Y-D Chan
- Nuclear Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | | | - P-H Chu
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - M L Clark
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - C Cuesta
- Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas, CIEMAT 28040, Madrid, Spain
| | - J A Detwiler
- Center for Experimental Nuclear Physics and Astrophysics, and Department of Physics, University of Washington, Seattle, Washington 98195, USA
| | - Yu Efremenko
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37916, USA
| | - H Ejiri
- Research Center for Nuclear Physics, Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - S R Elliott
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - G K Giovanetti
- Physics Department, Williams College, Williamstown, Massachusetts 01267, USA
| | - M P Green
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - J Gruszko
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - I S Guinn
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - V E Guiseppe
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - C R Haufe
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - R Henning
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - D Hervas Aguilar
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - E W Hoppe
- Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - A Hostiuc
- Center for Experimental Nuclear Physics and Astrophysics, and Department of Physics, University of Washington, Seattle, Washington 98195, USA
| | - M F Kidd
- Tennessee Tech University, Cookeville, Tennessee 38505, USA
| | - I Kim
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - R T Kouzes
- Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - T E Lannen V
- Department of Physics and Astronomy, University of South Carolina, Columbia, South Carolina 29208, USA
| | - A Li
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - A M Lopez
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37916, USA
| | | | - E L Martin
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - R D Martin
- Department of Physics, Engineering Physics and Astronomy, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - R Massarczyk
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - S J Meijer
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - S Mertens
- Max-Planck-Institut für Physik, München 80805, Germany
- Physik Department and Excellence Cluster Universe, Technische Universität, München 85748, Germany
| | - T K Oli
- Department of Physics, University of South Dakota, Vermillion, South Dakota 57069, USA
| | - G Othman
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - L S Paudel
- Department of Physics, University of South Dakota, Vermillion, South Dakota 57069, USA
| | - W Pettus
- IU Center for Exploration of Energy and Matter, and Department of Physics, Indiana University, Bloomington, Indiana 47405, USA
| | - A W P Poon
- Nuclear Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - D C Radford
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - J Rager
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
| | - A L Reine
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - K Rielage
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - N W Ruof
- Center for Experimental Nuclear Physics and Astrophysics, and Department of Physics, University of Washington, Seattle, Washington 98195, USA
| | - D C Schaper
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - D Tedeschi
- Department of Physics and Astronomy, University of South Carolina, Columbia, South Carolina 29208, USA
| | - R L Varner
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - S Vasilyev
- Joint Institute for Nuclear Research, Dubna 141980, Russia
| | - J F Wilkerson
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - C Wiseman
- Center for Experimental Nuclear Physics and Astrophysics, and Department of Physics, University of Washington, Seattle, Washington 98195, USA
| | - W Xu
- Department of Physics, University of South Dakota, Vermillion, South Dakota 57069, USA
| | - C-H Yu
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - B X Zhu
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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Park S, Kim I, Chhetri G, Jung Y, Woo H, Seo T. Cellulomonas alba sp. nov. and Cellulomonas edaphi sp. nov., isolated from wetland soils. Int J Syst Evol Microbiol 2024; 74. [PMID: 38214698 DOI: 10.1099/ijsem.0.006235] [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: 01/13/2024] Open
Abstract
Two novel strains were isolated from wetland soils in Goyang, Republic of Korea. The two Gram-stain-positive, facultatively anaerobic, rod-shaped bacterial-type strains were designated MW4T and MW9T. Phylogenomic analysis based on whole-genome sequences suggested that both strains belonged to the genus Cellulomonas. The cells of strain MW4T were non-motile and grew at 20-40 °C (optimum, 35 °C), at pH 6.0-10.0 (optimum, pH 8.0) and in the presence of 0-1.0% NaCl (optimum, 0 %). The cells of strain MW9T were non-motile and grew at 20-40 °C (optimum, 35 °C), at pH 5.0-9.0 (optimum, pH 8.0) and in the presence of 0-1.0% NaCl (optimum, 0 %). The average nucleotide identity (77.1-88.1 %) and digital DNA-DNA hybridization values (21.0-34.8 %) between the two novel strains and with their closely related strains fell within the range for the genus Cellulomonas. The novel strains MW4T and MW9T and reference strains possessed alkane synthesis gene clusters (oleA, oleB, oleC and oleD). Phylogenomic, phylogenetic, average nucleotide identity, digital DNA-DNA hybridization, physiological and biochemical data indicated that the novel strains were distinct from other members of the family Cellulomonadaceae. We propose the names Cellulomonas alba sp. nov. (type strain MW4T=KACC 23260T=TBRC 17645T) and Cellulomons edaphi sp. nov. (type strain MW9T=KACC 23261T=TBRC 17646T) for the two strains.
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Affiliation(s)
- Sunho Park
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Yonghee Jung
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Haejin Woo
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
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Arnquist IJ, Avignone FT, Barabash AS, Barton CJ, Bhimani KH, Blalock E, Bos B, Busch M, Buuck M, Caldwell TS, Christofferson CD, Chu PH, Clark ML, Cuesta C, Detwiler JA, Efremenko Y, Ejiri H, Elliott SR, Giovanetti GK, Goett J, Green MP, Gruszko J, Guinn IS, Guiseppe VE, Haufe CR, Henning R, Hervas Aguilar D, Hoppe EW, Hostiuc A, Kim I, Kouzes RT, Lannen V TE, Li A, López-Castaño JM, Massarczyk R, Meijer SJ, Meijer W, Oli TK, Paudel LS, Pettus W, Poon AWP, Radford DC, Reine AL, Rielage K, Rouyer A, Ruof NW, Schaper DC, Schleich SJ, Smith-Gandy TA, Tedeschi D, Thompson JD, Varner RL, Vasilyev S, Watkins SL, Wilkerson JF, Wiseman C, Xu W, Yu CH, Alves DSM, Hebenstiel L, Ramani H. Constraints on the Decay of ^{180m}Ta. Phys Rev Lett 2023; 131:152501. [PMID: 37897780 DOI: 10.1103/physrevlett.131.152501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/15/2023] [Accepted: 09/12/2023] [Indexed: 10/30/2023]
Abstract
^{180m}Ta is a rare nuclear isomer whose decay has never been observed. Its remarkably long lifetime surpasses the half-lives of all other known β and electron capture decays due to the large K-spin differences and small energy differences between the isomeric and lower-energy states. Detecting its decay presents a significant experimental challenge but could shed light on neutrino-induced nucleosynthesis mechanisms, the nature of dark matter, and K-spin violation. For this study, we repurposed the Majorana Demonstrator, an experimental search for the neutrinoless double-beta decay of ^{76}Ge using an array of high-purity germanium detectors, to search for the decay of ^{180m}Ta. More than 17 kg, the largest amount of tantalum metal ever used for such a search, was installed within the ultralow-background detector array. In this Letter, we present results from the first year of Ta data taking and provide an updated limit for the ^{180m}Ta half-life on the different decay channels. With new limits up to 1.5×10^{19} yr, we improved existing limits by 1-2 orders of magnitude which are the most sensitive searches for a single β and electron capture decay ever achieved. Over all channels, the decay can be excluded for T_{1/2}<0.29×10^{18} yr.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - D S M Alves
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - L Hebenstiel
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
- IU Center for Exploration of Energy and Matter, and Department of Physics, Indiana University, Bloomington, Indiana 47405, USA
| | - H Ramani
- Stanford Institute for Theoretical Physics, Stanford University, Stanford, California 94305, USA
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So Y, Chhetri G, Kim I, Kim J, Park S, Jung Y, Seo T. Neoroseomonas alba sp. nov., Neoroseomonas nitratireducens sp. nov., Paraoseomonas indoligenes sp. nov and Paraoseomonas baculiformis sp. nov., isolated from the rhizosphere of paddy soil. Antonie Van Leeuwenhoek 2023; 116:1009-1022. [PMID: 37587352 DOI: 10.1007/s10482-023-01863-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 07/27/2023] [Indexed: 08/18/2023]
Abstract
Four novel Gram-stain negative bacteria, designated as HAJ6T, PWR1T, SG15T and SSH11T, were isolated from the soil sample of paddy fields from Goyang in the Republic of Korea. The isolated strains were aerobic, short-rod or rod shaped, non-sporulating. They grew optimally at 30 °C, pH 7 and without additional NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that they belong to the genus of Neoroseomonas and Pararoseomonas and closely relate to Neoroseomonas terrae DS-48T (97.5%; HJA6T), Neoroseomonas rubea MO17T (99.4%; PWR1T), Pararoseomonas pecuniae N75T (97.3%; SG15T) and Pararoseomonas rosea 173-96T (97.8%; SSH11T). The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of the isolates with the most closely related strains were 72.9-90.9% and 19.1-42.5%, respectively. The major fatty acids in the isolates were C16:0, C19:0 cyclo ω8c, C18:1 2-OH and summed feature 8 (composed of C18:1 ω7c and/or C18:1 ω6c), and the predominant quinone was ubiquinone 10. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, and other unidentified polar lipids. Based on the draft genome sequences, the genomic DNA G + C content of HAJ6T, PWR1T, SG15T and SSH11T were 69.5%, 72.0%, 70.8% and 69.7%, respectively. All isolates produced indole-3-acetic acid (IAA), a type of plant growth hormone in the presence of L-tryptophan. Physiological and biochemical tests and 16S rRNA sequence analysis clearly revealed that the isolates were novel species belonging to the genus Neoroseomonas and Pararoseomonas. Their proposed names were as follows: Neoroseomonas alba sp. nov. for strain HJA6T (= KACC 21545T = NBRC 114316T), Neoroseomonas nitratireducens sp. nov. for strain PWR1T (= KCTC 82687T = NBRC 114490T), Pararoseomonas indoligenes sp. nov. for strain SG15T (= KCTC 82686T = NBRC 114481T) and Paraoseomonas baculiformis sp. nov. for strain SSH11T (= KCTC 82685T = NBRC 11482T).
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Affiliation(s)
- Yoonseop So
- Department of Life Science, Dongguk University Seoul, Goyang, 10326, South Korea
| | - Geeta Chhetri
- Department of Life Science, Dongguk University Seoul, Goyang, 10326, South Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University Seoul, Goyang, 10326, South Korea
| | - Jiyoun Kim
- Department of Life Science, Dongguk University Seoul, Goyang, 10326, South Korea
| | - Sunho Park
- Department of Life Science, Dongguk University Seoul, Goyang, 10326, South Korea
| | - Yonghee Jung
- Department of Life Science, Dongguk University Seoul, Goyang, 10326, South Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University Seoul, Goyang, 10326, South Korea.
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Kim I, Chhetri G, So Y, Park S, Jung Y, Woo H, Seo T. Mesorhizobium liriopis sp. nov., isolated from the fermented fruit of Liriope platyphylla a medicinal plant. Int J Syst Evol Microbiol 2023; 73. [PMID: 37801075 DOI: 10.1099/ijsem.0.006086] [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: 10/07/2023] Open
Abstract
A facultative anaerobic and Gram-negative strain, designated RP14T, was isolated from the fruit of Liriope platyphylla fermented for 60 days at 25°C. Strain RP14T showed 98.0 % 16S rRNA similarity to Mesorhizobium huakuii IFO 15243T, but in the phylogenetic tree, Mesorhizobium terrae NIBRBAC000500504T was its closest neighbour. The average nucleotide identity and digital DNA-DNA hybridization values between strain RP14T and 15 genomes of type strains of Mesorhizobium, were 73.8-74.4% and 16.4-20.2 %, respectively, which were lower than the recommended thresholds for species delineation. The strain grew at 25-32°C (optimum, 28°C), at pH 7.0-12.0 (optimum, pH 9.0) and with 0-2% NaCl (optimum, 0 %; w/v). Cells of strain RP14T were catalase-positive, oxidase-negative, rod-shaped and formed yellow-coloured colonies. The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The major fatty acid were C16 : 0, C19 : 0 cyclo ω8c and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The DNA G+C content was 62.8 mol%. Based on polyphasic evidence, we propose Mesorhizobium liriopis sp. nov as a novel species within the genus Mesorhizobium. The type strain is RP14T (=KACC 22720T=TBRC 16341T).
