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Lee H, Chaudhary DK, Kim DU. Sphingomonas flavescens sp. nov., isolated from soil. Arch Microbiol 2024; 206:119. [PMID: 38396312 DOI: 10.1007/s00203-024-03851-6] [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: 12/18/2023] [Revised: 01/11/2024] [Accepted: 01/17/2024] [Indexed: 02/25/2024]
Abstract
An aerobic bacterium, designated as PT-12T, was isolated from soil collected from agriculture field, and its taxonomic position was validated through a comprehensive polyphasic methodology. The strain was identified as Gram-stain-negative, non-motile, rod-shaped, and catalase- and oxidase-positive. The yellow-colored colonies showed growth ability at temperature range of 18-37 °C, NaCl content of 0-1.0% (w/v), and at a pH of 6.0-8.0. The 16S rRNA gene and phylogenetic analysis showed that strain PT-12T affiliated with the genus Sphingomonas in the family Sphingomonadaceae, and displayed the highest 16S rRNA nucleotide sequence similarity with Sphingomonas limnosediminicola 03SUJ6T (98.4%). The genome size of strain PT-12T was 2,656,862 bp and the DNA G + C content estimated from genome was 63.5%. The highest values of average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) were observed between strain PT-12T and Sphingomonas segetis YJ09T, accounting to 76.2% and 20.2%, respectively. In addition, both ANI and dDDH values between strain PT-12T and other phylogenetically related neighbors ranged between 69.6% and 76.2% and 18.4% and 20.2%, respectively. Chemotaxonomic features exhibited Q-10 as the only ubiquinone; homospermidine as the major polyamine; summed feature 8 (C18:1ω7c and/or C18:1ω6c), C16:0, and 10-methyl C18:0 as the notable fatty acids; and phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, and sphingoglycolipid as dominating polar lipids. Overall, the comprehensive polyphasic data supported that strain PT-12T represents a novel bacterial species within the genus Sphingomonas. Accordingly, we propose the name Sphingomonas flavescens sp. nov. The type strain is PT-12T (= KCTC 92114T = NBRC 115717T).
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Affiliation(s)
- Hyosun Lee
- Department of Biological Science, College of Science and Engineering, Sangji University, Wonju, 26339, Republic of Korea
| | - Dhiraj Kumar Chaudhary
- Department of Biomaterials, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, 600077, India
| | - Dong-Uk Kim
- Department of Biological Science, College of Science and Engineering, Sangji University, Wonju, 26339, Republic of Korea.
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Zhu L, Yang B, Guo W, Hu X, Liu S, Xiao X, Wei W. Nocardioides limicola sp. nov., an alkaliphilic alkane degrading bacterium isolated from oilfield alkali-saline soil. Antonie Van Leeuwenhoek 2024; 117:14. [PMID: 38170333 DOI: 10.1007/s10482-023-01907-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: 07/24/2023] [Accepted: 11/20/2023] [Indexed: 01/05/2024]
Abstract
A Gram-stain-positive, rod-shaped, non-spore-forming, alkane degrading bacterium, designated DJM-14T, was isolated from oilfield alkali-saline soil in Heilongjiang, Northeast China. On the basis of 16 S rRNA gene sequencing, strain DJM-14T was shown to belong to the genus Nocardioides, and related most closely to Nocardioides terrigena KCTC 19,217T (95.53% 16 S rRNA gene sequence similarity). Strain DJM-14T was observed to grow at 25-35 °C, pH 7.0-11.0, in the presence of 0-6.0% (w/v) NaCl. The predominant respiratory quinone was MK-8 (H4) and LL-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. The major fatty acids were identified as iso-C16:0 and C18:1 ω9c. It contained diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol as the polar lipids. The genome (3,722,608 bp), composed of 24 contigs, had a G + C content of 69.6 mol%. Out of the 3667 predicted genes, 3618 were protein-coding genes, and 49 were ncRNAs. Digital DNA-DNA hybridization (dDDH) estimation and average nucleotide identity (ANI) of strain DJM-14T against genomes of the type strains of related species in the same family ranged between 18.7% and 20.0%; 68.8% and 73.6%, respectively. According to phenotypic, genotypic and phylogenetic data, strain DJM-14T represents a novel species in the genus Nocardioides, for which the name Nocardioides limicola sp. nov. is proposed and the type strain is DJM-14T (= CGMCC 4.7593T, =JCM 33,692T). In addition, novel strains were able to grow with n-alkane (C24-C36) as the sole carbon source. Multiple copies of alkane 1-monooxygenase (alkB) gene, as well as alcohol dehydrogenase gene and aldehyde dehydrogenase gene involved in the alkane assimilation were annotated in the genome of type strain DJM-14T.
