Complete Genome Analysis of Glutamicibacter Creatinolyticus From
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Arthrobacter Paludis Sp. Nov., Isolated from a Marsh
TAXONOMIC DESCRIPTION Zhang et al., Int J Syst Evol Microbiol 2018;68:47–51 DOI 10.1099/ijsem.0.002426 Arthrobacter paludis sp. nov., isolated from a marsh Qi Zhang,1 Mihee Oh,1 Jong-Hwa Kim,1 Rungravee Kanjanasuntree,1 Maytiya Konkit,1 Ampaitip Sukhoom,2 Duangporn Kantachote2 and Wonyong Kim1,* Abstract A novel Gram-stain-positive, strictly aerobic, non-endospore-forming bacterium, designated CAU 9143T, was isolated from a hydric soil sample collected from Seogmo Island in the Republic of Korea. Strain CAU 9143T grew optimally at 30 C, at pH 7.0 and in the presence of 1 % (w/v) NaCl. The phylogenetic trees based on 16S rRNA gene sequences revealed that strain CAU 9143T belonged to the genus Arthrobacter and was closely related to Arthrobacter ginkgonis SYP-A7299T (97.1 % T similarity). Strain CAU 9143 contained menaquinone MK-9 (H2) as the major respiratory quinone and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, two glycolipids and two unidentified phospholipids as the major polar lipids. The whole-cell sugars were glucose and galactose. The peptidoglycan type was A4a (L-Lys–D-Glu2) and the major cellular fatty T acid was anteiso-C15 : 0. The DNA G+C content was 64.4 mol% and the level of DNA–DNA relatedness between CAU 9143 and the most closely related strain, A. ginkgonis SYP-A7299T, was 22.3 %. Based on phenotypic, chemotaxonomic and genetic data, strain CAU 9143T represents a novel species of the genus Arthrobacter, for which the name Arthrobacter paludis sp. nov. is proposed. The type strain is CAU 9143T (=KCTC 13958T,=CECT 8917T). -
Taxonomy and Systematics of Plant Probiotic Bacteria in the Genomic Era
AIMS Microbiology, 3(3): 383-412. DOI: 10.3934/microbiol.2017.3.383 Received: 03 March 2017 Accepted: 22 May 2017 Published: 31 May 2017 http://www.aimspress.com/journal/microbiology Review Taxonomy and systematics of plant probiotic bacteria in the genomic era Lorena Carro * and Imen Nouioui School of Biology, Newcastle University, Newcastle upon Tyne, UK * Correspondence: Email: [email protected]. Abstract: Recent decades have predicted significant changes within our concept of plant endophytes, from only a small number specific microorganisms being able to colonize plant tissues, to whole communities that live and interact with their hosts and each other. Many of these microorganisms are responsible for health status of the plant, and have become known in recent years as plant probiotics. Contrary to human probiotics, they belong to many different phyla and have usually had each genus analysed independently, which has resulted in lack of a complete taxonomic analysis as a group. This review scrutinizes the plant probiotic concept, and the taxonomic status of plant probiotic bacteria, based on both traditional and more recent approaches. Phylogenomic studies and genes with implications in plant-beneficial effects are discussed. This report covers some representative probiotic bacteria of the phylum Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes, but also includes minor representatives and less studied groups within these phyla which have been identified as plant probiotics. Keywords: phylogeny; plant; probiotic; PGPR; IAA; ACC; genome; metagenomics Abbreviations: ACC 1-aminocyclopropane-1-carboxylate ANI average nucleotide identity FAO Food and Agriculture Organization DDH DNA-DNA hybridization IAA indol acetic acid JA jasmonic acid OTUs Operational taxonomic units NGS next generation sequencing PGP plant growth promoters WHO World Health Organization PGPR plant growth-promoting rhizobacteria 384 1. -
Data of Read Analyses for All 20 Fecal Samples of the Egyptian Mongoose