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Affiliation(s)
- Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Yoonseop So
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Sunho Park
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Yonghee Jung
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Haejin Woo
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
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Park S, Kim I, Chhetri G, So Y, Jung Y, Woo H, Seo T. Roseateles albus sp. nov., Roseateles koreensis sp. nov. and Janthinobacterium fluminis sp. nov., isolated from freshwater at Jucheon River, and emended description of Roseateles aquaticus comb. nov. Int J Syst Evol Microbiol 2023; 73. [PMID: 37750754 DOI: 10.1099/ijsem.0.006043] [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: 09/27/2023] Open
Abstract
Three Gram-stain-negative, facultatively anaerobic, rod-shaped, catalase-positive, oxidase-negative bacterial strains were designated as hw1T, hw8T and hw3T. Strains hw1T, hw8T and hw3T grew at 15-28 °C (optimum, 25 °C), 15-35 °C (optimum, 30 °C) and 4-28 °C (optimum, 20 °C), respectively, and at pH 7.0-12.0 (optimum, pH 9.0), pH 6.0-11.0 (optimum, pH 9.0) and 5.0-12.0 (optimum, pH 7.0), respectively. Additionally, strains hw1T and hw8T only grew when the NaCl concentration was 0 %, while strain hw3T grew at between 0 and 0.5 % (w/v; optimum, 0 %). The average nucleotide identity (ANI) values between strains hw1T, hw8T and the Roseateles type strains ranged from 73.8 to 84.2 %, while the digital DNA-DNA hybridization (dDDH) values ranged from 19.7 to 27.5 %. The ANI values between strain hw3T and the Janthinobacterium type strains ranged from 78.7 to 80.7 %, while dDDH values ranged from 22.3 to 23.0 %. The draft genomes of strains hw1T, hw8T and hw3T consisted of 5.5, 4.4 and 5.9 Mbp, with DNA G+C contents of 61.7, 61.8 and 66.0 mol%, respectively. The results of the dDDH, ANI, phylogenetic, biochemical and physiological analyses indicated that the novel strains were distinct from other members of their genera. Thus, we proposed the names Roseateles albus sp. nov. (type strain hw1T= KACC 22887T= TBRC 16613T), Roseateles koreensis sp. nov. (type strain hw8T= KACC 22885T= TBRC 16614T) and Janthinobacterium fluminis sp. nov. (type strain hw3T= KACC 22886T= TBRC 16615T).
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Affiliation(s)
- Sunho Park
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Yoonseop So
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Yonghee Jung
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Haejin Woo
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
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Chhetri G, Kim I, Park S, Jung Y, Seo T. Planobacterium oryzisoli sp. nov., a novel bacterium isolated from roots of rice plant. Arch Microbiol 2023; 205:324. [PMID: 37656250 DOI: 10.1007/s00203-023-03657-y] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 09/02/2023]
Abstract
A Gram-negative, aerobic, short rod-shaped, non-motile, non-spore forming bacterium, designated strain GCR5T, was isolated from soil of paddy field. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain GCR5T belongs to the genus Planobacterium and is related to Planobacterium taklimakanense NCTC 13490 T (96.1%, 16S rRNA gene sequence similarity). Colonies on R2A were white but they turn into bright yellow after exponential growth. They produce carotenoid pigment after 5-6 days of incubation, before that carotenoid pigment was not found. The major isoprenoid quinone was MK-6, and major cellular fatty acids were iso-C15:0, anteiso-C15:0 and iso-C17:0 3OH. Polar lipids include phosphatidylethanolamine, three unidentified phosphoglycolipids, three unidentified glycolipids, one unidentified aminophosphoglycolipid and five unidentified polar lipids. The strain GCR5T was found to have a 2,106,200 bp linear genome with G + C content of 43.7%. The ANI, dDDH and AAI values between the strain GCR5T and the type strains of phylogenetically related species were 60.2-71.1%, 19-24.3%, and 60.2-69.6%, respectively. The strain designated GCR5T produced indole acetic acid (IAA) in the presence of tryptophan only, and auxin responsive genes and tryptophan biosynthesis genes were found in its genome. Based on its polyphasic characteristics, strain GCR5T represents a novel species within the genus Planobacterium, for which the name Planobacterium oryzisoli sp. nov. was proposed. The type strain is GCR5T (= KCTC 82713 T = TISTR 2996 T = TBRC 15746 T).Repositories: The draft genome and 16S rRNA gene sequences of strain GCR5T have been deposited at GenBank/EMBL/DDBJ under accession numbers JADKYY000000000 and MN955408, respectively.
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Affiliation(s)
- Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Sunho Park
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Yonghee Jung
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea.
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Park S, Kim I, Chhetri G, So Y, Jung Y, Woo H, Seo T. Alteromonas gilva sp. nov. and Erythrobacter fulvus sp. nov., isolated from a tidal mudflat. Int J Syst Evol Microbiol 2023; 73. [PMID: 37676705 DOI: 10.1099/ijsem.0.006032] [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: 09/08/2023] Open
Abstract
Strains chi3T and sf7T were collected from a tidal mudflat around Dongmak beach in Ganghwa, Republic of Korea. Both strains were Gram-stain-negative, aerobic or facultatively anaerobic, and rod-shaped. Results of phylogenetic tree analysis based on 16S rRNA and whole-genome sequences suggested that strains chi3T and sf7T belong to the genera Alteromonas and Erythrobacter, respectively. The cells of strain chi3T were non-motile and grew at 15-45 °C (optimum, 38 °C), at pH 6.0-10.0 (optimum, pH 8.0) and in the presence of 0-9.0 % (w/v) NaCl (optimum, 2.0 %). The cells of strain sf7T were motile as they had flagella and grew at 20-48 °C (optimum, 38 °C), at pH 6.0-10.0 (optimum, pH 9.0) and in the presence of 0-5.0 % (w/v) NaCl (optimum, 1.0 %). Strains chi3T and sf7T have average nucleotide identity values (70.0-70.4% and 78.9-81.7 %) and digital DNA-DNA hybridization values (21.8-22.3% and 21.0-25.6 %) with reference strains in the genera Alteromonas and Erythrobacter, respectively. Data from digital DNA-DNA hybridization, as well as phylogenetic, biochemical and physiological analyses, indicated the distinction of the two strains from the genera Alteromonas and Erythrobacter, respectively, and we thus propose the names Alteromonas gilva sp. nov. (type strain chi3T=KACC 22866T=TBRC 16612T) and Erythrobacter fulvus sp. nov. (type strain sf7T=KACC 22865T=TBRC 16611T).
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Affiliation(s)
- Sunho Park
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Yoonseop So
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Yonghee Jung
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Haejin Woo
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
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So Y, Chhetri G, Kim I, Park S, Jung Y, Woo H, Seo T. Nocardioides pini sp. nov. and Nocardioides pinisoli sp. nov., two novel actinomycetes isolated from Pinus densiflora. Int J Syst Evol Microbiol 2023; 73. [PMID: 37755157 DOI: 10.1099/ijsem.0.006062] [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: 09/28/2023] Open
Abstract
Two novel Gram-positive bacteria designated as strains STR2T and STR3T were isolated from the rhizosphere of a Pinus densiflora sample collected from Goyang-si, Republic of Korea. Strains STR2T and STR3T were aerobic, rod shaped, non-sporulated, catalase negative, oxidase negative and non-motile bacteria. They grew at 15-37 °C (optimum, 25-30 °C), at pH 6.0-11.0 (optimum, pH 7.0) and in the presence of 0-2% NaCl (optimum, 0 %, w/v). The chemotaxonomic and morphological characteristics of the novel strains were consistent with those of the members of Nocardioides. The phylogenetic analysis of the 16S rRNA gene sequences revealed that STR2T was closely related to N. cavernae YIM A1136T (99.3 %) and N. flavus Y4T (99.1 %), and STR3T was closely related to N. exalbidus DSM 22017T (99.0 %), N. baculatus G10T (98.8 %) and N. hwasunensis HFW-21T (98.7 %). The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values of STR2T and STR3T with the most closely related strains that have publicly available whole genomes were 83.1-89.8 %, 80.9-89.6% and 26.2-39.1 %, respectively. The cell-wall peptidoglycan of strain STR2T and STR3T contained ll-diaminopimelic acid as the diagnostic amino acid. The major fatty acids in STR2T and STR3T were iso-C16 : 0 and C17 : 1 ω8c, and the predominant quinone was MK-8(H4). Their polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and other polar lipids. The draft genome sequences showed that the genomic DNA G+C content of STR2T and STR3T were both 72.2 mol%. Physiological and biochemical tests and 16S rRNA sequence analysis clearly revealed that STR2T and STR3T could represent novel Nocardioides species. Their proposed names were as follows: Nocardioides pini sp. nov. for strain STR2T (=KACC 22784T=TBRC 16336T) and Nocardioides pinisoli sp. nov. for strain STR3T (= KACC 22785T=TBRC 16337T).
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Affiliation(s)
- Yoonseop So
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Sunho Park
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Yonghee Jung
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Haejin Woo
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
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Kim I, Chhetri G, So Y, Park S, Jung Y, Woo H, Seo T. Characterization and Antioxidant Activity of Exopolysaccharides Produced by Lysobacter soyae sp. nov Isolated from the Root of Glycine max L. Microorganisms 2023; 11:1900. [PMID: 37630460 PMCID: PMC10456730 DOI: 10.3390/microorganisms11081900] [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: 06/30/2023] [Revised: 07/24/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Microbial exopolysaccharides (EPSs) have attracted attention from several fields due to their high industrial applicability. In the present study, rhizosphere strain CJ11T was isolated from the root of Glycine max L. in Goyang-si, Republic of Korea, and a novel exopolysaccharide was purified from the Lysobacter sp. CJ11T fermentation broth. The exopolysaccharide's average molecular weight was 0.93 × 105 Da. Its monosaccharide composition included 72.2% mannose, 17.2% glucose, 7.8% galactose, and 2.8% arabinose. Fourier-transform infrared spectroscopy identified the exopolysaccharide carbohydrate polymer functional groups, and the structural properties were investigated using nuclear magnetic resonance. In addition, a microstructure of lyophilized EPS was determined by scanning electron microscopy. Using thermogravimetric analysis, the degradation of the exopolysaccharide produced by strain CJ11T was determined to be 210 °C. The exopolysaccharide at a concentration of 4 mg/mL exhibited 2,2-diphenyl-1-picrylhydrazyl free-radical-scavenging activity of 73.47%. Phylogenetic analysis based on the 16S rRNA gene sequencing results revealed that strain CJ11T was a novel isolate for which the name Lysobacter soyae sp. nov is proposed.
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Affiliation(s)
| | | | | | | | | | | | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea; (I.K.); (G.C.); (Y.S.); (S.P.); (Y.J.); (H.W.)
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Jung Y, Chhetri G, Kim I, So Y, Park S, Woo H, Lee KH, Seo T. Chryseobacterium edaphi sp. nov. and Chryseobacterium gilvum sp. nov., isolated from soil. Int J Syst Evol Microbiol 2023; 73. [PMID: 37490399 DOI: 10.1099/ijsem.0.005989] [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: 07/27/2023] Open
Abstract
Two Gram-stain-negative, aerobic, yellow and rod-shaped bacteria, designated as strains PBS4-4T and GMJ5T, were isolated from soil samples collected in Goyang-si and Paju-si, Gyeonggi-do, Republic of Korea. Strains PBS4-4T and GMJ5T were both positive for catalase and oxidase. Strain PBS4-4T grew at 15-37 °C and pH 5.0-12.0. Strain GMJ5T grew at 15-37 °C and pH 5.0-11.0. Neither strain required NaCl for growth. 16S rRNA sequence analysis revealed that strains PBS4-4T and GMJ5T form a closely related cluster with the genus Chryseobacterium. The average nucleotide identity and digital DNA-DNA hybridization values between strain PBS4-4T and its closely related strains were 79.4-84.5% and 23.2-28.7 %, respectively. For GMJ5T, the values were 78.3-79.3% and 22.0-22.6 %, respectively. The major fatty acids shared by both novel strains were iso-C15 : 0 and summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c). Strain GMJ5T had one other major fatty acid: iso-C17 : 0 3OH. Based on phenotypic, genomic and phylogenetic results, strains PBS4-4T and GMJ5T represent novel species within the genus Chryseobacterium, and the names Chryseobacterium edaphi sp. nov. and Chryseobacterium gilvum sp. nov. are proposed, respectively. The type strain of C. edaphi is PBS4-4T (=KACC 22882T=TBRC 17052T) and the type strain of C. gilvum is GMJ5T (=KACC 22883T=TBRC 17053T).
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Affiliation(s)
- Yonghee Jung
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Yoonseop So
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Sunho Park
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Haejin Woo
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Ki-Ho Lee
- Department of Biochemistry and Molecular Biology, College of Medicine, Eulji University, Daejeon 34824, Republic of Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
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Jung Y, Chhetri G, Kim I, So Y, Park S, Seo T. Ideonella oryzae sp. nov., isolated from soil, and Spirosoma liriopis sp. nov., isolated from fruits of Liriope platyphylla. Int J Syst Evol Microbiol 2023; 73. [PMID: 37409567 DOI: 10.1099/ijsem.0.005943] [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: 07/07/2023] Open
Abstract
Gram-negative, aerobic, motile by means of two or more polar or subpolar flagella, rod-shaped strain NS12-5T and Gram-negative, facultatively anaerobic, yellow-coloured, rod-shaped strain RP8T were isolated from rice rhizosphere soil and fermented fruits of Liriope platyphylla in the Republic of Korea, respectively. The result of phylogenetic analyses based on 16S rRNA gene sequences showed that strain NS12-5T was most closely related to Ideonella aquatica 4Y11T with 99.79 % sequence similarity. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain NS12-5T and species of the genus Ideonella were 75.6-91.7 % and 20.3-43.9 %, respectively. Growth occurred at 15-40 °C and pH 5-11, and NaCl was not needed for growth. The major fatty acids of strain NS12-5T were summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c) and C16 : 0, and the major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C content of strain NS12-5T was 69.03 mol%. The result of phylogenetic analyses based on 16S rRNA gene sequences revealed that strain RP8T was most closely related to Spirosoma aureum BT328T with 96.01 % sequence similarity. The ANI and dDDH values between strain RP8T and reference strains of the genus Spirosoma were 72.9-76.4 % and 18.6-20.0 %, respectively. Growth occurred at 15-37 °C and pH 5-11, and NaCl was not needed for growth. The major fatty acids of strain RP8T were summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 1 ω5c and iso-C15 : 0. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C contents of strain RP8T were 54.9 mol%. Based on phenotypic, genomic and phylogenetic results, strains NS12-5T and RP8T represent novel species in the genus Ideonella and Spirosoma, respectively, and the names Ideonella oryzae sp. nov. and Spirosoma liriopis sp. nov. are proposed. The type strain of I. oryzae sp. nov. is NS12-5T (=KACC 22691T=TBRC 16346T) and the type strain of S. liriopis is RP8T (=KACC 22688T=TBRC 16345T).