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Affiliation(s)
- Lin Zhu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Biyue Yang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Wenjun Guo
- School of Agricultural Engineering, Jiangsu University, Zhenjiang, China
| | - Xinyu Hu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Shenkui Liu
- State Key Laboratory of Subtropical Forest Cultivation, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Xiang Xiao
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Wei Wei
- School of Agricultural Engineering, Jiangsu University, Zhenjiang, China.
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Chen X, Zheng Z, Li F, Ma X, Chen F, Chen M, Tuo L. Description and genomic characterization of Nocardioides bruguierae sp. nov., isolated from Bruguiera gymnorhiza. Syst Appl Microbiol 2023; 46:126391. [PMID: 36621108 DOI: 10.1016/j.syapm.2022.126391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 11/21/2022] [Accepted: 12/28/2022] [Indexed: 01/04/2023]
Abstract
Strains BSK12Z-3T and BSK12Z-4, two Gram-stain-positive, aerobic, non-spore-forming strains, were isolated from Shankou Mangrove Nature Reserve, Guangxi Zhuang Autonomous Region, China. The diagnostic diamino acid in the cell-wall peptidoglycan of strain BSK12Z-3T was LL-diaminopimelic acid and MK-8(H4) was the predominant menaquinone. The polar lipids comprised diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and phospholipid (PL). The major fatty acids was iso-C16:0. Phylogenetic analysis based on 16S rRNA gene sequences suggested that the two strains fell within the genus Nocardioides, appearing most closely related to Nocardioides ginkgobilobae KCTC 39594T (97.5-97.6 % sequence similarity) and Nocardioides marinus DSM 18248T (97.4-97.6 %). Genome-based phylogenetic analysis confirmed that strains BSK12Z-3T and BSK12Z-4 formed a distinct phylogenetic cluster within the genus Nocardioides. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of strains BSK12Z-3T, BSK12Z-4 with their most related species N. marinus DSM18248T were within the ranges of 77.2-77.3 % and 21.3-21.4 %, respectively, clearly indicated that strains BSK12Z-3T, BSK12Z-4 represented novel species. Strains BSK12Z-3T and BSK12Z-4 exhibited 99.9 % 16S rRNA gene sequence similarity. The ANI and dDDH values between the two strains were 97.8 % and 81.1 %, respectively, suggesting that they belong to the same species. However, DNA fingerprinting discriminated that they were not from one clonal origin. Based on phylogenomic and phylogenetic analyses coupled with phenotypic and chemotaxonomic characterizatons, strains BSK12Z-3T and BSK12Z-4 could be classified as a novel species of the genus Nocardioides, for which the name Nocardioides bruguierae sp. nov., is proposed. The type strain is BSK12Z-3T (=CGMCC 4.7709T = JCM 34554T).