Supplementary Table S1 – Data of read analyses for all 20 fecal samples of the Egyptian mongoose Number of Good's No-target Chimeric reads ID at ID Total reads Low-quality amplicons Min length Average length Max length Valid reads coverage of amplicons amplicons the species library (%) level 383 2083 33 0 281 1302 1407.0 1442 1769 1722 99.72 466 2373 50 1 212 1310 1409.2 1478 2110 1882 99.53 467 1856 53 3 187 1308 1404.2 1453 1613 1555 99.19 516 2397 36 0 147 1316 1412.2 1476 2214 2161 99.10 460 2657 297 0 246 1302 1416.4 1485 2114 1169 98.77 463 2023 34 0 189 1339 1411.4 1561 1800 1677 99.44 471 2290 41 0 359 1325 1430.1 1490 1890 1833 97.57 502 2565 31 0 227 1315 1411.4 1481 2307 2240 99.31 509 2664 62 0 325 1316 1414.5 1463 2277 2073 99.56 674 2130 34 0 197 1311 1436.3 1463 1899 1095 99.21 396 2246 38 0 106 1332 1407.0 1462 2102 1953 99.05 399 2317 45 1 47 1323 1420.0 1465 2224 2120 98.65 462 2349 47 0 394 1312 1417.5 1478 1908 1794 99.27 501 2246 22 0 253 1328 1442.9 1491 1971 1949 99.04 519 2062 51 0 297 1323 1414.5 1534 1714 1632 99.71 636 2402 35 0 100 1313 1409.7 1478 2267 2206 99.07 388 2454 78 1 78 1326 1406.6 1464 2297 1929 99.26 504 2312 29 0 284 1335 1409.3 1446 1999 1945 99.60 505 2702 45 0 48 1331 1415.2 1475 2609 2497 99.46 508 2380 30 1 210 1329 1436.5 1478 2139 2133 99.02 1 Supplementary Table S2 – PERMANOVA test results of the microbial community of Egyptian mongoose comparison between female and male and between non-adult and adult. -
Micrococcus Luteus), a Pyridine-Degrading Bacterium
UC San Diego UC San Diego Previously Published Works Title Draft Genome Sequence of Pseudarthrobacter sp. Strain ATCC 49442 (Formerly Micrococcus luteus), a Pyridine-Degrading Bacterium. Permalink https://escholarship.org/uc/item/5sw2j66q Journal Microbiology resource announcements, 9(38) ISSN 2576-098X Authors Gupta, Nidhi Skinner, Kelly A Summers, Zarath M et al. Publication Date 2020-09-17 DOI 10.1128/mra.00299-20 Peer reviewed eScholarship.org Powered by the California Digital Library University of California GENOME SEQUENCES crossm Draft Genome Sequence of Pseudarthrobacter sp. Strain ATCC 49442 (Formerly Micrococcus luteus), a Pyridine-Degrading Bacterium Nidhi Gupta,a,b Kelly A. Skinner,a Zarath M. Summers,c Janaka N. Edirisinghe,a,b Pamela B. Weisenhorn,a José P. Faria,a,b Christopher W. Marshall,a* Anukriti Sharma,b* Neil R. Gottel,b* Jack A. Gilbert,a,b* Christopher S. Henry,a,b Edward J. O’Loughlina aArgonne National Laboratory, Lemont, Illinois, USA bUniversity of Chicago, Chicago, Illinois, USA cExxonMobil Research and Engineering Company, Annandale, New Jersey, USA ABSTRACT We present here the draft genome sequence of a pyridine-degrading bacterium, Micrococcus luteus ATCC 49442, which was reclassified as Pseudarthrobac- ter sp. strain ATCC 49442 based on its draft genome sequence. Its genome length is 4.98 Mbp, with 64.81% GC content. icrococcus luteus ATCC 49442 was isolated from a Chalmers silt loam soil, which Mhad not previously been exposed to pyridine, by enrichment using pyridine as a carbon, nitrogen, and energy source (1), with growth on pyridine leading to overpro- duction of riboflavin (2). To obtain material for sequencing, ATCC 49442 was cultured in tryptic soy broth at 30°C for 16 h, after which DNA was isolated using a DNeasy PowerSoil kit (Qiagen, catalog number 12888-50) following the manufacturer’s proto- col. -
This Article Appeared in a Journal Published by Elsevier. the Attached
This article appeared in a journal published by Elsevier. The attached copy is furnished to the author for internal non-commercial research and education use, including for instruction at the authors institution and sharing with colleagues. Other uses, including reproduction and distribution, or selling or licensing copies, or posting to personal, institutional or third party websites are prohibited. In most cases authors are permitted to post their version of the article (e.g. in Word or Tex form) to their personal website or institutional repository. Authors requiring further information regarding Elsevier’s archiving and manuscript policies are encouraged to visit: http://www.elsevier.com/copyright Author's personal copy Pharmacological Research 69 (2013) 32–41 Contents lists available at SciVerse ScienceDirect Pharmacological Research journa l homepage: www.elsevier.com/locate/yphrs Invited review Microbiota of male genital tract: Impact on the health of man and his partner a,b,∗ Reet Mändar a Department of Microbiology, University of Tartu, Ravila 19, Tartu 50411, Estonia b Competence Centre on Reproductive Medicine and Biology, Tiigi 61b, Tartu 50410, Estonia a r t i c l e i n f o a b s t r a c t Article history: This manuscript describes the male genital tract microbiota and the significance of it on the host’s and Received 10 July 2012 his partner’s health. Microbiota exists in male lower genital tract, mostly in urethra and coronal sulcus Received in revised form 16 October 2012 while high inter-subject variability exists. Differences appear between sexually transmitted disease pos- Accepted 29 October 2012 itive and negative men as well as circumcised and uncircumcised men. -