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Affiliation(s)
- Yonghee Jung
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Yoonseop So
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Sunho Park
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
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Arnquist IJ, Avignone FT, Barabash AS, Barton CJ, Bhimani KH, Blalock E, Bos B, Busch M, Buuck M, Caldwell TS, Chan YD, Christofferson CD, Chu PH, Clark ML, Cuesta C, Detwiler JA, Efremenko Y, Ejiri H, Elliott SR, Giovanetti GK, Green MP, Gruszko J, Guinn IS, Guiseppe VE, Haufe CR, Henning R, Hervas Aguilar D, Hoppe EW, Hostiuc A, Kim I, Kouzes RT, Lannen V TE, Li A, Lopez AM, López-Castaño JM, Martin EL, Martin RD, Massarczyk R, Meijer SJ, Oli TK, Othman G, Paudel LS, Pettus W, Poon AWP, Radford DC, Reine AL, Rielage K, Ruof NW, Tedeschi D, Varner RL, Vasilyev S, Wilkerson JF, Wiseman C, Xu W, Yu CH, Zhu BX. Erratum: Search for Spontaneous Radiation from Wave Function Collapse in the Majorana Demonstrator [Phys. Rev. Lett. 129, 080401 (2022)]. Phys Rev Lett 2023; 130:239902. [PMID: 37354428 DOI: 10.1103/physrevlett.130.239902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Indexed: 06/26/2023]
Abstract
This corrects the article DOI: 10.1103/PhysRevLett.129.080401.
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Park S, Kim I, Chhetri G, So Y, Jung Y, Woo H, Seo T. Runella salmonicolor sp. nov. and Dyella lutea sp. nov., isolated from paddy field soil. Int J Syst Evol Microbiol 2023; 73. [PMID: 37358382 DOI: 10.1099/ijsem.0.005938] [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
Bacterial strains were collected from the soil of a paddy field around Dongguk University in Goyang, Republic of Korea. Two Gram-stain-negative, rod-shaped, aerobic or facultatively anaerobic bacterial strains were designated S5T and SaT. The results of analysis of phylogenetic trees based on 16S rRNA and whole-genome sequences indicated that these two strains represented a member of the genus Runella and a member of the genus Dyella, respectively. S5T exhibited 99.22, 98.10 and 97.68 % similarity to Runella rosea HYN0085T, Runella aurantiaca YX9T and Runella slithyformis DSM 19594T, respectively. S5T grew at 15-40 °C (optimum, 25 °C), at pH 6.5-12.0 (optimum, pH 9.5) and in the presence of 0-0.5 % (w/v) NaCl (optimum, 0 %). SaT exhibited 99.18 %, 98.36 %, 97.82 % and 97.68 % similarity to Dyella thiooxydans ATSB10T, Frateruia defendens DHoT, Fulvimonas yonginensis 5HGs31-2T and Dyella ginsengisoli Gsoil 3046T, respectively, and grew at 20-40 °C (optimum, 30 °C), at pH 5.5-11.0 (optimum, pH 8) and in the presence of 0-4.5 % (w/v) NaCl (optimum, 2.5 %). The average nucleotide identity difference values of S5T, SaT and the species reference strains were 92.16-93.62 % and 92.71-93.43%, which confirms that the S5T and SaT represent two novel species of the genera Runella and Dyella, respectively. The draft genome of S5T consisted of 7 048 502 bp, with a DNA G+C content of 44.9 % and that of SaT of 4 398 720 bp with a DNA G+C content of 67.9 %. The phylogenetic, phenotypic and physiological characteristics permitted the distinction of the two strains from their families, and we thus propose the names Runella salmonicolor sp. nov. (type strain S5T = KACC 22689T = TBRC 16343T) and Dyella lutea sp. nov. (type strain SaT=KACC 22690T = TBRC 16344T).
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Affiliation(s)
- Sunho Park
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
| | - Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
| | - Yoonseop So
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
| | - Yonghee Jung
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
| | - Haejin Woo
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
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Lee G, Park S, Lee S, Song K, Kim Y, Chang W, Kim J, Park N, Kim J, Park S, Hwang I, Kim H, Kim I. Bioimpedance Analysis as a Screening Tool in Heart-Transplanted Patients. J Heart Lung Transplant 2023. [DOI: 10.1016/j.healun.2023.02.1265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
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Kim D, Youn J, Kim J, Kim I, Choi J, Kransdorf E, Chang D, Kittleson M, Patel J, Cole R, Moriguchi J, Esmailian F, Kobashigawa J. Clinical Outcomes of Heart Transplantation in Desensitized Durable Mechanical Circulatory Support Patients. J Heart Lung Transplant 2023. [DOI: 10.1016/j.healun.2023.02.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
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Kim I, Youn J, Chang D, Nishihara K, Kransdorf E, Kittleson M, Patel J, Cole R, Nikolova A, Esmailian F, Czer L, Kobashigawa J. The Validation of Cardiac Rehabilitation after Heart Transplantation from Anonymized Patient-Reported Outcomes. J Heart Lung Transplant 2023. [DOI: 10.1016/j.healun.2023.02.1262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
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Kim E, Lee S, Jang D, Kyoung Y, Kim J, Kim I, Kim J, Youn J. Proteomic Discovery of Molecular Pathways in Patients with Biopsy-Proven Myocarditis. J Heart Lung Transplant 2023. [DOI: 10.1016/j.healun.2023.02.603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
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21
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Chhetri G, Kim I, Seo T. Devosia oryzisoli sp. nov., a novel moderately halotolerant bacterium isolated from the roots of rice plants and genome mining revealed the biosynthesis potential as plant growth promoter. Antonie Van Leeuwenhoek 2023; 116:231-242. [PMID: 36525157 DOI: 10.1007/s10482-022-01800-1] [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: 06/22/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022]
Abstract
A Gram-stain-negative, halotolerant bacterium designated as PTR5T was isolated from the roots of rice plants, collected in Ilsan, South Korea. Cells were, aerobic, asporogenous, motile, rod-shaped, white in color, and grew at 5-38 °C (optimum 30 °C), at pH 5.0-0-8.0 (optimum, 7.0) and tolerates up to 10% (w/v) NaCl (optimum, 0% NaCl). According to the EZbioCloud server the most closely related Devosia species to strain PTR5T based on 16 S rRNA gene sequence comparison are Devosia crocina (97.4%), followed by D. soli (97.2%), D. lucknowensis (96.9%) and D. marina (96.5%). The respiratory quinone was identified as Q-10. The major polar lipids were phosphatidylglycerol and diphosphatidylglycerol. C16:0, C18:1 ω7c 11-methyl and summed feature 8 (comprising C18:1 ω7c/C18:1 ω6c) constituted the main cellular fatty acids. The draft genome sequence of strain PTR5T was 3,689,283 bp in size. The average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH) and amino acid identity (AAI) values between strain PTR5T and its close relative were 72.8-76.8%, 19-20.7% and 70.3-75%, respectively. The G + C content was 63.7%. Strain PTR5T was able to produce siderophore and indole acetic acid (IAA) in the presence of L-tryptophan. Genes for siderophore production, auxin responsive and tryptophan biosynthesis were present in the genome of novel strain. Also, gene clusters involved in detoxification of various metal pollutants and antibiotics were also revealed in the genome of novel strain PTR5T, this suggest that novel strain can facilitate bioremediation of heavy metals and antibiotics in contaminated areas. This study aimed to determine the detailed taxonomic position of the strain PTR5T using the modern polyphasic approach. On the basis of evidence presented in this study, strain PTR5T is considered to represent a novel species of the genus Devosia, for which the name Devosia oryzisoli sp. nov. (type strain PTR5T (KCTC 82691T = TBRC 15163T) is proposed.
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Affiliation(s)
- Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, 10326, Goyang, South Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, 10326, Goyang, South Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, 10326, Goyang, South Korea.
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22
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Arnquist IJ, Avignone FT, Barabash AS, Barton CJ, Barton PJ, Bhimani KH, Blalock E, Bos B, Busch M, Buuck M, Caldwell TS, Chan YD, Christofferson CD, Chu PH, Clark ML, Cuesta C, Detwiler JA, Efremenko Y, Ejiri H, Elliott SR, Giovanetti GK, Green MP, Gruszko J, Guinn IS, Guiseppe VE, Haufe CR, Henning R, Hervas Aguilar D, Hoppe EW, Hostiuc A, Kidd MF, Kim I, Kouzes RT, Lannen V TE, Li A, Lopez AM, López-Castaño JM, Martin EL, Martin RD, Massarczyk R, Meijer SJ, Mertens S, Oli TK, Othman G, Paudel LS, Pettus W, Poon AWP, Radford DC, Reine AL, Rielage K, Ruof NW, Schaper DC, Tedeschi D, Varner RL, Vasilyev S, Wilkerson JF, Wiseman C, Xu W, Yu CH, Zhu BX. Final Result of the Majorana Demonstrator's Search for Neutrinoless Double-β Decay in ^{76}Ge. Phys Rev Lett 2023; 130:062501. [PMID: 36827565 DOI: 10.1103/physrevlett.130.062501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 11/09/2022] [Accepted: 12/16/2022] [Indexed: 06/18/2023]
Abstract
The Majorana Demonstrator searched for neutrinoless double-β decay (0νββ) of ^{76}Ge using modular arrays of high-purity Ge detectors operated in vacuum cryostats in a low-background shield. The arrays operated with up to 40.4 kg of detectors (27.2 kg enriched to ∼88% in ^{76}Ge). From these measurements, the Demonstrator has accumulated 64.5 kg yr of enriched active exposure. With a world-leading energy resolution of 2.52 keV FWHM at the 2039 keV Q_{ββ} (0.12%), we set a half-life limit of 0νββ in ^{76}Ge at T_{1/2}>8.3×10^{25} yr (90% C.L.). This provides a range of upper limits on m_{ββ} of (113-269) meV (90% C.L.), depending on the choice of nuclear matrix elements.