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Kim DY, Jeong IC, Lee SY, Jeong YS, Han JE, Tak EJ, Lee JY, Kim PS, Hyun DW, Bae JW. Nocardioides palaemonis sp. nov. and Tessaracoccus palaemonis sp. nov., isolated from the gastrointestinal tract of lake prawn. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748471 DOI: 10.1099/ijsem.0.005643] [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: 12/24/2022] Open
Abstract
Two novel Gram-stain-positive, non-motile and non-spore-forming bacterial strains, designated J2M5T and J1M15T, were isolated from the gastrointestinal tract of a lake prawn Palaemon paucidens. Strain J2M5T was an obligately aerobic bacterium that formed milky-coloured colonies and showed a rod-coccus cell cycle, while strain J1M15T was a facultatively aerobic bacterium that formed orangish-yellow-coloured colonies and showed rod-shaped cells. Strains J2M5T and J1M15T showed the highest 16S rRNA gene sequence similarity to Nocardioides ganghwensis JC2055T (98.63 %) and Tessaracoccus flavescens SST-39T (98.08 %), respectively. The whole-genome sequence of strain J2M5T was 4.52 Mbp in size and the genomic G+C content directly calculated from the genome sequence of strain J2M5T was 72.5 mol%. The whole-genome sequence of strain J1M15T was 3.20 Mbp in size and the genomic G+C content directly calculated from the genome sequence of strain J1M15T was 69.6mol %. Strains J2M5T and J1M15T showed high OrthoANI similarity to N. ganghwensis JC2055T (83.6 %) and T. flavescens (77.2 %), respectively. We analysed the genome sequences of strains J2M5T and J1M15T in terms of carbohydrate-active enzymes, antibiotic resistance genes and virulence factor genes. Strains J2M5T and J1M15T contained MK-8 (H4) and MK-9 (H4) as the predominant respiratory quinones, respectively. The major polar lipids of both strains were phosphatidylglycerol and diphosphatidylglycerol. Additionally, strain J2M5T possessed phosphatidylcholine, phosphatidylserine and phosphatidylethanolamine. The cellular sugar components of strain J2M5T were ribose, mannose, glucose and galactose, and its cellular amino acid components were l-alanine and l-lysine. The cellular sugar components of strain J1M15T were rhamnose, ribose, mannose and glucose, and its cellular amino acid component was l-alanine. The major cellular fatty acids of strains J2M5T and J1M15T were iso-C16 : 0 and anteiso-C15 : 0, respectively. The multiple taxonomic analyses indicated that strains J2M5T and J1M15T represent novel species of the genus Nocardioides and Tessaracoccus, respectively. We propose the names Nocardioides palaemonis sp. nov. and Tessaracoccus palaemonis sp. nov. for strain J2M5T (=KCTC 49461T=CCUG 74767T) and strain J1M15T (=KCTC 49462T=CCUG 74766T), respectively.
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Affiliation(s)
- Do-Yeon Kim
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - In-Chul Jeong
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - So-Yeon Lee
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Yun-Seok Jeong
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Jeong Eun Han
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Euon Jung Tak
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - June-Young Lee
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Pil Soo Kim
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Dong-Wook Hyun
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Jin-Woo Bae
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea.,Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
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Yoo JH, Han JE, Lee JY, Jeong SW, Jeong YS, Lee JY, Lee SY, Sung H, Tak EJ, Kim HS, Kim PS, Choi JW, Kim DY, Jeong IC, Gim DH, Kang SM, Bae JW. Parasphingorhabdus cellanae sp. nov., isolated from the gut of a Korean limpet, Cellana toreuma. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005470] [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 novel bacterium, designated strain JHSY0214T, was isolated from the gut of a Korean limpet, Cellana toreuma. Cells of strain JHSY0214T were Gram-stain-negative, strictly aerobic, yellow-pigmented, non-spore-forming, non-motile and showed a rod–coccus growth cycle. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain belonged to the genus
Parasphingorhabdus
, and was most closely related to
Parasphingorhabdus litoris
KCTC 12764T (98.71 %). Strain JHSY0214T had two fluoroquinolone-resistance genes and seven multidrug-resistance efflux pump genes, but did not have beta-lactamase genes and zinc resistance genes compared with
P. litoris
KCTC 12764T. Strain JHSY0214T grew optimally at 30 °C, pH 7.0 and in the presence of 2 % (w/v) NaCl. The predominant cellular fatty acids of strain JHSY0214T were summed feature 8 (C18 : 1
ω6c and/or C18 : 1
ω7c; 41.2 %), summed feature 3 (C16 : 1
ω7c and/or C16 : 1
ω6c; 21 %) and C16 : 0 (18.9 %). The major isoprenoid quinone was ubiquinone-10. The major polar lipids were sphingoglycolipid and phosphatidylethanolamine. The genomic DNA G+C content was 52.8 mol%. Based on phylogenetic, genotypic and phenotypic data, strain JHSY0214T represents a novel species of the genus
Parasphingorhabdus
, for which the name Parasphingorhabdus cellanae is proposed. The type strain is JHSY0214T (=KCTC 82387T=DSM 112279T).