Fish Bacterial Flora Identification Via Rapid Cellular Fatty Acid Analysis
Fish bacterial flora identification via rapid cellular fatty acid analysis Item Type Thesis Authors Morey, Amit Download date 09/10/2021 08:41:29 Link to Item http://hdl.handle.net/11122/4939 FISH BACTERIAL FLORA IDENTIFICATION VIA RAPID CELLULAR FATTY ACID ANALYSIS By Amit Morey /V RECOMMENDED: $ Advisory Committe/ Chair < r Head, Interdisciplinary iProgram in Seafood Science and Nutrition /-■ x ? APPROVED: Dean, SchooLof Fisheries and Ocfcan Sciences de3n of the Graduate School Date FISH BACTERIAL FLORA IDENTIFICATION VIA RAPID CELLULAR FATTY ACID ANALYSIS A THESIS Presented to the Faculty of the University of Alaska Fairbanks in Partial Fulfillment of the Requirements for the Degree of MASTER OF SCIENCE By Amit Morey, M.F.Sc. Fairbanks, Alaska h r A Q t ■ ^% 0 /v AlA s ((0 August 2007 ^>c0^b Abstract Seafood quality can be assessed by determining the bacterial load and flora composition, although classical taxonomic methods are time-consuming and subjective to interpretation bias. A two-prong approach was used to assess a commercially available microbial identification system: confirmation of known cultures and fish spoilage experiments to isolate unknowns for identification. Bacterial isolates from the Fishery Industrial Technology Center Culture Collection (FITCCC) and the American Type Culture Collection (ATCC) were used to test the identification ability of the Sherlock Microbial Identification System (MIS). Twelve ATCC and 21 FITCCC strains were identified to species with the exception of Pseudomonas fluorescens and P. putida which could not be distinguished by cellular fatty acid analysis. The bacterial flora changes that occurred in iced Alaska pink salmon ( Oncorhynchus gorbuscha) were determined by the rapid method. -
Complete Genome Sequence of Arthrobacter Sp
Complete genome sequence of Arthrobacter sp. PAMC25564 and comparative genome analysis for elucidating the role of CAZymes in cold adaptation So-Ra Han Sun Moon University Byeollee Kim Sun Moon University Jong Hwa Jang Dankook University Hyun Park Korea University Tae-Jin Oh ( [email protected] ) Sun Moon University Research Article Keywords: Arthrobacter species, CAZyme, cold-adapted bacteria, genetic patterns, glycogen metabolism, trehalose pathway Posted Date: December 16th, 2020 DOI: https://doi.org/10.21203/rs.3.rs-118769/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/17 Abstract Background: The Arthrobacter group is a known isolate from cold areas, the species of which are highly likely to play diverse roles in low temperatures. However, their role and survival mechanisms in cold regions such as Antarctica are not yet fully understood. In this study, we compared the genomes of sixteen strains within the Arthrobacter group, including strain PAMC25564, to identify genomic features that adapt and survive life in the cold environment. Results: The genome of Arthrobacter sp. PAMC25564 comprised 4,170,970 bp with 66.74 % GC content, a predicted genomic island, and 3,829 genes. This study provides an insight into the redundancy of CAZymes for potential cold adaptation and suggests that the isolate has glycogen, trehalose, and maltodextrin pathways associated to CAZyme genes. This strain can utilize polysaccharide or carbohydrate degradation as a source of energy. Moreover, this study provides a foundation on which to understand how the Arthrobacter strain produces energy in an extreme environment, and the genetic pattern analysis of CAZymes in cold-adapted bacteria can help to determine how bacteria adapt and survive in such environments. -