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Affiliation(s)
- I J Arnquist
- Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - F T Avignone
- Department of Physics and Astronomy, University of South Carolina, Columbia, South Carolina 29208, USA
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - A S Barabash
- National Research Center "Kurchatov Institute" Institute for Theoretical and Experimental Physics, Moscow, 117218 Russia
| | - C J Barton
- Department of Physics, University of South Dakota, Vermillion, South Dakota 57069, USA
| | - P J Barton
- Nuclear Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - K H Bhimani
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - E Blalock
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - B Bos
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - M Busch
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
- Department of Physics, Duke University, Durham, North Carolina 27708, USA
| | - M Buuck
- Center for Experimental Nuclear Physics and Astrophysics, and Department of Physics, University of Washington, Seattle, Washington 98195, USA
| | - T S Caldwell
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - Y-D Chan
- Nuclear Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | | | - P-H Chu
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - M L Clark
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - C Cuesta
- Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas, CIEMAT, 28040 Madrid, Spain
| | - J A Detwiler
- Center for Experimental Nuclear Physics and Astrophysics, and Department of Physics, University of Washington, Seattle, Washington 98195, USA
| | - Yu Efremenko
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37916, USA
| | - H Ejiri
- Research Center for Nuclear Physics, Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - S R Elliott
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - G K Giovanetti
- Physics Department, Williams College, Williamstown, Massachusetts 01267, USA
| | - M P Green
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - J Gruszko
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - I S Guinn
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - V E Guiseppe
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - C R Haufe
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - R Henning
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - D Hervas Aguilar
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - E W Hoppe
- Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - A Hostiuc
- Center for Experimental Nuclear Physics and Astrophysics, and Department of Physics, University of Washington, Seattle, Washington 98195, USA
| | - M F Kidd
- Tennessee Tech University, Cookeville, Tennessee 38505, USA
| | - I Kim
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - R T Kouzes
- Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - T E Lannen V
- Department of Physics and Astronomy, University of South Carolina, Columbia, South Carolina 29208, USA
| | - A Li
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - A M Lopez
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37916, USA
| | | | - E L Martin
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - R D Martin
- Department of Physics, Engineering Physics and Astronomy, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - R Massarczyk
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - S J Meijer
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - S Mertens
- Max-Planck-Institut für Physik, München 80805, Germany
- Physik Department and Excellence Cluster Universe, Technische Universität, München, 85748 Germany
| | - T K Oli
- Department of Physics, University of South Dakota, Vermillion, South Dakota 57069, USA
| | - G Othman
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - L S Paudel
- Department of Physics, University of South Dakota, Vermillion, South Dakota 57069, USA
| | - W Pettus
- Department of Physics, Indiana University, Bloomington, Indiana 47405, USA
- IU Center for Exploration of Energy and Matter, Bloomington, Indiana 47408, USA
| | - A W P Poon
- Nuclear Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - D C Radford
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - A L Reine
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - K Rielage
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - N W Ruof
- Center for Experimental Nuclear Physics and Astrophysics, and Department of Physics, University of Washington, Seattle, Washington 98195, USA
| | - D C Schaper
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - D Tedeschi
- Department of Physics and Astronomy, University of South Carolina, Columbia, South Carolina 29208, USA
| | - R L Varner
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - S Vasilyev
- Joint Institute for Nuclear Research, Dubna, 141980 Russia
| | - J F Wilkerson
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - C Wiseman
- Center for Experimental Nuclear Physics and Astrophysics, and Department of Physics, University of Washington, Seattle, Washington 98195, USA
| | - W Xu
- Department of Physics, University of South Dakota, Vermillion, South Dakota 57069, USA
| | - C-H Yu
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - B X Zhu
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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Abstract
A Gram-stain-positive, facultatively aerobic, rod-shaped and non-motile bacterial strain designated RMG13T was isolated from the soil near Gaetgol Eco Park and collected in Siheung-si, Republic of Korea. It was taxonomically characterized through polyphasic analysis. Phylogenetic analysis based on the 16S rRNA gene revealed that the novel isolate was most closely related to the type strains of species of the genus Pseudarthrobacter. RMG13T shared the highest similarities with Pseudarthrobacter sulfonivorans ALLT (99.2 %) and Pseudarthrobacter psychrotolerans YJ56T (99.0 %). In silico DNA-DNA hybridization values of RMG13T with P. sulfonivorans ALLT and P. psychrotolerans YJ56T were 28.1 and 41.8 %, respectively. The average nucleotide identities of RMG13T with P. sulfonivorans ALLT and P. psychrotolerans YJ56T were 84.2 and 70.3 %, respectively, whilst the average amino acid identities of RMG13T with P. sulfonivorans ALLT and P. psychrotolerans YJ56T were 90.5 and 74.6 %, respectively. Two-dimensional thin-layer chromatography showed that the major polar lipids of RMG13T were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol, and its major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0. MK-9 (H2) was the sole menaquinone. Cells grew at 4-37 °C (optimum 30 °C) and pH 5.0-12.0 (optimum pH 8.0) in Reasoner's 2A (MB cell). The cells tolerated 0-5% NaCl (w/v) but not 6 % NaCl. The DNA G+C content of RMG13T was 65.0 %. The results of phenotypic, genotypic, chemotaxonomic and phylogenetic analyses indicated that RMG13T represents a novel member of the genus Pseudarthrobacter, and the proposed name is P. humi sp. nov. The type strain of P. humi is RMG13T (= KACC 22359T = TBRC 15115T).
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Affiliation(s)
- Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
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Chhetri G, Kim I, Kim J, So Y, Park S, Jung Y, Seo T. Paraburkholderia tagetis sp. nov., a novel species isolated from roots of Tagetes patula enhances the growth and yield of Solanum lycopersicum L. (tomato). Front Microbiol 2023; 14:1140484. [PMID: 37082173 PMCID: PMC10110911 DOI: 10.3389/fmicb.2023.1140484] [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: 01/11/2023] [Accepted: 03/21/2023] [Indexed: 04/22/2023] Open
Abstract
A multifunctional, Gram-stain-negative, aerobic, motile by flagella, short-rod shaped bacteria, designated strain RG36T was isolated from roots of marigold plant (Tagetes patula) sampled at Dongguk University, Republic of Korea. A 16S rRNA sequences indicated that the closest phylogenetic neighbors were Paraburkholderia acidiphila 7Q-K02T (99.0%) and Paraburkholderia sacchari IPT101T (98.9%) of the family Burkholderiaceae. The draft genome size was 8.52 Mb (63.7% GC). The genome contained 7,381 coding sequences. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values of strain RG36T with its most closely related species were only 83.1-88.7 and 27.6-36.7%, respectively. Strain RG36T contained Q-8 as the major respiratory quinone and its main fatty acids (>10%) were C16:0, C17:0 cyclo, C19:0 cyclo ω8c, and summed feature 8 (comprising C18:1 ω7c and/or C18:1 ω6c). Strain RG36T accumulates polyhydroxybutyrates (PHB) and exhibits multiple plant growth-promoting properties including production of indole-3-acetic acid (IAA), siderophores, protease, phosphate solubilization, and harboring gene clusters for its multifunctional properties. A pot experiment was conducted to evaluate the effect of PGPR on the growth of Solanum lycopersicum L. (Tomato). Result also confirmed the ability of strain RG36T to promote tomato plant growth, especially it increases the yield of tomatoes. Structural assessment of the bioplastic by Fourier transform infrared (FTIR), nuclear magnetic resonance (NMR), and GC-MS spectroscopy, which confirmed the structure of the polymer as PHB. Our study revealed the potential of strain RG36T to promote the growth of tomato plant and fruit yield by stimulating the various phytohormones, which could be use as bio-fertilizers to reduce the use of chemical fertilizers and promotes sustainable agricultural production. The phenotypic, chemotaxonomic and phylogenetic data, and genome analysis showed that strain RG36T represents a novel species of the genus Paraburkholderia, for which the name Paraburkholderia tagetis sp. nov. is proposed. The type strain is RG36T (=KACC 22685T = TBRC 15696T).
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Kang M, Chhetri G, Kim I, So Y, Seo T. Comparative genomic analyses of four novel Ramlibacter species and the cellulose-degrading properties of Ramlibacter cellulosilyticus sp. nov. Sci Rep 2022; 12:21233. [PMID: 36482214 PMCID: PMC9731981 DOI: 10.1038/s41598-022-25718-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
In this study, four novel bacterial strains, USB13T, AW1T, GTP1T, and HM2T, were isolated from various environments in Busan and Jeju Island, Republic of Korea. The 16S rRNA sequencing results indicated that the four novel strains belong to the genus Ramlibacter. All four strains were tested for their potential cellulolytic properties, where strain USB13T was identified as the only novel bacterium and the first within its genus to show cellulolytic activity. When tested, the highest activities of endoglucanase, exoglucanase, β-glucosidase, and filter paper cellulase (FPCase) were 1.91 IU/mL, 1.77 IU/mL, 0.76 IU/mL, and 1.12 IU/mL, respectively at pH 6.0. Comparisons of draft whole genome sequences (WGS) were also made using average nucleotide identity, digital DNA-DNA hybridization values, and average amino acid identity values, while whole genome comparison was visualized using the BLAST Ring Image Generator. The G + C contents of the strains ranged from 67.9 to 69.9%, while genome sizes ranged from 4.31 to 6.15 Mbp. Based on polyphasic evidence, the novel strains represent four new species within the genus Ramlibacter, for which the names Ramlibacter cellulosilyticus sp. nov. (type strain, USB13T = KACC 21656T = NBRC 114839T) Ramlibacter aurantiacus sp. nov. (type strain, AW1T = KACC 21544T = NBRC 114862T), Ramlibacter albus sp. nov. (type strain, GTP1T = KACC 21702T = NBRC 114488T), and Ramlibacter pallidus sp. nov. (type strain, HM2T = KCTC 82557T = NBRC 114489T) are proposed.
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Affiliation(s)
- Minchung Kang
- grid.255168.d0000 0001 0671 5021Department of Life Science, Dongguk University-Seoul, Goyang, 10326 Korea
| | - Geeta Chhetri
- grid.255168.d0000 0001 0671 5021Department of Life Science, Dongguk University-Seoul, Goyang, 10326 Korea
| | - Inhyup Kim
- grid.255168.d0000 0001 0671 5021Department of Life Science, Dongguk University-Seoul, Goyang, 10326 Korea
| | - Yoonseop So
- grid.255168.d0000 0001 0671 5021Department of Life Science, Dongguk University-Seoul, Goyang, 10326 Korea
| | - Taegun Seo
- grid.255168.d0000 0001 0671 5021Department of Life Science, Dongguk University-Seoul, Goyang, 10326 Korea
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Kim I, Chhetri G, So Y, Jung Y, Park S, Seo T. Sphingomonas liriopis sp. nov., Sphingomonas donggukensis sp. nov., and Sphingomonas tagetis sp. nov., isolated from Liriope platyphylla fruit, soil, and Tagetes patula roots. Arch Microbiol 2022; 205:16. [PMID: 36477930 DOI: 10.1007/s00203-022-03360-4] [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: 08/24/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022]
Abstract
Three bacterial strains, designated RP10T, RMG20T, and MG17T, were isolated from Liriope platyphylla fruit (strain RP10T), soil (RMG20T), and Tagetes patula roots (MG17T) collected in Goyang, Republic of Korea. The 16S rRNA gene sequences revealed that strains RP10T, RMG20T, and MG17T were closely related to Sphingomonas melonis DSM 14444 T (highest similarity of the strain RP10T), Sphingomonas asaccharolytica DSM 10564 T (strain RMG20T), and Sphingomonas suaedae JCM 33850 T (strain MG17T) with 98.0-99.0% highest sequence similarity. The 16S rRNA gene sequences similarity between strains RP10T, RMG20T, and MG17T was 96.6-97.4%. Strains RP10T, RMG20T, MG17T, and the closely related type strains have digital DNA-DNA hybridization and average nucleotide identity values of 19.4-65.3% and 74.0-95.7%, respectively. Based on phylogenetic, biochemical, chemotaxonomic, and phenotypic data, strains RP10T, RMG20T, and MG17T are considered to represent novel species of the genus Sphingomonas, for which the name Sphingomonas liriopis sp. nov. (type strain RP10T = KACC 22357 T = TBRC 15161 T), Sphingomonas donggukensis sp. nov. (type strain RMG20T = KACC 22358 T = TBRC 15162 T), and Sphingomonas tagetis sp. nov. (type strain MG17T = KACC 22355 T = TBRC 15160 T), are proposed.
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Affiliation(s)
- Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Yoonseop So
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Yonghee Jung
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Sunho Park
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea.
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Kim I, Chhetri G, Kim J, So Y, Seo T. Chryseolinea lacunae sp. nov. and Piscinibacter lacus sp. nov. Isolated from Artificial Pond Water. Curr Microbiol 2022; 80:25. [PMID: 36473949 DOI: 10.1007/s00284-022-03133-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022]
Abstract
Two Gram stain-negative bacterial strains designated Jin1T and Jin2T were isolated from artificial pond water in the Republic of Korea and investigated in the present study using a polyphasic taxonomic approach. Phylogenetic analysis of the 16S rRNA gene sequences indicated that these two strains belonged to the genera Chryseolinea and Piscinibacter due to their highest similarities with the 16S rRNA gene sequences of Chryseolinea serpens RYGT (98.7%) and Piscinibacter aquaticus IMCC1728T (97.1%), respectively. The dDDH and ANI values were 18.1-20.5% and 68.9-76.8% between whole-genome sequences of strain Jin1T and type trains of the selected taxa, Chryseolinea species, and 20.1-20.2% and 75.5-76.1% between those of strain Jin2T and the type strains of the selected taxa, Piscinibacter species, respectively. A threshold AAI value of 44.7-64.8% for the species boundary (95-96%) was established for strains Jin1T, Jin2T, and type strains of other species involved in the system incidence, which confirms that strains Jin1T and Jin2T represent two new species of the genera Chryseolinea and Piscinibacter, respectively. Based on the phylogenetic, chemotaxonomic, and phenotypic analyses, strains Jin1T and Jin2T represent novel species of the genera Chryseolinea and Piscinibacter, respectively, for which the names Chryseolinea lacunae sp. nov. (type strain Jin1T = KCTC 82562T = NBRC 114837T) and Piscinibacter lacus sp. nov. (type strain Jin2T = KCTC 82556T = NBRC 114838T) have been proposed.
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Affiliation(s)
- Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Jiyoun Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Yoonseop So
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea.
