Effect of Long Pasteurization Run Times on Bacterial Numbers in Milk
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Kaistella Soli Sp. Nov., Isolated from Oil-Contaminated Soil
A001 Kaistella soli sp. nov., Isolated from Oil-contaminated Soil Dhiraj Kumar Chaudhary1, Ram Hari Dahal2, Dong-Uk Kim3, and Yongseok Hong1* 1Department of Environmental Engineering, Korea University Sejong Campus, 2Department of Microbiology, School of Medicine, Kyungpook National University, 3Department of Biological Science, College of Science and Engineering, Sangji University A light yellow-colored, rod-shaped bacterial strain DKR-2T was isolated from oil-contaminated experimental soil. The strain was Gram-stain-negative, catalase and oxidase positive, and grew at temperature 10–35°C, at pH 6.0– 9.0, and at 0–1.5% (w/v) NaCl concentration. The phylogenetic analysis and 16S rRNA gene sequence analysis suggested that the strain DKR-2T was affiliated to the genus Kaistella, with the closest species being Kaistella haifensis H38T (97.6% sequence similarity). The chemotaxonomic profiles revealed the presence of phosphatidylethanolamine as the principal polar lipids;iso-C15:0, antiso-C15:0, and summed feature 9 (iso-C17:1 9c and/or C16:0 10-methyl) as the main fatty acids; and menaquinone-6 as a major menaquinone. The DNA G + C content was 39.5%. In addition, the average nucleotide identity (ANIu) and in silico DNA–DNA hybridization (dDDH) relatedness values between strain DKR-2T and phylogenically closest members were below the threshold values for species delineation. The polyphasic taxonomic features illustrated in this study clearly implied that strain DKR-2T represents a novel species in the genus Kaistella, for which the name Kaistella soli sp. nov. is proposed with the type strain DKR-2T (= KACC 22070T = NBRC 114725T). [This study was supported by Creative Challenge Research Foundation Support Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (NRF- 2020R1I1A1A01071920).] A002 Chitinibacter bivalviorum sp. -
Proposal of Two New Species in the Genus Microbacterium Dextranolyticum Sp. Microbacterium
INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, July 1993, p. 549-554 Vol. 43, No. 3 0020-7713/93/030549-06$02.00/0 Copyright 0 1993, International Union of Microbiological Societies Proposal of Two New Species in the Genus Microbacterium : Microbacterium dextranolyticum sp. nov. and Microbacterium aurum sp. nov. AKIRA YOKOTA,l* MARIKO TAKEUCH1,l AND NOBERT WEISS2 Institute for Fermentation, Osaka, 17-85, Juso-honmachi 2-chome, Yodogawa-ku, Osaka 532, Japan, and Deutsche Sammlung von Mikroolganismen und Zellkulturen 0-3300 Braunschweig, Germany2 The taxonomic positions of Flavobacterium sp. strain IF0 14592= (= M-73T) (T = type strain), a dextran-a-l,2-debranchingenzyme producer, and Microbacterium sp. strain IF0 15204T (= H-5T), an isolate obtained from corn steep liquor, were investigated; on the basis of the results of chemotaxonomic and phenetic studies and DNA-DNA similarity data, we propose that these bacteria should be classified in the genus Microbacterium as Microbacterium dextranolyticum sp. nov. and Microbacterium aurum sp. nov., respectively. The type strain of M. dextranolyticum is strain IF0 14592, and the type strain of M. aurum is strain IF0 15204. The genus Microbacterium was proposed by Orla-Jensen of 1% tetramethyl-p-phenylenediamineon filter paper. Acid (15), and its description was emended by Collins et al. (1). production from carbohydrates was studied in a medium Four species have been described previously: Microbacte- containing 0.3% peptone, 0.25% NaCl, 0.003% bromcresol rium lacticum, Microbacterium imperiale, Microbacterium purple, and 0.5% carbohydrate (pH 7.2). Assimilation of laevaniformans, and Microbacterium arborescens (1, 5, 6). organic acids was studied in a medium containing 0.5% During a taxonomic study of Flavobacterium strains in the organic acid (sodium salt), 0.02% D-glucose, 0.01% yeast Institute for Fermentation at Osaka (IFO) culture collection, extract, 0.01% peptone, 0.01% Bacto brain heart infusion, we found that Flavobacterium sp. -