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SUPPLEMENTARY DATA Characterization of microbial communities associated with ceramic raw materials as potential contributors for the improvement of ceramic rheological properties Angela M. Garcia-Sanchez 1, Bernardino Machado-Moreira 2, Mário Freire 3, Ricardo Santos 3, Sílvia Monteiro 3, Diamantino Dias 4, Orquídia Neves 2, Amélia Dionísio 2 and Ana Z. Miller 5* 1 Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville. Profesor García González 2, 41012 Seville, Spain; 2 CERENA, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001, Lisboa, Portugal; 3 Laboratorio de Análises do Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal; 4 Rauschert Portuguesa, SA., Estrada Nacional 249-4, Trajouce, 2785-653 São Domingos de Rana, Portugal; 5 Instituto de Recursos Naturales y Agrobiologia de Sevilla (IRNAS-CSIC), Av. Reina Mercedes 10, 41012 Sevilla, Spain; 6 HERCULES Laboratory, University of Évora, Largo Marquês de Marialva 8, 7000-809 Évora, Portugal. * Correspondence: [email protected] The Supplementary data include: Figure S1. Rarefaction curves. Table S1. Phylogenetic affiliations of the 16S rRNA gene sequences of total bacteria obtained from sample 1A (74 sequences, 64 OTUs). Table S2. Phylogenetic affiliations of the 16S rRNA gene sequences of total bacteria obtained from sample 2B (69 sequences, 51 OTUs). Table S3. Phylogenetic affiliations of the 16S rRNA gene sequences of total bacteria obtained from sample 4D (80 sequences, 54 OTUs). Table S4. Phylogenetic affiliations of the 16S rRNA gene sequences of total bacteria obtained from sample 6F (86 sequences, 38 OTUs). Table S5. Phylogenetic affiliations of the 16S rRNA gene sequences of total bacteria obtained from sample 7G (79 sequences, 48 OTUs). -
Comparative Genomics and Physiological Investigation
Comparative Genomics and Physiological Investigation Supported Safety, Cold Adaptation, Ecient Hydrolytic and Plant Growth-promoting Potential of Psychrotrophic Glutamicibacter Arilaitensis LJH19, Isolated from Night-Soil Compost Shruti Borker Institute of Himalayan Bioresource Technology Aman Thakur Institute of Himalayan Bioresource Technology Sanjeet Kumar Institute of Himalayan Bioresource Technology Sareeka Kumari Institute of Himalayan Bioresource Technology Rakshak Kumar ( [email protected] ) Institute of Himalayan Bioresource Technology Sanjay Kumar Institute of Himalayan Bioresource Technology Research Article Keywords: Winter dry toilet, polysaccharide metabolism, indole acetic acid, siderophore, type III PKS Posted Date: December 10th, 2020 DOI: https://doi.org/10.21203/rs.3.rs-122385/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Version of Record: A version of this preprint was published on April 28th, 2021. See the published version at https://doi.org/10.1186/s12864-021-07632-z. Page 1/37 Abstract Background: Night-soil compost (NSC) has traditionally been conserving water and a source of organic manure in northwestern Himalaya. Lately, this traditional method is declining due to modernization, its unhygienic conditions, and social apprehensions. Reduction in the age-old traditional practice has led to excessive chemical fertilizers and water shortage in the eco-sensitive region. In the current study, a bacterium has been analysed for its safety, cold-adaptation, ecient degradation, and plant growth potential attributes for its possible application as a safe bioinoculant in psychrotrophic bacterial consortia for improved night-soil composting. Results: Glutamicibacter arilaitensis LJH19, a psychrotrophic bacterium, was isolated from the night-soil compost of Lahaul valley in northwestern Himalaya. -
2018-02-20-A.Globiforum FSAR-EN
Final Screening Assessment for Arthrobacter globiformis strain ATCC 8010 Environment and Climate Change Canada Health Canada February 2018 Cat. No.: En14-312/2018E-PDF ISBN 978-0-660-24723-6 Information contained in this publication or product may be reproduced, in part or in whole, and by any means, for personal or public non-commercial purposes, without charge or further permission, unless otherwise specified. You are asked to: • Exercise due diligence in ensuring the accuracy of the materials reproduced; • Indicate both the complete title of the materials reproduced, as well as the author organization; and • Indicate that the reproduction is a copy of an official work that is published by the Government of Canada and that the reproduction has not been produced in affiliation with or with the endorsement of the Government of Canada. Commercial reproduction and distribution is prohibited except with written permission from the author. For more