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Kim J, Chhetri G, Kim I, So Y, Seo T. Paenibacillus agilis sp. nov., Paenibacillus cremeus sp. nov. and Paenibacillus terricola sp. nov., isolated from rhizosphere soils. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748605 DOI: 10.1099/ijsem.0.005640] [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: 12/23/2022] Open
Abstract
Members of the genus Paenibacillus are well known for their metabolic versatility and great application potential in plant growth promotion. Three novel bacterial strains, designated N4T, JC52T and PR3T, were isolated from rhizosphere soils and characterized by using a polyphasic taxonomic approach. The 16S rRNA gene sequence phylogenetic and phylogenomic analysis revealed that the three strains belonged to the genus Paenibacillus and formed three independent branches distinct from all reference strains. The results of DNA-DNA hybridization (DDH) and average nucleotide identity (ANI) analyses between the three strains and their relatives further demonstrated that the three strains represented different novel genospecies. Strain N4T exhibited the highest similarity, ANI and digital DDH values with Paenibacillus assamensis DSM 18201T (99.0/87.5/33.9 %) and Paenibacillus insulae DS80T (97.2/-/18.2±1.2 %). Values for JC52T with Paenibacillus validus NBRC 15382T were 96.9, 73.3 and 19.6 %, and with Paenibacillus rigui JCM 16352T were 96.1, 72.1 and 19.3 %. Values for PR3T with Paenibacillus ginsengiterrae DCY89T were 98.2, - and 31.8±1.5 %, with Paenibacillus cellulosilyticus ASM318225v1T were 97.8, 83.3 and 26.7 %, and with Paenibacillus kobensis NBRC 15729T were 97.6, 75.7 and 20.4 %. Cells of the three novel bacterial strains were Gram-positive, spore-forming, motile and rod-shaped. The novel species contained anteiso-C15 : 0 and MK-7 as the predominant fatty acid and menaquinone, respectively. The novel strains have numerous similar known clusters of non-ribosomal peptide synthetases, siderophores, lanthipeptide, lassopeptide-like bacillibactin, paeninodin and polyketide-like chejuenolide A/B lankacidin C. Based on the distinct morphological, physiological, chemotaxonomic and phylogenetic differences from their closest phylogenetic neighbours, we propose that strains N4T, JC52T and PR3T represent novel species of the genus Paenibacillus, with the names Paenibacillus agilis sp. nov. (=KACC 19717T=JCM 32775T), Paenibacillus cremeus sp. nov. (=KACC 21221T=NBRC 113867T) and Paenibacillus terricola sp. nov. (=KACC 21455T=NBRC 114385T), respectively.
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Affiliation(s)
- Jiyoun Kim
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
| | - Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
| | - Yoonseop So
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
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Moon Y, Lee S, Lee J, Kim S, Kim I, Joo W, Jung S, Choi M, Park H, Lee C, Chung YG, Kim K, Park Y, Seong R. OD2-4 Efficient and noninvasive T cell therapy platform using autologous peripheral blood PD-1+CD8+ T cells instead of tumor-infiltrating lymphocytes in solid tumors: Ex vivo efficacy. ESMO Open 2022. [DOI: 10.1016/j.esmoop.2022.100668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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Muhizi S, Kim I. Microbial agent spraying in pig housing and slurry can potentially
reduce harmful gas emissions – a preliminary study. J Anim Feed Sci 2022. [DOI: 10.22358/jafs/154037/2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Boshra M, Lee A, Kim I, Malek-Adamian E, Yau M, LaDonna KA. When patients teach students empathy: a systematic review of interventions for promoting medical student empathy. Can Med Educ J 2022; 13:46-56. [PMID: 36440084 PMCID: PMC9684039 DOI: 10.36834/cmej.73058] [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] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
BACKGROUND Despite growing emphasis on empathic care, numerous studies demonstrate diminishing empathy in medical students. Involving patient educators in medical curricula may be a solution. Therefore, we conducted a systematic review to evaluate patient-involved interventions that promote empathy among medical students. METHOD A literature search of MEDLINE, Embase, PsycINFO, and ERIC databases was performed using the keywords "empathy," "medical student," and their synonyms. Results were independently screened in duplicate. Conflicts were resolved by group consensus. All English studies describing interventions that promote empathy in medical students engaging patient educators were included. Relevant data was extracted and summarized. RESULTS 1467 studies were screened. 14 studies were included, of which 10 were pilot studies. Studies included patient involved interventions such as storytelling (5/14), shadowing patients (3/14), recorded videos (3/14), or combinations of methods (3/14). Qualitative measurements of empathy included written feedback and group discussions. Quantitative measurements included validated scales measuring empathy. All studies demonstrated increase in empathy among medical students. Participants reported satisfaction with training and patients reported being proud of giving back by training future physicians. CONCLUSION Interventions engaging patient educators were shown to have a positive impact on medical student empathy. Furthermore, patient-led education was shown to increase medical student understanding of subject and knowledge retention while empowering patients. Further implementation of patient-involved education is an important step forward in patient-partnered care and may identify additional advantages of patient engagement in medical education.
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Affiliation(s)
- M Boshra
- Faculty of Medicine, University of Ottawa, Ontario, Canada
| | - A Lee
- Faculty of Medicine, University of Ottawa, Ontario, Canada
| | - I Kim
- Faculty of Medicine, University of Ottawa, Ontario, Canada
| | | | - M Yau
- Faculty of Medicine, University of Ottawa, Ontario, Canada
| | - KA LaDonna
- Faculty of Medicine, University of Ottawa, Ontario, Canada
- Department of Innovation in Medical Education and Department of Medicine, University of Ottawa, Ontario, Canada
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Ajani J, Sharpe D, De T, Kim I, Gricar J, Kurt M. 1218P Long-term survivorship rates among chemotherapy refractory or intolerant advanced esophageal squamous cell carcinoma (aESCC) patients treated with nivolumab (NIVO). Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.1336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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Yoo C, Kim KP, Kim I, Kang M, Cheon J, Kang B, Ryu H, Jeong J, Lee J, Kim K, Ryoo BY, Abou-Alfa G. 55P Final results from the NIFTY trial, a phase IIb, randomized, open-label study of liposomal Irinotecan (nal-IRI) plus fluorouracil (5-FU)/leucovorin (LV) in patients (pts) with previously treated metastatic biliary tract cancer (BTC). Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Arnquist IJ, Avignone FT, Barabash AS, Barton CJ, Bhimani KH, Blalock E, Bos B, Busch M, Buuck M, Caldwell TS, Chan YD, Christofferson CD, Chu PH, Clark ML, Cuesta C, Detwiler JA, Efremenko Y, Ejiri H, Elliott SR, Giovanetti GK, Green MP, Gruszko J, Guinn IS, Guiseppe VE, Haufe CR, Henning R, Hervas Aguilar D, Hoppe EW, Hostiuc A, Kim I, Kouzes RT, Lannen V TE, Li A, Lopez AM, López-Castaño JM, Martin EL, Martin RD, Massarczyk R, Meijer SJ, Oli TK, Othman G, Paudel LS, Pettus W, Poon AWP, Radford DC, Reine AL, Rielage K, Ruof NW, Tedeschi D, Varner RL, Vasilyev S, Wilkerson JF, Wiseman C, Xu W, Yu CH, Zhu BX. Search for Spontaneous Radiation from Wave Function Collapse in the Majorana Demonstrator. Phys Rev Lett 2022; 129:080401. [PMID: 36053678 DOI: 10.1103/physrevlett.129.080401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 06/14/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
The Majorana Demonstrator neutrinoless double-beta decay experiment comprises a 44 kg (30 kg enriched in ^{76}Ge) array of p-type, point-contact germanium detectors. With its unprecedented energy resolution and ultralow backgrounds, Majorana also searches for rare event signatures from beyond standard model physics in the low energy region below 100 keV. In this Letter, we test the continuous spontaneous localization (CSL) model, one of the mathematically well-motivated wave function collapse models aimed at solving the long-standing unresolved quantum mechanical measurement problem. While the CSL predicts the existence of a detectable radiation signature in the x-ray domain, we find no evidence of such radiation in the 19-100 keV range in a 37.5 kg-y enriched germanium exposure collected between December 31, 2015, and November 27, 2019, with the Demonstrator. We explored both the non-mass-proportional (n-m-p) and the mass-proportional (m-p) versions of the CSL with two different assumptions: that only the quasifree electrons can emit the x-ray radiation and that the nucleus can coherently emit an amplified radiation. In all cases, we set the most stringent upper limit to date for the white CSL model on the collapse rate, λ, providing a factor of 40-100 improvement in sensitivity over comparable searches. Our limit is the most stringent for large parts of the allowed parameter space. If the result is interpreted in terms of the Diòsi-Penrose gravitational wave function collapse model, the lower bound with a 95% confidence level is almost an order of magnitude improvement over the previous best limit.
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Affiliation(s)
- I J Arnquist
- Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - F T Avignone
- Department of Physics and Astronomy, University of South Carolina, Columbia, South Carolina 29208, USA
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - A S Barabash
- National Research Center "Kurchatov Institute" Institute for Theoretical and Experimental Physics, Moscow, 117218 Russia
| | - C J Barton
- Department of Physics, University of South Dakota, Vermillion, South Dakota 57069, USA
| | - K H Bhimani
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - E Blalock
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - B Bos
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - M Busch
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
- Department of Physics, Duke University, Durham, North Carolina 27708, USA
| | - M Buuck
- Center for Experimental Nuclear Physics and Astrophysics, and Department of Physics, University of Washington, Seattle, Washington 98195, USA
| | - T S Caldwell
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - Y-D Chan
- Nuclear Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | | | - P-H Chu
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - M L Clark
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - C Cuesta
- Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas, CIEMAT 28040 Madrid, Spain
| | - J A Detwiler
- Center for Experimental Nuclear Physics and Astrophysics, and Department of Physics, University of Washington, Seattle, Washington 98195, USA
| | - Yu Efremenko
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37916, USA
| | - H Ejiri
- Research Center for Nuclear Physics, Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - S R Elliott
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - G K Giovanetti
- Physics Department, Williams College, Williamstown, Massachusetts 01267, USA
| | - M P Green
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - J Gruszko
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - I S Guinn
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - V E Guiseppe
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - C R Haufe
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - R Henning
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - D Hervas Aguilar
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - E W Hoppe
- Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - A Hostiuc
- Center for Experimental Nuclear Physics and Astrophysics, and Department of Physics, University of Washington, Seattle, Washington 98195, USA
| | - I Kim
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - R T Kouzes
- Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - T E Lannen V
- Department of Physics and Astronomy, University of South Carolina, Columbia, South Carolina 29208, USA
| | - A Li
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - A M Lopez
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37916, USA
| | | | - E L Martin
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - R D Martin
- Department of Physics, Engineering Physics and Astronomy, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - R Massarczyk
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - S J Meijer
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - T K Oli
- Department of Physics, University of South Dakota, Vermillion, South Dakota 57069, USA
| | - G Othman
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - L S Paudel
- Department of Physics, University of South Dakota, Vermillion, South Dakota 57069, USA
| | - W Pettus
- Department of Physics, Indiana University, Bloomington, Indiana 47405, USA
- IU Center for Exploration of Energy and Matter, Bloomington, Indiana 47408, USA
| | - A W P Poon
- Nuclear Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - D C Radford
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - A L Reine
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - K Rielage
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - N W Ruof
- Center for Experimental Nuclear Physics and Astrophysics, and Department of Physics, University of Washington, Seattle, Washington 98195, USA
| | - D Tedeschi
- Department of Physics and Astronomy, University of South Carolina, Columbia, South Carolina 29208, USA
| | - R L Varner
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - S Vasilyev
- Joint Institute for Nuclear Research, Dubna, 141980 Russia
| | - J F Wilkerson
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - C Wiseman
- Center for Experimental Nuclear Physics and Astrophysics, and Department of Physics, University of Washington, Seattle, Washington 98195, USA
| | - W Xu
- Department of Physics, University of South Dakota, Vermillion, South Dakota 57069, USA
| | - C-H Yu
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - B X Zhu
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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Arnquist IJ, Avignone FT, Barabash AS, Barton CJ, Bhimani KH, Blalock E, Bos B, Busch M, Buuck M, Caldwell TS, Chan YD, Christofferson CD, Chu PH, Clark ML, Cuesta C, Detwiler JA, Efremenko Y, Ejiri H, Elliott SR, Giovanetti GK, Green MP, Gruszko J, Guinn IS, Guiseppe VE, Haufe CR, Henning R, Hervas Aguilar D, Hoppe EW, Hostiuc A, Kidd MF, Kim I, Kouzes RT, Lannen V TE, Li A, Lopez AM, López-Castaño JM, Martin EL, Martin RD, Massarczyk R, Meijer SJ, Oli TK, Othman G, Paudel LS, Pettus W, Poon AWP, Radford DC, Reine AL, Rielage K, Ruof NW, Schaper DC, Tedeschi D, Varner RL, Vasilyev S, Wilkerson JF, Wiseman C, Xu W, Yu CH, Zhu BX. Search for Solar Axions via Axion-Photon Coupling with the Majorana Demonstrator. Phys Rev Lett 2022; 129:081803. [PMID: 36053699 DOI: 10.1103/physrevlett.129.081803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
Axions were originally proposed to explain the strong-CP problem in QCD. Through axion-photon coupling, the Sun could be a major source of axions, which could be measured in solid state detection experiments with enhancements due to coherent Primakoff-Bragg scattering. The Majorana Demonstrator experiment has searched for solar axions with a set of ^{76}Ge-enriched high purity germanium detectors using a 33 kg-yr exposure collected between January, 2017 and November, 2019. A temporal-energy analysis gives a new limit on the axion-photon coupling as g_{aγ}<1.45×10^{-9} GeV^{-1} (95% confidence level) for axions with mass up to 100 eV/c^{2}. This improves laboratory-based limits between about 1 eV/c^{2} and 100 eV/c^{2}.