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Affiliation(s)
- Ji-Ho Yoo
- Department of Biomedical and Pharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Jeong Eun Han
- Department of Biomedical and Pharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - June-Young Lee
- Department of Biomedical and Pharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Su-Won Jeong
- Department of Biomedical and Pharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Yun-Seok Jeong
- Department of Biomedical and Pharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Jae-Yun Lee
- Department of Biomedical and Pharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - So-Yeon Lee
- Department of Biomedical and Pharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Hojun Sung
- Department of Biomedical and Pharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Euon Jung Tak
- Department of Biomedical and Pharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Hyun Sik Kim
- Department of Biomedical and Pharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Pil Soo Kim
- Department of Biomedical and Pharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Jee-Won Choi
- Department of Biomedical and Pharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Do-Yeon Kim
- Department of Biomedical and Pharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - In Chul Jeong
- Department of Biomedical and Pharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Do-Hun Gim
- Department of Biomedical and Pharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Seo Min Kang
- Department of Biomedical and Pharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
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Abdelhafiz Y, Fernandes JMO, Donati C, Pindo M, Kiron V. Intergenerational Transfer of Persistent Bacterial Communities in Female Nile Tilapia. Front Microbiol 2022; 13:879990. [PMID: 35655994 PMCID: PMC9152445 DOI: 10.3389/fmicb.2022.879990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 04/11/2022] [Indexed: 11/30/2022] Open
Abstract
Resident microbial communities that can support various host functions play a key role in their development and health. In fishes, microbial symbionts are vertically transferred from the parents to their progeny. Such transfer of microbes in mouthbrooder fish species has not been reported yet. Here, we employed Nile tilapia (Oreochromis niloticus) to investigate the vertical transmission of microbes across generations using a 16S rRNA amplicon sequencing approach, based on the presence of bacteria in different generations. Our analysis revealed that the core microbiome in the buccal cavity and posterior intestine of parents shapes the gut microbiome of the progeny across generations. We speculate that the route of this transmission is via the buccal cavity. The identified core microbiome bacteria, namely Nocardioides, Propionibacterium, and Sphingomonas have been reported to play an essential role in the health and development of offspring. These core microbiome members could have specific functions in fish, similar to mammals.
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Affiliation(s)
- Yousri Abdelhafiz
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | | | - Claudio Donati
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Massimo Pindo
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Viswanath Kiron
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
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Oren A, Garrity GM. Valid publication of new names and new combinations effectively published outside the IJSEM. Validation List no. 203. Int J Syst Evol Microbiol 2022; 72. [PMID: 35108178 DOI: 10.1099/ijsem.0.005167] [Citation(s) in RCA: 275] [Impact Index Per Article: 137.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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Lee JY, Kang W, Shin NR, Hyun DW, Kim PS, Kim HS, Lee JY, Tak EJ, Sung H, Bae JW. Anaerostipes hominis sp. nov., a novel butyrate-producing bacteria isolated from faeces of a patient with Crohn's disease. Int J Syst Evol Microbiol 2021; 71. [PMID: 34870576 DOI: 10.1099/ijsem.0.005129] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Cultivation and isolation of gut bacteria are necessary for understanding their role in the intestinal ecosystem. We isolated a novel bacterium, designated strain BG01T, from the faeces of a patient with Crohn's disease. Strain BG01T was a strictly anaerobic, rod-shaped, Gram-variable and endospore-forming bacterium. Strain BG01T possessed C12 : 0, C18 : 0 dimethyl aldehyde (DMA) and C18 : 1 ω9c DMA as predominant cellular fatty acids and meso-diaminopimelic acid as a diagnostic diamino acid. Strain BG01T grew at 15-45 °C (optimum, 37 °C), with 0-4 % (w/v) NaCl (optimum, 0-1 %), at pH 6-10 (optimum, pH 7) and was resistant to bile salt, but not to ampicillin, metronidazole, vancomycin and cefoperazone. Butyrate, propionate, oxalacetate and fumarate were produced as fermentation end products from Gifu anaerobic medium broth. Strain BG01T showed 97.7 % 16S rRNA gene sequence similarity, and 92.0 and 48.5 % of average nucleotide identity and digital DNA-DNA hybridization values, respectively, with Anaerostipes caccae KCTC 15019T. Genomic analysis indicated that strain BG01T had a butyrate-producing pathway. The genomic G+C content of the strain was 43.5 mol%. Results of the phenotypic, phylogenetic and genotypic analyses indicated that strain BG01T represents a novel butyrate-producing species of the genus Anaerostipes, for which the name Anaerostipes hominis sp. nov. is proposed. The type strain is BG01T (=KCTC 15617T=JCM 32275T).