information, please contact Environment and Climate Change Canada’s Inquiry Centre at 1-800-668-6767 (in Canada only) or 819-997-2800 or email to [email protected]. © Her Majesty the Queen in Right of Canada, represented by the Minister of the Environment and Climate Change, 2016. Aussi disponible en français ii Synopsis Pursuant to paragraph 74(b) of the Canadian Environmental Protection Act, 1999 (CEPA), the Minister of the Environment and the Minister of Health have conducted a screening assessment of Arthrobacter globiformis (A. globiformis) strain ATCC 8010. A. globiformis strain ATCC 8010 is a soil bacterium that has characteristics in common with other strains of the species. -
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Iraqi Journal of Agricultural Sciences –2019:50(5):1425-1431 Abdulrazzaq et al. ISOLATION AND MOLECULAR DETECTION OF ARTHROBACTER SPECIES GROWN ON THE SURFACE OF DATE PALM TISSUE CULTURE MEDIA A. Abdulrazzaq H. S.Khierallah S. M. H. Al-Rubaye S.M. Bader Assist.Prof., Assist.Prof., Lecturer C.S. Researchers Dept. Microbiology,Coll. Veterinary Medicine, University of Baghdad Email: [email protected] ABSTRACT This study was aimed to found out the type of bacterial species grown on the surface of date palm tissue culture media. Shoot tips of date palm (Barhi cv.) were cultured on MS media supplemented with various combinations of hormones. During growth an infection was appeared in all cultures with gray colour. Primarily identification, proved a bacterial infection due to its colour and appearance. The genus Arthrobacter was isolated Antibiotic sensitivity test showed that the isolate was sensitive to ciprofloxacin,Trimethoprim, and Amikacin and resistant to Clarithromycin,Ceftriaxone and Gentamycin. Sequence analysis of 16 rRNA indicated a new isolates were closely related to the Glutamicibacter arilaitensis strain ebst40 and Arthrobacter arilaitensis strain L11 with the highest sequence similarity (100%) . Keywords: shoot tips, Glutamicibacter arilaitensis ,polymerase chain reaction, hormons, antibiotic sensitivity. مجلة العلوم الزراعية العراقية -2019 :50(5(:1425-1431 عبد الرزاق وآخرون العزل والنشخيص الجزيئي لبكتريا Arthrobacter النامية على سطح الوسط الزرعي لنسيج نخلة التمر اثير عبد الرزاق حسام سعد الدين خيراهلل سحر مهدي الربيعي صالح محسن بدر استاذ مساعد استاذ مساعد مدرس رئيس باحثين قسم أﻷحياء المجهرية كلية الطب البيطري جامعة بغداد المستخلص زرعت اطراف اﻻفرع لفسائل البرحي في وسط موراشيح وسكوج المجهزبتوليفات مختلفة من الهرمونات . -
Complete Genome Sequence of Drought Tolerant Plant Growth
Korean Journal of Microbiology (2019) Vol. 55, No. 3, pp. 300-302 pISSN 0440-2413 DOI https://doi.org/10.7845/kjm.2019.9087 eISSN 2383-9902 Copyright ⓒ 2019, The Microbiological Society of Korea Complete genome sequence of drought tolerant plant growth-promoting rhizobacterium Glutamicibacter halophytocola DR408 Susmita Das Nishu, Hye Rim Hyun, and Tae Kwon Lee* Department of Environmental Engineering, Yonsei University, Wonju 26493, Republic of Korea 내건성 식물생장 촉진 균주인 Glutamicibacter halophytocola DR408의 유전체 분석 수스미타 다스 니슈 ・ 현혜림 ・ 이태권* 연세대학교 환경공학부 (Received August 9, 2019; Revised September 5, 2019; Accepted September 5, 2019) Glutamicibacter halophytocola DR408 isolated from the rhi- spheric soil of the soybean (Glycine max) exposed to periodic zospheric soil of soybean plant at Jecheon showed drought drought in Jecheon, Republic of Korea. Phylogenetic analysis tolerance and plant growth promotion capacity. The complete of its 16S rRNA gene sequence revealed that the strain DR408 genome of strain DR408 comprises 3,770,186 bp, 60.2% GC- closed to genus Glutamicibacter and had the highest similarity content, which include 3,352 protein-coding genes, 64 tRNAs, to Glutamicibacter halophytocola KCTC 39692 (99%) (Feng 19 rRNA, and 3 ncRNA. The genome analysis revealed gene et al. clusters encoding osmolyte synthesis and plant growth pro- , 2017). Unexpectedly, only one complete genome se- motion enzymes, which are known to contribute to improve quence belonging to this species are available in public drought tolerance of the plant. database (NZ_CP012750). Here, we describe the complete Glutamicibacter halo- Keywords: Glutamicibacter halophytocola, complete genome, genome sequence and annotation of drought tolerance, plant growth promotion phytocola DR408.