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Affiliation(s)
- I J Arnquist
- Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - F T Avignone
- Department of Physics and Astronomy, University of South Carolina, Columbia, South Carolina 29208, USA
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - A S Barabash
- National Research Center "Kurchatov Institute" Institute for Theoretical and Experimental Physics, Moscow, 117218 Russia
| | - C J Barton
- Department of Physics, University of South Dakota, Vermillion, South Dakota 57069, USA
| | - K H Bhimani
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - E Blalock
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - B Bos
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - M Busch
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
- Department of Physics, Duke University, Durham, North Carolina 27708, USA
| | - M Buuck
- Center for Experimental Nuclear Physics and Astrophysics, and Department of Physics, University of Washington, Seattle, Washington 98195, USA
| | - T S Caldwell
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - Y-D Chan
- Nuclear Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | | | - P-H Chu
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - M L Clark
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - C Cuesta
- Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas, CIEMAT 28040, Madrid, Spain
| | - J A Detwiler
- Center for Experimental Nuclear Physics and Astrophysics, and Department of Physics, University of Washington, Seattle, Washington 98195, USA
| | - Yu Efremenko
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37916, USA
| | - H Ejiri
- Research Center for Nuclear Physics, Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - S R Elliott
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - G K Giovanetti
- Physics Department, Williams College, Williamstown, Massachusetts 01267, USA
| | - M P Green
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - J Gruszko
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - I S Guinn
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - V E Guiseppe
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - C R Haufe
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - R Henning
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - D Hervas Aguilar
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - E W Hoppe
- Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - A Hostiuc
- Center for Experimental Nuclear Physics and Astrophysics, and Department of Physics, University of Washington, Seattle, Washington 98195, USA
| | - M F Kidd
- Tennessee Tech University, Cookeville, Tennessee 38505, USA
| | - I Kim
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - R T Kouzes
- Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - T E Lannen V
- Department of Physics and Astronomy, University of South Carolina, Columbia, South Carolina 29208, USA
| | - A Li
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - A M Lopez
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37916, USA
| | | | - E L Martin
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - R D Martin
- Department of Physics, Engineering Physics and Astronomy, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - R Massarczyk
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - S J Meijer
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - T K Oli
- Department of Physics, University of South Dakota, Vermillion, South Dakota 57069, USA
| | - G Othman
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - L S Paudel
- Department of Physics, University of South Dakota, Vermillion, South Dakota 57069, USA
| | - W Pettus
- Department of Physics, Indiana University, Bloomington, Indiana 47405, USA
- IU Center for Exploration of Energy and Matter, Bloomington, Indiana 47408, USA
| | - A W P Poon
- Nuclear Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - D C Radford
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - A L Reine
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - K Rielage
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - N W Ruof
- Center for Experimental Nuclear Physics and Astrophysics, and Department of Physics, University of Washington, Seattle, Washington 98195, USA
| | - D C Schaper
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - D Tedeschi
- Department of Physics and Astronomy, University of South Carolina, Columbia, South Carolina 29208, USA
| | - R L Varner
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - S Vasilyev
- Joint Institute for Nuclear Research, Dubna, 141980 Russia
| | - J F Wilkerson
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - C Wiseman
- Center for Experimental Nuclear Physics and Astrophysics, and Department of Physics, University of Washington, Seattle, Washington 98195, USA
| | - W Xu
- Department of Physics, University of South Dakota, Vermillion, South Dakota 57069, USA
| | - C-H Yu
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - B X Zhu
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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Kim I, Chhetri G, Kim J, So Y, Seo T. Quadrisphaera setariae sp. nov., polyphosphate-accumulating bacterium occurring as tetrad or aggregate cocci and isolated from Setaria viridis. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, orange-pigmented, aerobic, cocci (occurring in tetrads), non-spore-forming, non-motile bacterium, designated as DD2AT, was isolated from Setaria viridis collected at Dongguk University, Republic of Korea. Phylogenetic analysis based on the 16S rRNA gene revealed that strain DD2AT was most closely related to type strains of the genus
Quadrisphaera
. Strain DD2AT showed the highest 16S rRNA gene sequence similarities to
Quadrisphaera oryzae
TBRC 8486T (99.4 %) and
Quadrisphaera granulorum
JCM 16010T (98.8 %). Strain DD2AT also showed auto-aggregation ability. The digital DNA–DNA hybridization values between strain DD2AT and the reference strains,
Q. oryzae
TBRC 8486T and
Q. granulorum
JCM 16010T were 31.1 and 27.4 %, respectively. The average nucleotide identity values between strain DD2AT and
Q. oryzae
TBRC 8486T and
Q. granulorum
JCM 16010T were 86.3 and 84.1 %, respectively. The major polar lipids of strain DD2AT were diphosphatidylglycerol and phosphatidylglycerol. The major cellular fatty acid of strain DD2AT was anteiso-C15 : 0. The cell-wall peptidoglycan contained meso-diaminopimelic acid (which is a diagnostic cell-wall diamino acid), alanine and glutamic acid. The respiratory quinones was found to be menaquinone-8. The DNA G+C content of strain DD2AT was 74.8 mol%. On the basis of the findings of genotypic, phenotypic, chemotaxonomic and phylogenetic analyses, strain DD2AT was considered to represent a novel member in the genus
Quadrisphaera
, for which the name Quadrisphaera setariae sp. nov. is proposed. The type strain of Quadrisphaera setariae is DD2AT (=KACC 21165T=NBRC 113770T).
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Affiliation(s)
- Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, Republic of Korea
| | - Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang, Republic of Korea
| | - Jiyoun Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, Republic of Korea
| | - Yoonseop So
- Department of Life Science, Dongguk University-Seoul, Goyang, Republic of Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang, Republic of Korea
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Klosowicz A, Crouch J, Zhan Q, Kim I, Gehad A, Teague J, Kupper T, Clark R. 085 Senescent dendritic cells drive ROS-induced DNA damage in CTCL. J Invest Dermatol 2022. [DOI: 10.1016/j.jid.2022.05.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Wahid S, Lee B, Kim I. Effect of purified docosahexaenoic acid supplementation
on production performance, meat quality,
and intestinal microbiome of finishing pigs. J Anim Feed Sci 2022. [DOI: 10.22358/jafs/150033/2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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39
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Kim J, Lee B, Chhetri G, Kim I, So Y, Jang W, Seo T. Identification of Mucilaginibacter conchicola sp. nov., Mucilaginibacter achroorhodeus sp. nov. and Mucilaginibacter pallidiroseus sp. nov. and emended description of the genus Mucilaginibacter. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005431] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three chitinolytic, Gram-negative, light pink, capsule-forming, rod-shaped bacterial strains with gliding motion (MYSH2T, MJ1aT and dk17T) were isolated from seashells, soil and foxtail, respectively. Phylogenetic analysis of the 16S rRNA gene sequences and concatenated alignment of 92 core genes indicated that strains MYSH2T, MJ1aT and dk17T were novel species of the genus
Mucilaginibacter
and exhibited a high 16S rRNA sequence similarity (i.e. more than 97.2 %) among each other. These novel strains contained summed feature 3 (C16:1 ω7c and/or C16:1 ω6), iso-C15:0 and MK-7 as the predominant fatty acids and menaquinone. According to the CAZys coding gene of KAAS, MYSH2T and MJ1aT were interpreted as strains containing both GH18 and 19 family coding genes, except for dk17T, which shows only GH19 family genes. These strains likely degrade chitin to chitobiose or directly to N-acetyl-d-glucosamine, which may enhance their chitinolytic capacity, thus making these stains potentially useful for industrial chitin degradation. Based on distinct morphological, physiological, chemotaxonomic and phylogenetic differences from their closest phylogenetic neighbours, we propose that strains MYSH2T, MJ1aT and dk17T represent three novel species in the genus
Mucilaginibacter
, for which the names Mucilaginibacter conchicola sp. nov. (=KACC 19716T=JCM 32787T), Mucilaginibacter achroorhodeus sp. nov. (=KACC 19906T=NBRC 113667T) and Mucilaginibacter pallidiroseus sp. nov. (=KACC 19907T=NBRC 113666T) are proposed. An emended description of the genus
Mucilaginibacter
is proposed.
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Affiliation(s)
- Jiyoun Kim
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
| | - Byungjo Lee
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
| | - Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
| | - Yoonseop So
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
| | - Wonhee Jang
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
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40
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Barinov VV, Cleveland BT, Danshin SN, Ejiri H, Elliott SR, Frekers D, Gavrin VN, Gorbachev VV, Gorbunov DS, Haxton WC, Ibragimova TV, Kim I, Kozlova YP, Kravchuk LV, Kuzminov VV, Lubsandorzhiev BK, Malyshkin YM, Massarczyk R, Matveev VA, Mirmov IN, Nico JS, Petelin AL, Robertson RGH, Sinclair D, Shikhin AA, Tarasov VA, Trubnikov GV, Veretenkin EP, Wilkerson JF, Zvir AI. Results from the Baksan Experiment on Sterile Transitions (BEST). Phys Rev Lett 2022; 128:232501. [PMID: 35749172 DOI: 10.1103/physrevlett.128.232501] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 01/18/2022] [Accepted: 02/28/2022] [Indexed: 06/15/2023]
Abstract
The Baksan Experiment on Sterile Transitions (BEST) was designed to investigate the deficit of electron neutrinos ν_{e} observed in previous gallium-based radiochemical measurements with high-intensity neutrino sources, commonly referred to as the "gallium anomaly," which could be interpreted as evidence for oscillations between ν_{e} and sterile neutrino (ν_{s}) states. A 3.414-MCi ^{51}Cr ν_{e} source was placed at the center of two nested Ga volumes and measurements were made of the production of ^{71}Ge through the charged current reaction, ^{71}Ga(ν_{e},e^{-})^{71}Ge, at two average distances. The measured production rates for the inner and the outer targets, respectively, are [54.9_{-2.4}^{+2.5}(stat)±1.4(syst)] and [55.6_{-2.6}^{+2.7}(stat)±1.4(syst)] atoms of ^{71}Ge/d. The ratio (R) of the measured rate of ^{71}Ge production at each distance to the expected rate from the known cross section and experimental efficiencies are R_{in}=0.79±0.05 and R_{out}=0.77±0.05. The ratio of the outer to the inner result is 0.97±0.07, which is consistent with unity within uncertainty. The rates at each distance were found to be similar, but 20%-24% lower than expected, thus reaffirming the anomaly. These results are consistent with ν_{e}→ν_{s} oscillations with a relatively large Δm^{2} (>0.5 eV^{2}) and mixing sin^{2}2θ (≈0.4).
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Affiliation(s)
- V V Barinov
- Institute for Nuclear Research of the Russian Academy of Sciences, Moscow 117312, Russia
| | | | - S N Danshin
- Institute for Nuclear Research of the Russian Academy of Sciences, Moscow 117312, Russia
| | - H Ejiri
- Research Center for Nuclear Physics, Osaka University, Osaka 567-0047, Japan
| | - S R Elliott
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - D Frekers
- Institut für Kernphysik, Westfälische Wilhelms-Universität Munster, D-48149 Munster, Germany
| | - V N Gavrin
- Institute for Nuclear Research of the Russian Academy of Sciences, Moscow 117312, Russia
| | - V V Gorbachev
- Institute for Nuclear Research of the Russian Academy of Sciences, Moscow 117312, Russia
| | - D S Gorbunov
- Institute for Nuclear Research of the Russian Academy of Sciences, Moscow 117312, Russia
| | - W C Haxton
- Nuclear Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- Department of Physics, University of California, Berkeley, California 94720, USA
| | - T V Ibragimova
- Institute for Nuclear Research of the Russian Academy of Sciences, Moscow 117312, Russia
| | - I Kim
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Yu P Kozlova
- Institute for Nuclear Research of the Russian Academy of Sciences, Moscow 117312, Russia
| | - L V Kravchuk
- Institute for Nuclear Research of the Russian Academy of Sciences, Moscow 117312, Russia
| | - V V Kuzminov
- Institute for Nuclear Research of the Russian Academy of Sciences, Moscow 117312, Russia
| | - B K Lubsandorzhiev
- Institute for Nuclear Research of the Russian Academy of Sciences, Moscow 117312, Russia
| | - Yu M Malyshkin
- Institute for Nuclear Research of the Russian Academy of Sciences, Moscow 117312, Russia
| | - R Massarczyk
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - V A Matveev
- Joint Institute for Nuclear Research (JINR) Joliot-Curie 6, 141980 Dubna, Moscow Region, Russia
| | - I N Mirmov
- Institute for Nuclear Research of the Russian Academy of Sciences, Moscow 117312, Russia
| | - J S Nico
- National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, USA
| | - A L Petelin
- JSC "State Scientific Center Research Institute of Atomic Reactors," Dimitrovgrad 433510, Russia
| | - R G H Robertson
- Center for Experimental Nuclear Physics and Astrophysics, and Department of Physics, University of Washington, Seattle, Washington 98195, USA
| | - D Sinclair
- Carleton University 1125 Colonel By Drive, Ottawa K1S 5B6, Canada
| | - A A Shikhin
- Institute for Nuclear Research of the Russian Academy of Sciences, Moscow 117312, Russia
| | - V A Tarasov
- JSC "State Scientific Center Research Institute of Atomic Reactors," Dimitrovgrad 433510, Russia
| | - G V Trubnikov
- Joint Institute for Nuclear Research (JINR) Joliot-Curie 6, 141980 Dubna, Moscow Region, Russia
| | - E P Veretenkin
- Institute for Nuclear Research of the Russian Academy of Sciences, Moscow 117312, Russia
| | - J F Wilkerson
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27599, USA
- Triangle Universities Nuclear Laboratory, Durham, North Carolina 27708, USA
| | - A I Zvir
- JSC "State Scientific Center Research Institute of Atomic Reactors," Dimitrovgrad 433510, Russia
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Alagoz O, Ajani J, Srinivasan S, Kim I, Singh P, Xiao H, Kurt M. P-56 Estimating endpoint correlation between surrogate measures and overall survival using reconstructed survival data: Case studies from adjuvant and metastatic gastric cancer trials. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.04.146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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42
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Abstract
A starch-degrading novel strain, designated as strain ITR2T, was isolated from a soil sample collected from a garden near Dongguk University located in Goyang, Republic of Korea. The strain was identified as Gram-stain-positive, rod-shaped, and motile by means of peritrichous flagella. Moreover, 16S rRNA gene analysis revealed the novel strain to form a separate clade with
Tumebacillus permanentifrigoris
Eur1 9.5T (98.3 %) while also clustering with
Tumebacillus flagellatus
GST4T (97.9 %). Strain ITR2T grew optimally at temperatures of 20–30 °C, at pH 6.0–7.0 and at NaCl concentrations of 0–1 %. The sole quinone was menaquinone-7 and the cell-wall peptidoglycan comprised alanine, aspartic acid, glutamic acid, lysine and meso-diaminopimelic acid (type-A1γ peptidoglycan). The major fatty acids (>10%) of the novel strain were C16 : 0, iso-C14 : 0, iso-C15 : 0 and anteiso-C15 : 0, while the major polar lipids were phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol and one unidentified phospholipid. Other polar lipids of the novel strain included, two unidentified glycolipids, three unidentified phospholipids and one unidentified lipid. The in silico DNA–DNA hybridization values between strain ITR2T and its reference strains (
T. permanentifrigoris
DSM 18773T and
T. flagellatus
GST4T) were 21.3 and 23.9 %, respectively, while the average nucleotide identity values were 78.5 and 81.2 %, respectively. The genomic DNA G+C content was 54.9 mol%. Based on the phylogenetic, chemotaxonomic and genomic data obtained in the present study, we propose Tumebacillus amylolyticus sp. nov. to be a novel species within the genus
Tumebacillus
. The type strain is ITR2T (=KCTC 43280T=NBRC 114753T).