( 12 ) United States Patent
US009956282B2 (12 ) United States Patent ( 10 ) Patent No. : US 9 ,956 , 282 B2 Cook et al. (45 ) Date of Patent: May 1 , 2018 ( 54 ) BACTERIAL COMPOSITIONS AND (58 ) Field of Classification Search METHODS OF USE THEREOF FOR None TREATMENT OF IMMUNE SYSTEM See application file for complete search history . DISORDERS ( 56 ) References Cited (71 ) Applicant : Seres Therapeutics , Inc. , Cambridge , U . S . PATENT DOCUMENTS MA (US ) 3 ,009 , 864 A 11 / 1961 Gordon - Aldterton et al . 3 , 228 , 838 A 1 / 1966 Rinfret (72 ) Inventors : David N . Cook , Brooklyn , NY (US ) ; 3 ,608 ,030 A 11/ 1971 Grant David Arthur Berry , Brookline, MA 4 ,077 , 227 A 3 / 1978 Larson 4 ,205 , 132 A 5 / 1980 Sandine (US ) ; Geoffrey von Maltzahn , Boston , 4 ,655 , 047 A 4 / 1987 Temple MA (US ) ; Matthew R . Henn , 4 ,689 ,226 A 8 / 1987 Nurmi Somerville , MA (US ) ; Han Zhang , 4 ,839 , 281 A 6 / 1989 Gorbach et al. Oakton , VA (US ); Brian Goodman , 5 , 196 , 205 A 3 / 1993 Borody 5 , 425 , 951 A 6 / 1995 Goodrich Boston , MA (US ) 5 ,436 , 002 A 7 / 1995 Payne 5 ,443 , 826 A 8 / 1995 Borody ( 73 ) Assignee : Seres Therapeutics , Inc. , Cambridge , 5 ,599 ,795 A 2 / 1997 McCann 5 . 648 , 206 A 7 / 1997 Goodrich MA (US ) 5 , 951 , 977 A 9 / 1999 Nisbet et al. 5 , 965 , 128 A 10 / 1999 Doyle et al. ( * ) Notice : Subject to any disclaimer , the term of this 6 ,589 , 771 B1 7 /2003 Marshall patent is extended or adjusted under 35 6 , 645 , 530 B1 . 11 /2003 Borody U . -
From Genotype to Phenotype: Inferring Relationships Between Microbial Traits and Genomic Components
From genotype to phenotype: inferring relationships between microbial traits and genomic components Inaugural-Dissertation zur Erlangung des Doktorgrades der Mathematisch-Naturwissenschaftlichen Fakult¨at der Heinrich-Heine-Universit¨atD¨usseldorf vorgelegt von Aaron Weimann aus Oberhausen D¨usseldorf,29.08.16 aus dem Institut f¨urInformatik der Heinrich-Heine-Universit¨atD¨usseldorf Gedruckt mit der Genehmigung der Mathemathisch-Naturwissenschaftlichen Fakult¨atder Heinrich-Heine-Universit¨atD¨usseldorf Referent: Prof. Dr. Alice C. McHardy Koreferent: Prof. Dr. Martin J. Lercher Tag der m¨undlichen Pr¨ufung: 24.02.17 Selbststandigkeitserkl¨ arung¨ Hiermit erkl¨areich, dass ich die vorliegende Dissertation eigenst¨andigund ohne fremde Hilfe angefertig habe. Arbeiten Dritter wurden entsprechend zitiert. Diese Dissertation wurde bisher in dieser oder ¨ahnlicher Form noch bei keiner anderen Institution eingereicht. Ich habe bisher keine erfolglosen Promotionsversuche un- ternommen. D¨usseldorf,den . ... ... ... (Aaron Weimann) Statement of authorship I hereby certify that this dissertation is the result of my own work. No other person's work has been used without due acknowledgement. This dissertation has not been submitted in the same or similar form to other institutions. I have not previously failed a doctoral examination procedure. Summary Bacteria live in almost any imaginable environment, from the most extreme envi- ronments (e.g. in hydrothermal vents) to the bovine and human gastrointestinal tract. By adapting to such diverse environments, they have developed a large arsenal of enzymes involved in a wide variety of biochemical reactions. While some such enzymes support our digestion or can be used for the optimization of biotechnological processes, others may be harmful { e.g. mediating the roles of bacteria in human diseases. -