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Affiliation(s)
- Jae-Yun Lee
- Department of Biology, Department of Life and Nanopharmaceutical Sciences and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Woorim Kang
- Department of Biology, Department of Life and Nanopharmaceutical Sciences and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Na-Ri Shin
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Dong-Wook Hyun
- Department of Biology, Department of Life and Nanopharmaceutical Sciences and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Pil Soo Kim
- Department of Biology, Department of Life and Nanopharmaceutical Sciences and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Hyun Sik Kim
- Department of Biology, Department of Life and Nanopharmaceutical Sciences and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - June-Young Lee
- Department of Biology, Department of Life and Nanopharmaceutical Sciences and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Euon Jung Tak
- Department of Biology, Department of Life and Nanopharmaceutical Sciences and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Hojun Sung
- Department of Biology, Department of Life and Nanopharmaceutical Sciences and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Jin-Woo Bae
- Department of Biology, Department of Life and Nanopharmaceutical Sciences and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 130-701, Republic of Korea
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9
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Hyun DW, Lee JY, Kim MS, Shin NR, Whon TW, Kim KH, Kim PS, Tak EJ, Jung MJ, Lee JY, Kim HS, Kang W, Sung H, Jeon CO, Bae JW. Pathogenomics of Streptococcus ilei sp. nov., a newly identified pathogen ubiquitous in human microbiome. J Microbiol 2021; 59:792-806. [PMID: 34302622 DOI: 10.1007/s12275-021-1165-x] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/08/2021] [Accepted: 06/14/2021] [Indexed: 01/09/2023]
Abstract
Viridans group streptococci are a serious health concern because most of these bacteria cause life-threatening infections, especially in immunocompromised and hospitalized individuals. We focused on two alpha-hemolytic Streptococcus strains (I-G2 and I-P16) newly isolated from an ileostomy effluent of a colorectal cancer patient. We examined their pathogenic potential by investigating their prevalence in human and assessing their pathogenicity in a mouse model. We also predicted their virulence factors and pathogenic features by using comparative genomic analysis and in vitro tests. Using polyphasic and systematic approaches, we identified the isolates as belonging to a novel Streptococcus species and designated it as Streptococcus ilei. Metagenomic survey based on taxonomic assignment of datasets from the Human Microbiome Project revealed that S. ilei is present in most human population and at various body sites but is especially abundant in the oral cavity. Intraperitoneal injection of S. ilei was lethal to otherwise healthy C57BL/6J mice. Pathogenomics and in vitro assays revealed that S. ilei possesses a unique set of virulence factors. In agreement with the in vivo and in vitro data, which indicated that S. ilei strain I-G2 is more pathogenic than strain I-P16, only the former displayed the streptococcal group A antigen. We here newly identified S. ilei sp. nov., and described its prevalence in human, virulence factors, and pathogenicity. This will help to prevent S. ilei strain misidentification in the future, and improve the understanding and management of streptococcal infections.
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Affiliation(s)
- Dong-Wook Hyun
- Department of Biology, Department of Biomedical and Pharmaceutical Sciences, and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Jae-Yun Lee
- Department of Biology, Department of Biomedical and Pharmaceutical Sciences, and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Min-Soo Kim
- Department of Biology, Department of Biomedical and Pharmaceutical Sciences, and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Na-Ri Shin
- Department of Biology, Department of Biomedical and Pharmaceutical Sciences, and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Tae Woong Whon
- Department of Biology, Department of Biomedical and Pharmaceutical Sciences, and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Kyung Hyun Kim
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Pil Soo Kim
- Department of Biology, Department of Biomedical and Pharmaceutical Sciences, and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Euon Jung Tak
- Department of Biology, Department of Biomedical and Pharmaceutical Sciences, and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Mi-Ja Jung
- Department of Biology, Department of Biomedical and Pharmaceutical Sciences, and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - June Young Lee
- Department of Biology, Department of Biomedical and Pharmaceutical Sciences, and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Hyun Sik Kim
- Department of Biology, Department of Biomedical and Pharmaceutical Sciences, and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Woorim Kang
- Department of Biology, Department of Biomedical and Pharmaceutical Sciences, and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Hojun Sung
- Department of Biology, Department of Biomedical and Pharmaceutical Sciences, and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Jin-Woo Bae
- Department of Biology, Department of Biomedical and Pharmaceutical Sciences, and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, 02447, Republic of Korea.
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