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Affiliation(s)
- Minchung Kang
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Jiyoun Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Yoonseop So
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
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43
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Lee S, Dong-Won Y, Cheon J, Lee S, Cho H, Kim I. M231 Application trial of moving average as a tool of realtime quality control of clinical chemistry. Clin Chim Acta 2022. [DOI: 10.1016/j.cca.2022.04.419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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44
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Arnquist IJ, Avignone FT, Barabash AS, Barton CJ, Bertrand FE, Blalock E, Bos B, Busch M, Buuck M, Caldwell TS, Chan YD, Christofferson CD, Chu PH, Clark ML, Cuesta C, Detwiler JA, Drobizhev A, Edwards TR, Edwins DW, Edzards F, Efremenko Y, Elliott SR, Gilliss T, Giovanetti GK, Green MP, Gruszko J, Guinn IS, Guiseppe VE, Haufe CR, Hegedus RJ, Henning R, Aguilar DH, Hoppe EW, Hostiuc A, Kim I, Kouzes RT, Lopez AM, López-Castaño JM, Martin EL, Martin RD, Massarczyk R, Meijer SJ, Mertens S, Myslik J, Oli TK, Othman G, Pettus W, Poon AWP, Radford DC, Rager J, Reine AL, Rielage K, Ruof NW, Saykı B, Schönert S, Stortini MJ, Tedeschi D, Varner RL, Vasilyev S, Wilkerson JF, Willers M, Wiseman C, Xu W, Yu CH, Zhu BX. α -event characterization and rejection in point-contact HPGe detectors. Eur Phys J C Part Fields 2022; 82:226. [PMID: 35310515 PMCID: PMC8921096 DOI: 10.1140/epjc/s10052-022-10161-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 02/23/2022] [Indexed: 06/14/2023]
Abstract
P-type point contact (PPC) HPGe detectors are a leading technology for rare event searches due to their excellent energy resolution, low thresholds, and multi-site event rejection capabilities. We have characterized a PPC detector's response to α particles incident on the sensitive passivated and p + surfaces, a previously poorly-understood source of background. The detector studied is identical to those in the Majorana Demonstrator experiment, a search for neutrinoless double-beta decay ( 0 ν β β ) in 76 Ge. α decays on most of the passivated surface exhibit significant energy loss due to charge trapping, with waveforms exhibiting a delayed charge recovery (DCR) signature caused by the slow collection of a fraction of the trapped charge. The DCR is found to be complementary to existing methods of α identification, reliably identifying α background events on the passivated surface of the detector. We demonstrate effective rejection of all surface α events (to within statistical uncertainty) with a loss of only 0.2% of bulk events by combining the DCR discriminator with previously-used methods. The DCR discriminator has been used to reduce the background rate in the 0 ν β β region of interest window by an order of magnitude in the Majorana Demonstrator and will be used in the upcoming LEGEND-200 experiment.
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Affiliation(s)
- I. J. Arnquist
- Pacific Northwest National Laboratory, Richland, WA 99354 USA
| | - F. T. Avignone
- Department of Physics and Astronomy, University of South Carolina, Columbia, SC 29208 USA
- Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - A. S. Barabash
- National Research Center “Kurchatov Institute” Institute for Theoretical and Experimental Physics, Moscow, 117218 Russia
| | - C. J. Barton
- Department of Physics, University of South Dakota, Vermillion, SD 57069 USA
| | | | - E. Blalock
- Department of Physics, North Carolina State University, Raleigh, NC 27695 USA
- Triangle Universities Nuclear Laboratory, Durham, NC 27708 USA
| | - B. Bos
- Triangle Universities Nuclear Laboratory, Durham, NC 27708 USA
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, NC 27514 USA
| | - M. Busch
- Triangle Universities Nuclear Laboratory, Durham, NC 27708 USA
- Department of Physics, Duke University, Durham, NC 27708 USA
| | - M. Buuck
- Center for Experimental Nuclear Physics and Astrophysics, and Department of Physics, University of Washington, Seattle, WA 98195 USA
- Present Address: SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - T. S. Caldwell
- Triangle Universities Nuclear Laboratory, Durham, NC 27708 USA
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, NC 27514 USA
| | - Y.-D. Chan
- Nuclear Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | | | - P.-H. Chu
- Los Alamos National Laboratory, Los Alamos, NM 87545 USA
| | - M. L. Clark
- Triangle Universities Nuclear Laboratory, Durham, NC 27708 USA
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, NC 27514 USA
| | - C. Cuesta
- Center for Experimental Nuclear Physics and Astrophysics, and Department of Physics, University of Washington, Seattle, WA 98195 USA
- Present Address: Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas, CIEMAT, 28040 Madrid Spain
| | - J. A. Detwiler
- Center for Experimental Nuclear Physics and Astrophysics, and Department of Physics, University of Washington, Seattle, WA 98195 USA
| | - A. Drobizhev
- Nuclear Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - T. R. Edwards
- Department of Physics, University of South Dakota, Vermillion, SD 57069 USA
- Los Alamos National Laboratory, Los Alamos, NM 87545 USA
| | - D. W. Edwins
- Department of Physics and Astronomy, University of South Carolina, Columbia, SC 29208 USA
| | - F. Edzards
- Max-Planck-Institut für Physik, 80805 Munich, Germany
- Present Address: Physik-Department, Technische Universität, 85748 Munich, Germany
| | - Y. Efremenko
- Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- Department of Physics and Astronomy, University of Tennessee, Knoxville, TN 37916 USA
| | - S. R. Elliott
- Los Alamos National Laboratory, Los Alamos, NM 87545 USA
| | - T. Gilliss
- Triangle Universities Nuclear Laboratory, Durham, NC 27708 USA
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, NC 27514 USA
- Present Address: Applied Physics Laboratory, Johns Hopkins University, Laurel, MD 20723 USA
| | - G. K. Giovanetti
- Physics Department, Williams College, Williamstown, MA 01267 USA
| | - M. P. Green
- Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- Department of Physics, North Carolina State University, Raleigh, NC 27695 USA
- Triangle Universities Nuclear Laboratory, Durham, NC 27708 USA
| | - J. Gruszko
- Triangle Universities Nuclear Laboratory, Durham, NC 27708 USA
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, NC 27514 USA
| | - I. S. Guinn
- Triangle Universities Nuclear Laboratory, Durham, NC 27708 USA
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, NC 27514 USA
| | | | - C. R. Haufe
- Triangle Universities Nuclear Laboratory, Durham, NC 27708 USA
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, NC 27514 USA
| | - R. J. Hegedus
- Triangle Universities Nuclear Laboratory, Durham, NC 27708 USA
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, NC 27514 USA
| | - R. Henning
- Triangle Universities Nuclear Laboratory, Durham, NC 27708 USA
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, NC 27514 USA
| | - D. Hervas Aguilar
- Triangle Universities Nuclear Laboratory, Durham, NC 27708 USA
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, NC 27514 USA
| | - E. W. Hoppe
- Pacific Northwest National Laboratory, Richland, WA 99354 USA
| | - A. Hostiuc
- Center for Experimental Nuclear Physics and Astrophysics, and Department of Physics, University of Washington, Seattle, WA 98195 USA
| | - I. Kim
- Los Alamos National Laboratory, Los Alamos, NM 87545 USA
| | - R. T. Kouzes
- Pacific Northwest National Laboratory, Richland, WA 99354 USA
| | - A. M. Lopez
- Department of Physics and Astronomy, University of Tennessee, Knoxville, TN 37916 USA
| | | | - E. L. Martin
- Triangle Universities Nuclear Laboratory, Durham, NC 27708 USA
- Department of Physics, Duke University, Durham, NC 27708 USA
| | - R. D. Martin
- Department of Physics, Engineering Physics and Astronomy, Queen’s University, Kingston, ON K7L 3N6 Canada
| | - R. Massarczyk
- Los Alamos National Laboratory, Los Alamos, NM 87545 USA
| | - S. J. Meijer
- Los Alamos National Laboratory, Los Alamos, NM 87545 USA
| | - S. Mertens
- Max-Planck-Institut für Physik, 80805 Munich, Germany
- Present Address: Physik-Department, Technische Universität, 85748 Munich, Germany
| | - J. Myslik
- Nuclear Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - T. K. Oli
- Department of Physics, University of South Dakota, Vermillion, SD 57069 USA
| | - G. Othman
- Triangle Universities Nuclear Laboratory, Durham, NC 27708 USA
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, NC 27514 USA
- Universität Hamburg, 20146 Hamburg, Germany
| | - W. Pettus
- Department of Physics, Indiana University, Bloomington, IN 47405 USA
- IU Center for Exploration of Energy and Matter, Bloomington, IN 47408 USA
| | - A. W. P. Poon
- Nuclear Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - D. C. Radford
- Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - J. Rager
- Triangle Universities Nuclear Laboratory, Durham, NC 27708 USA
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, NC 27514 USA
- Present Address: Applied Research Associated, Raleigh, NC 27615 USA
| | - A. L. Reine
- Triangle Universities Nuclear Laboratory, Durham, NC 27708 USA
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, NC 27514 USA
| | - K. Rielage
- Los Alamos National Laboratory, Los Alamos, NM 87545 USA
| | - N. W. Ruof
- Center for Experimental Nuclear Physics and Astrophysics, and Department of Physics, University of Washington, Seattle, WA 98195 USA
| | - B. Saykı
- Los Alamos National Laboratory, Los Alamos, NM 87545 USA
| | - S. Schönert
- Present Address: Physik-Department, Technische Universität, 85748 Munich, Germany
| | - M. J. Stortini
- Los Alamos National Laboratory, Los Alamos, NM 87545 USA
| | - D. Tedeschi
- Department of Physics and Astronomy, University of South Carolina, Columbia, SC 29208 USA
| | - R. L. Varner
- Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - S. Vasilyev
- Joint Institute for Nuclear Research, Dubna, 141980 Russia
| | - J. F. Wilkerson
- Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- Triangle Universities Nuclear Laboratory, Durham, NC 27708 USA
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, NC 27514 USA
| | - M. Willers
- Present Address: Physik-Department, Technische Universität, 85748 Munich, Germany
| | - C. Wiseman
- Center for Experimental Nuclear Physics and Astrophysics, and Department of Physics, University of Washington, Seattle, WA 98195 USA
| | - W. Xu
- Department of Physics, University of South Dakota, Vermillion, SD 57069 USA
| | - C.-H. Yu
- Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - B. X. Zhu
- Los Alamos National Laboratory, Los Alamos, NM 87545 USA
- Present Address: Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109 USA
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So Y, Chhetri G, Kim I, Kang M, Kim J, Lee B, Jang W, Seo T. Halomonas antri sp. nov., a carotenoid-producing bacterium isolated from surface seawater. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005272] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, moderately halophilic bacterium, designated as strain Y3S6T, was isolated from a surface seawater sample collected from Dongangyoeng cave, Udo-myeon, Jeju-si, Jeju-do, Repulic of Korea. Cells of strain Y3S6T were aerobic, rod-shaped, non-sporulated, yellow, catalase- negative, oxidase-negative and motile with one polar flagellum. Growth of strain Y3S6T occurred at 15–40 °C (optimum: 25–30 °C), at pH 6.0–9.0 (optimum: pH 7.0) and in the presence of 0–13% NaCl (optimum: 1–6 %, w/v). The novel strain was able to produce carotenoids. Its chemotaxonomic and morphological characteristics were consistent with those of members of the genus
Halomonas
. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain Y3S6T formed a clade with
Halomonas pellis
L5T (98.97 %) and
Halomonas saliphila
LCB169T(98.90%). The average nucleotide identity and digital DNA–DNA hybridization values of strain Y3S6T with the most closely related strains for which whole genomes are publicly available were 82.3–85.2% and 62.8–66.1 %, respectively. The major fatty acids in strain Y3S6T were C16 : 0, C19 : 0 cyclo ω8c and summed feature 8 (composed of C18 : 1 ω7c and/or C18 : 1 ω6c), and the predominant quinone was Q-9. Its polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified phosphoglycolipid, one unidentified phosphoaminoglycolipid and one unidentified phospholipid. The genomic DNA G+C content based on the draft genome sequence was 64.2 mol%. The results of physiological and biochemical tests and 16S rRNA sequence analysis clearly revealed that strain Y3S6T represents a novel species in the genus
Halomonas
, for which the name Halomonas antri sp. nov. has been proposed. The type strain is Y3S6T (=KACC 21536T=NBRC 114315=TBRC 15164T).