Microbacterium Flavum Sp. Nov. and Microbacterium Lacus Sp. Nov
Actinomycetologica (2007) 21:53–58 Copyright Ó 2007 The Society for Actinomycetes Japan VOL. 21, NO. 2 Microbacterium flavum sp. nov. and Microbacterium lacus sp. nov., isolated from marine environments. Akiko Kageyama1, Yoko Takahashi1Ã, Yoshihide Matsuo2, Kyoko Adachi2, Hiroaki Kasai2, Yoshikazu Shizuri2 and Satoshi O¯ mura1;3 1Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8642, Japan. 2Marine Biotechnology Institute, 3-75-1 Heita, Kamaishi, Iwate 026-0001, Japan. 3The Kitasato Institute, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8642, Japan. (Received Feb. 21, 2007 / Accepted Jul. 9, 2007 / Published Sep. 10, 2007) Strains YM18-098T and A5E-52T were both Gram-positive, aerobic, irregular rod-shaped bacteria, with lysine and ornithine as the diagnostic diamino acids of their peptidoglycans, respectively. The acyl type of the peptidoglycan in both cases was N-glycolyl. The major menaquinones were MK-11, -12 and -13. Mycolic acids were not detected. The G+C content of the DNA was 69–70 mol%. Comparative 16S rRNA studies revealed that the isolates belonged to the genus Microbacterium, that YM18-098T was closely related to the species Microbacterium lacticum and Microbacterium schleiferi, and that A5E-52T was closely related to the species Microbacterium aurum, Microbacterium aoyamense, Microbacterium deminutum and Microbacterium pumilum. DNA-DNA relatedness analysis showed that the isolated strains represented two separate genomic species. Based on both phenotypic and genotypic data, the following new species of the genus Microbacterium are proposed: Microbacterium flavum sp. nov. and Microbacterium lacus sp. nov., with the type strains YM18-098T (= MBIC08278T, DSM 18909T) and A5E-52T (= MBIC08279T, DSM 18910T), respectively. -
Organic Acid Production from Starchy Waste by Gut Derived Microorganisms”
Propositions 1. Actinomyces succiniciruminis has potential for industrial succinate production from starchy waste (this thesis) 2. Knowing the relative abundance of each microbial species in a mixed rumen inoculum does not help to predict the fermentation products (this thesis) 3. Phytoplanktons are the real-world savers for the global warming crisis as they are world’s biggest oxygen producers and carbon sequesters (Witman, S. (2017) World’s biggest oxygen producers living in swirling ocean waters. Eos, 98) 4. The best way to protect endangered floras is to bring them into a commercial breeding system 5. Studying abroad elevates cooking skills to the master level 6. There is no real waste in our world Propositions belonging to this thesis entitled: “Organic acid production from starchy waste by gut derived microorganisms” Susakul Palakawong Na Ayudthaya Wageningen, 7 September 2018 Organic acid production from starchy waste by gut derived microorganisms Susakul Palakawong Na Ayudthaya Thesis committee Promotors Prof. Dr Alfons J.M. Stams Personal chair at the Laboratory of Microbiology Wageningen University & Research Prof. Dr Willem M. de Vos Professor of Microbiology Wageningen University & Research Co-promotor Dr Caroline M. Plugge Associate professor, Laboratory of Microbiology Wageningen University & Research Other members Prof. Dr Grietje Zeeman, Wageningen University & Research Dr Bundit Fungsin, Thailand Institute of Scientific and Technological Research, Pathum Thani, Thailand Prof. Dr Gert-Jan W. Euverink, University of Groningen, The Netherlands Dr Marieke E. Bruins, Wageningen University & Research This research was conducted under the auspices of the Graduate School for Socio-Economic and Natural Sciences of the Environment (SENSE). Organic acid production from starchy waste by gut derived microorganisms Susakul Palakawong Na Ayudthaya Thesis submitted in fulfilment of the requirements for the degree of doctor at Wageningen University by the authority of the Rector Magnificus, Prof. -
Supplemental Tables for Plant-Derived Benzoxazinoids Act As Antibiotics and Shape Bacterial Communities
Supplemental Tables for Plant-derived benzoxazinoids act as antibiotics and shape bacterial communities Niklas Schandry, Katharina Jandrasits, Ruben Garrido-Oter, Claude Becker Contents Table S1. Syncom strains 2 Table S2. PERMANOVA 5 Table S3. ANOVA: observed taxa 6 Table S4. Observed diversity means and pairwise comparisons 7 Table S5. ANOVA: Shannon Diversity 9 Table S6. Shannon diversity means and pairwise comparisons 10 1 Table S1. Syncom strains Strain Genus Family Order Class Phylum Mixed Root70 Acidovorax Comamonadaceae Burkholderiales Betaproteobacteria Proteobacteria Root236 Aeromicrobium Nocardioidaceae Propionibacteriales Actinomycetia Actinobacteria Root100 Aminobacter Phyllobacteriaceae Rhizobiales Alphaproteobacteria Proteobacteria Root239 Bacillus Bacillaceae Bacillales Bacilli Firmicutes Root483D1 Bosea Bradyrhizobiaceae Rhizobiales Alphaproteobacteria Proteobacteria Root342 Caulobacter Caulobacteraceae Caulobacterales Alphaproteobacteria Proteobacteria Root137 Cellulomonas Cellulomonadaceae Actinomycetales Actinomycetia Actinobacteria Root1480D1 Duganella Oxalobacteraceae Burkholderiales Gammaproteobacteria Proteobacteria Root231 Ensifer Rhizobiaceae Rhizobiales Alphaproteobacteria Proteobacteria Root420 Flavobacterium Flavobacteriaceae Flavobacteriales Bacteroidia Bacteroidetes Root268 Hoeflea Phyllobacteriaceae Rhizobiales Alphaproteobacteria Proteobacteria Root209 Hydrogenophaga Comamonadaceae Burkholderiales Gammaproteobacteria Proteobacteria Root107 Kitasatospora Streptomycetaceae Streptomycetales Actinomycetia Actinobacteria -
As Microbacterium Resistens Comb. Nov
International Journal of Systematic and Evolutionary Microbiology (2001), 51, 1267–1276 Printed in Great Britain Description of Microbacterium foliorum sp. nov. and Microbacterium phyllosphaerae sp. nov., isolated from the phyllosphere of grasses and the surface litter after mulching the sward, and reclassification of Aureobacterium resistens (Funke et al. 1998) as Microbacterium resistens comb. nov. 1,2 Centre for Agricultural Undine Behrendt,1 Andreas Ulrich2 and Peter Schumann3 Landscape and Land Use Research Mu$ ncheberg (ZALF), Institute of Primary Production and Author for correspondence: Undine Behrendt. Tel: j49 33237 849357. Fax: j49 33237 849226. Microbial Ecology, e-mail: ubehrendt!zalf.de Gutshof 7, D 14641 Paulinenaue1 , Mu$ ncheberg2 , Germany The taxonomic position of a group of coryneform bacteria isolated from the phyllosphere of grasses and the surface litter after sward mulching was 3 DSMZ – German Collection of investigated. On the basis of restriction analyses of 16S rDNA, the isolates Microorganisms and Cell were divided into two genotypes. According to the 16S rDNA sequence Cultures, Braunschweig, analysis, representatives of both genotypes were related at a level of 99 2% Germany similarity and clustered within the genus Microbacterium. Chemotaxonomic features (major menaquinones MK-12, MK-11 and MK-10; predominating iso- and anteiso-branched cellular fatty acids; GMC content 64–67 mol%; peptidoglycan-type B2β with glycolyl residues) corresponded to this genus as well. DNA–DNA hybridization studies showed a reassociation value of less than 70% between representative strains of both subgroups, suggesting that two different species are represented. Although the extensive morphological and physiological analyses did not reveal any differentiating feature for the genotypes, differences in the presence of the cell-wall sugar mannose enabled the subgroups to be distinguished from one another. -