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Affiliation(s)
- Yoonseop So
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Minchung Kang
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Jiyoun Kim
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Byungjo Lee
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Wonhee Jang
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
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Kim I, Chhetri G, Kim J, Kang M, So Y, Lee B, Jang W, Seo T. Nocardioides donggukensis sp. nov. and Hyunsoonleella aquatilis sp. nov., isolated from Jeongbang Waterfall on Jeju Island. Int J Syst Evol Microbiol 2021; 71. [PMID: 34928203 DOI: 10.1099/ijsem.0.005176] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 11/18/2022] Open
Abstract
Two bacterial strains, designated MJB4T and SJ7T, were isolated from water samples collected from Jeongbang Falls on Jeju Island, Republic of Korea. Phylogenetic analysis of 16S rRNA gene sequences indicated that the two strains belonged to the genera Nocardioides and Hyunsoonleella, owing to their high similarities to Nocardioides jensenii DSM 29641T (97.5 %) and Hyunsoonleella rubra FA042 T (96.3 %), respectively. These values are much lower than the gold standard for bacterial species (98.7 %). The average nucleotide identity values between strains MJB4T, SJ7T and the reference strains, Nocardioides jensenii DSM 29641T, Nocardioides daejeonensis MJ31T and Hyunsoonleella flava T58T were 77.2, 75.9 and 75.4 %, respectively. Strains MJB4T and SJ7T and the type strains of the species involved in system incidence have average nucleotide identity and average amino acid threshold values of 60.1-82.6 % for the species boundary (95-96 %), which confirms that strains MJB4T and SJ7T represent two new species of genus Nocardioides and Hyunsoonleella, respectively. Based on phylogenetic and phenotypic data, strains MJB4T and SJ7T are considered to represent novel species of the genus Nocardioides and Hyunsoonleella, respectively, for which the names Nocardioides donggukensis sp. nov. (type strain MJB4T=KACC 21724T=NBRC 114402T) and Hyunsoonleella aquatilis sp. nov., (type strain SJ7T=KACC 21715T=NBRC 114486T) have been proposed.
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Affiliation(s)
- Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Jiyoun Kim
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Minchung Kang
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Yoonseop So
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Byungjo Lee
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Wonhee Jang
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
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Chhetri G, Kim I, Kang M, Kim J, So Y, Seo T. Devosia rhizoryzae sp. nov., and Devosia oryziradicis sp. nov., novel plant growth promoting members of the genus Devosia, isolated from the rhizosphere of rice plants. J Microbiol 2021; 60:1-10. [PMID: 34826099 DOI: 10.1007/s12275-022-1474-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [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: 09/09/2021] [Revised: 10/15/2021] [Accepted: 10/19/2021] [Indexed: 11/26/2022]
Abstract
Two novel Gram-negative, aerobic, asporogenous, motile, rod-shaped, orange and white pigmented, designated as LEGU1T and G19T, were isolated from the roots of rice plants, collected from Goyang, South Korea. Phylogenetic analysis based on their 16S rRNA gene sequences revealed that they belonged to the genus Devosia and formed a different lineage and clusters with different members of the genus Devosia. These strains shared common chemotaxonomic features. In particular, they had Q-10 as the sole quinone, phosphatidylglycerol, diphosphatidylglycerol as the principal polar lipids and C16:0, C18:1ω7c 11-methyl and summed feature 8 (comprising C18:1ω7c/C18:1ω6c) as the main fatty acids. The draft genome sequences of strains LEGU1T and G19T were 3,524,978 and 3,495,520 bp in size, respectively. Their average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values were 72.8-81.9% and 18.7-25.1%, respectively, with each other and type strains of related species belonging to the genus Devosia, suggesting that these two strains represent novel species. The G + C content of strains LEGU1T and G19T were 62.1 and 63.8%, respectively. Of the two strains, only LEGU1T produced carotenoid and flexirubin-type pigment. Both strains produced siderophore and indole acetic acid (IAA) in the presence of L-tryptophan. Siderophore biosynthesis genes, auxin responsive genes and tryptophan biosynthesis genes were present in their genomes. The present study aimed to determine the detailed taxonomic positions of the strains using the modern polyphasic approach. Based on the results of polyphasic analysis, these strains are suggested to be two novel bacterial species within the genus Devosia. The proposed names are D. rhizoryzae sp. nov., and Devosia oryziradicis sp. nov., respectively. The plant growth promoting effects of these strains suggest that they can be exploited to improve rice crop productivity. The type strain of D. rhizoryzae is LEGU1T (KCTC 82712T = NBRC 114485T) and D. oryziradicis is G19T (KCTC 82688T = NBRC 114842T).
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Affiliation(s)
- Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Minchung Kang
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Jiyoun Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Yoonseop So
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea.
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Kang M, Chhetri G, Kim J, Kim I, Seo T. Pontibacter cellulosilyticus sp. nov., a carboxymethyl cellulose-hydrolysing bacterium isolated from coastal water. Int J Syst Evol Microbiol 2021; 71. [PMID: 34694986 DOI: 10.1099/ijsem.0.005058] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, rod-shaped, non-motile, red-pink bacterium designated SD6T was isolated from coastal marine water at Sadong Beach, Ulleung Island, South Korea. Cells of SD6T grew at 10-42 °C (optimum, 30 °C), pH 5.0-9.0 (optimum, pH 6.0-7.0) and at 0-8.0 % (w/v) NaCl (optimum, 0-3 %). Moreover, 16S rRNA gene sequence analysis indicated that strain SD6T was a member of the genus Pontibacter, sharing similarities to Pontibacter aydingkolensis XAAS-1T (98.0 %), Pontibacter amylolyticus 9-2T (97.3 %), Pontibacter korlensis X14-1T (97.2 %) and Pontibacter soli HYL7-26T (96.8 %). The predominant fatty acids of strain SD6T were identified as iso-C15 : 0 and summed feature 4 (comprising anteiso-C17 : 1 B and/or iso-C17 : 1 I) and the sole respiratory quinone was identified as MK-7 (menaquinone 7). Major polar lipids included phosphatidylethanolamine, one unidentified phosphoglycolipid, two unidentified glycolipids and one unidentified lipid. The average nucleotide identity and in silico DNA-DNA hybridization values of strain SD6T with its closely related strains were 72.8-79.8 % and 19.2-22.6 %, respectively. The genomic DNA G+C content was 45.4 mol%. In accordance with the results of phenotypic, chemotaxonomic and phylogenetic data, strain SD6T represents a novel species of the genus Pontibacter, for which the name Pontibacter cellulosilyticus sp. nov. is proposed. The type strain is SD6T (=KACC 21543T=NBRC 114313T=JCM 31022T).
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Affiliation(s)
- Minchung Kang
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Jiyoun Kim
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
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Chhetri G, Kang M, Kim J, Kim I, So Y, Seo T. Sphingosinicella flava sp. nov., indole acetic acid producing bacteria isolated from maize field soil. Int J Syst Evol Microbiol 2021; 71. [PMID: 34605389 DOI: 10.1099/ijsem.0.005038] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel isolated yellow-pigmented bacterial designated strain UDD2T was isolated from a maize field soil sample collected in Ilsan, Republic of Korea. Cells of strain UDD2T were Gram-stain-negative, non-sporulating, long rod-shaped and exhibited flagellar motility. Cells could grow at 15-42 °C and pH 5.5-11.0. Strain UDD2T was sensitive to NaCl and barely tolerated up to 1 % NaCl (w/v). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain UDD2T formed a separate clade with the members of genus Sphingosinicella within the family Sphingomonadaceae. Strain UDD2T showed the highest 16S rRNA gene sequence similarity to Sphingosinicella vermicomposti KCTC 224446T (98.5 %) and Sphingosinicella humi KCTC 62519T (96.7 %), followed by members of the genus Sphingomonas (96.4-94.5 %) and Sphingobium (96.1-94.9 %), but they were located in other phylogenetic clusters. Average nucleotide identity and digital DNA-DNA hybridization values between strain UDD2T and S. vermicomposti KCTC 224446T and S. humi KCTC 62519T were 80.2/24.2 and 75.6/20.4 %, respectively. The total size of the genome was 2 421 697 bp and composed of one circular chromosome, with a G+C content of 63.7 mol%. Strain UDD2T produced indole acetic acid (IAA) in the presence of l-tryptophan. Bacterial IAA is a crucial phytohormone in plant growth and development. Gene clusters for indole-3-glycerol phosphate synthase and tryptophan synthase were found in the genome of strain UDD2T. To the best of our knowledge, no member of the genus Sphingosinicella has been reported to produce IAA to date. The major cellular fatty acids (>10 %) were found to be C16 : 0, C14 : 0 2OH and summed feature 3 (comprising C16 : 1 ω7c and/or iso-C15 : 0 2-OH). Strain UDD2T had ubiquinone Q-10 as the major respiratory quinone and homospermidine as the major polyamine. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, phosphatidylglycerol, phosphatidylcholine, three unidentified phosphoglycolipids, one unidentified phospholipid, one unidentified aminoglycophospholipid, one unidentified glycolipid and one unidentified polar lipid. Based on the phylogenetic, phenotypic, chemotaxonomic and genotypic data, strain UDD2T represents a novel species of the genus Sphingosinicella, for which the name Sphingosinicella flava is proposed. The type strain is UDD2T (=KCTC 82357T=NBRC 114507T).
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Affiliation(s)
- Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Minchung Kang
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Jiyoun Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Yoonseop So
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
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Chhetri G, Kim I, Kang M, Kim J, So Y, Seo T. Flavobacterium tagetis sp. nov., a novel urea-hydrolysing bacterium isolated from the roots of Tagetes patula. Int J Syst Evol Microbiol 2021; 71. [PMID: 34542390 DOI: 10.1099/ijsem.0.004984] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, rod-shaped, motile by gliding, non-sporulating and strictly aerobic bacterium, designated strain GN10T, was isolated from the roots of Tagetes patula, collected from the garden of Dongguk University, Goyang, Republic of Korea. The cells could grow at 10-42 °C and at pH 5.5-9.0. Strain GN10T was sensitive to NaCl and tolerated up to 4 % NaCl (w/v). Comparative analysis of 16S rRNA gene sequences revealed the highest similarities to Flavobacterium tistrianum GB 56.1T (98.9 %), Flavobacterium sharifuzzamanii A7.6T (98.6 %), Flavobacterium zhairuonense A5.7T (98.3 %) and Flavobacterium anhuiense D3T (98 %). Phylogenetic analysis showed that strain GN10T clustered within the genus Flavobacterium and formed a monophyletic cluster with its close relative members. The average nucleotide identity and digital DNA-DNA hybridization values between strain GN10T and related species belonging to the genus Flavobacterium were well below the standard threshold for prokaryotic species delineation. The DNA G+C content of strain GN10T was 33.6 mol%. The predominant cellular fatty acids (>10 %) were identified as iso-C15 : 0, C16 : 0 and summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c). Strain GN10T contained menaquinone 6 as the major respiratory quinone. The major polar lipids were phosphatidylethanolamine, three unidentified aminoglycolipids, two unidentified glycolipids, one unidentified phosphoglycolipid and five unidentified lipids. Urease is a nickel-containing enzyme found in archaea, bacteria, plants and unicellular eukaryotes. It serves as a virulence factor and is responsible for pathogenesis in humans and animals. Here, we describe a novel urease-hydrolysing bacterium, strain GN10T. The urease activity of this strain may serve as an indicator of pathogenic potential and drug resistance, which may facilitate the development of many diseases. The results of physiological and biochemical tests allowed the genotypic and phenotypic differentiation of strain GN10T from its closely related members and considered to represent novel species in the genus Flavobacterium, for which the name Flavobacterium tagetis (GN10T=KCTC 82695T=NBRC 114841T) is proposed.
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Affiliation(s)
- Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Minchung Kang
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Jiyoun Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Yoonseop So
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
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