Characterization of the Vaginal Microbiome in Pregnancy
CHARACTERIZATION OF THE VAGINAL MICROBIOME IN PREGNANCY A Thesis Submitted to the College of Graduate and Postdoctoral Studies In Partial Fulfillment of the Requirements For the Degree of Doctor of Philosophy In the Department of Veterinary Microbiology University of Saskatchewan Saskatoon By ALINE COSTA DE FREITAS © Copyright Aline C. Freitas, February, 2018. All rights reserved. PERMISSION TO USE In presenting this thesis in partial fulfillment of the requirements for a Postgraduate degree from the University of Saskatchewan, I agree that the Libraries of this University may make it freely available for inspection. I further agree that permission for copying of this thesis/dissertation in any manner, in whole or in part, for scholarly purposes may be granted by the professor or professors who supervised my thesis work or, in their absence, by the Head of the Department or the Dean of the College in which my thesis work was done. It is understood that any copying or publication or use of this thesis or parts thereof for financial gain shall not be allowed without my written permission. It is also understood that due recognition shall be given to me and to the University of Saskatchewan in any scholarly use which may be made of any material in my thesis/dissertation. Requests for permission to copy or to make other uses of materials in this thesis in whole or part should be addressed to: Head of Department of Veterinary Microbiology University of Saskatchewan Saskatoon, Saskatchewan S7N 5B4 Canada OR Dean College of Graduate and Postdoctoral Studies University of Saskatchewan 116 Thorvaldson Building, 110 Science Place Saskatoon, Saskatchewan S7N 5C9 Canada i ABSTRACT The vaginal microbiome plays an important role in women’s reproductive health. -
A Review on Bacterial Contribution to Lignocellulose Breakdown Into Useful Bio-Products
International Journal of Environmental Research and Public Health Review A Review on Bacterial Contribution to Lignocellulose Breakdown into Useful Bio-Products Ogechukwu Bose Chukwuma , Mohd Rafatullah * , Husnul Azan Tajarudin and Norli Ismail Division of Environmental Technology, School of Industrial Technology, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia; [email protected] (O.B.C.); [email protected] (H.A.T.); [email protected] (N.I.) * Correspondence: [email protected] or [email protected]; Tel.: +60-4-653-2111; Fax: +60-4-653-6375 Abstract: Discovering novel bacterial strains might be the link to unlocking the value in lignocel- lulosic bio-refinery as we strive to find alternative and cleaner sources of energy. Bacteria display promise in lignocellulolytic breakdown because of their innate ability to adapt and grow under both optimum and extreme conditions. This versatility of bacterial strains is being harnessed, with qualities like adapting to various temperature, aero tolerance, and nutrient availability driving the use of bacteria in bio-refinery studies. Their flexible nature holds exciting promise in biotechnology, but despite recent pointers to a greener edge in the pretreatment of lignocellulose biomass and lignocellulose-driven bioconversion to value-added products, the cost of adoption and subsequent Citation: Chukwuma, O.B.; scaling up industrially still pose challenges to their adoption. However, recent studies have seen Rafatullah, M.; Tajarudin, H.A.; the use of co-culture, co-digestion, and bioengineering to overcome identified setbacks to using Ismail, N. A Review on Bacterial bacterial strains to breakdown lignocellulose into its major polymers and then to useful products Contribution to Lignocellulose Breakdown into Useful Bio-Products. -
1 Diversity of Culturable Endophytic Bacteria from Wild and Cultivated Rice Showed 2 Potential Plant Growth Promoting Activities
bioRxiv preprint doi: https://doi.org/10.1101/310797; this version posted April 30, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 1 Diversity of Culturable Endophytic bacteria from Wild and Cultivated Rice showed 2 potential Plant Growth Promoting activities 3 Madhusmita Borah, Saurav Das, Himangshu Baruah, Robin C. Boro, Madhumita Barooah* 4 Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam 5 6 Authors Affiliations: 7 8 Madhusmita Borah: Department of Agricultural Biotechnology, Assam Agricultural 9 University, Jorhat, Assam. Email Id: [email protected] 10 11 Saurav Das: Department of Agricultural Biotechnology, Assam Agricultural University, 12 Jorhat, Assam. Email Id: [email protected] 13 14 Himangshu Baruah: Department of Agricultural Biotechnology, Assam Agricultural 15 University, Jorhat, Assam. Email Id: [email protected] 16 17 Robin Ch. Boro: Department of Agricultural Biotechnology, Assam Agricultural University, 18 Jorhat, Assam. Email Id: [email protected] 19 20 *Corresponding Author: 21 Madhumita Barooah: Professor, Department of Agricultural Biotechnology, Assam 22 Agricultural University, Jorhat, Assam. Emil Id: [email protected] 23 24 Present Address: 25 1. Saurav Das: DBT- Advanced Institutional Biotech Hub, Bholanath College, Dhubri, 26 Assam. 27 2. Himangshu Baruah: Department of Environmental Science, Cotton College State 28 University, Guwahati, Assam. 29 30 Abstract 31 In this paper, we report the endophytic microbial diversity of cultivated and wild Oryza 32 sativa plants including their functional traits related to multiple traits that promote plant 33 growth and development. -
Metabolic Roles of Uncultivated Bacterioplankton Lineages in the Northern Gulf of Mexico 2 “Dead Zone” 3 4 J
bioRxiv preprint doi: https://doi.org/10.1101/095471; this version posted June 12, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. 1 Metabolic roles of uncultivated bacterioplankton lineages in the northern Gulf of Mexico 2 “Dead Zone” 3 4 J. Cameron Thrash1*, Kiley W. Seitz2, Brett J. Baker2*, Ben Temperton3, Lauren E. Gillies4, 5 Nancy N. Rabalais5,6, Bernard Henrissat7,8,9, and Olivia U. Mason4 6 7 8 1. Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA 9 2. Department of Marine Science, Marine Science Institute, University of Texas at Austin, Port 10 Aransas, TX, USA 11 3. School of Biosciences, University of Exeter, Exeter, UK 12 4. Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, 13 FL, USA 14 5. Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, 15 LA, USA 16 6. Louisiana Universities Marine Consortium, Chauvin, LA USA 17 7. Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 18 13288 Marseille, France 19 8. INRA, USC 1408 AFMB, F-13288 Marseille, France 20 9. Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia 21 22 *Correspondence: 23 JCT [email protected] 24 BJB [email protected] 25 26 27 28 Running title: Decoding microbes of the Dead Zone 29 30 31 Abstract word count: 250 32 Text word count: XXXX 33 34 Page 1 of 31 bioRxiv preprint doi: https://doi.org/10.1101/095471; this version posted June 12, 2017.