Pyrosequencing-Based Analysis of the Bacterial Community During
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Enterobacter Massiliensis Sp. Nov
Standards in Genomic Sciences (2013) 7:399-412 DOI:10.4056/sigs.3396830 Non contiguous-finished genome sequence and descrip- tion of Enterobacter massiliensis sp. nov. Jean-Christophe Lagier1, Khalid El Karkouri1, Ajay Kumar Mishra1, Catherine Robert1, Didier Raoult1 and Pierre-Edouard Fournier1* 1Aix-Marseille Université, Faculté de médecine, Marseille, France *Corresponding author: Pierre-Edouard Fournier ([email protected]) Keywords: Enterobacter massiliensis, genome Enterobacter massiliensis strain JC163T sp. nov. is the type strain of E. massiliensis sp. nov., a new species within the genus Enterobacter. This strain, whose genome is described here, was isolated from the fecal flora of a healthy Senegalese patient. E. massiliensis is an aerobic rod. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,922,247 bp long genome (1 chromosome but no plasmid) exhibits a G+C content of 55.1% and contains 4,644 protein-coding and 80 RNA genes, including 5 rRNA genes. Introduction Enterobacter massiliensis strain JC163T (= CSUR Enterobacter spp. were isolated from the normal P161 = DSM 26120) is the type strain of E. fecal flora. massiliensis sp. nov. This bacterium is a Gram- negative, aerobic, flagellate, indole-positive bacil- Classification and features lus that was isolated from the feces of a healthy A stool sample was collected from a healthy 16- Senegalese patient in a study aiming at cultivating year-old male Senegalese volunteer patient living all bacterial species in human feces [1]. The cur- in Dielmo (rural village in the Guinean-Sudanian rent classification of prokaryotes, known as zone in Senegal), who was included in a research polyphasic taxonomy, relies on a combination of protocol. -
Preliminary MAIN RESEARCH LINES
Brothers, Sheila C From: Schroeder, Margaret <[email protected]> Sent: Tuesday, February 03, 2015 9:07 AM To: Brothers, Sheila C Subject: Proposed New Dual Degree Program: PhD in Plant Pathology with Universidade Federal de Vicosa Proposed New Dual Degree Program: PhD in Plant Pathology with Universidade Federal de Vicosa This is a recommendation that the University Senate approve, for submission to the Board of Trustees, the establishment of a new Dual Degree Program: PhD in Plant Pathology with Universidade Federal de Vicosa, in the Department of Plant Pathology within the College of Agriculture, Food, and Environment. Best- Margaret ---------- Margaret J. Mohr-Schroeder, PhD | Associate Professor of Mathematics Education | STEM PLUS Program Co-Chair | Department of STEM Education | University of Kentucky | www.margaretmohrschroeder.com 1 DUAL DOCTORAL DEGREE IN PLANT PATHOLOGY BETWEEN THE UNIVERSITY OF KENTUCKY AND THE UNIVERSIDADE FEDERAL DE VIÇOSA Program Goal This is a proposal for a dual Doctoral degree program between the University of Kentucky (UK) and the Universidade Federal de Viçosa (UFV) in Brazil. Students will acquire academic credits and develop part of the research for their Doctoral dissertations at the partner university. A stay of at least 12 consecutive months at the partner university will be required for the program. Students in the program will obtain Doctoral degrees in Plant Pathology from both UK and UFV. Students in the program will develop language skills in English and Portuguese, and become familiar with norms of the discipline in both countries. Students will fulfill the academic requirements of both institutions in order to obtain degrees from both. -
The Impact of Type VI Secretion System, Bacteriocins And
bioRxiv preprint doi: https://doi.org/10.1101/497016; this version posted December 17, 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 The impact of type VI secretion system, bacteriocins and antibiotics on competition 2 amongst Soft-Rot Enterobacteriaceae: Regulation of carbapenem biosynthesis by iron 3 and the transcriptional regulator Fur 4 Short title: Antimicrobial production by SRE and Fur-Fe2+ regulation of carbapenem 5 Divine Yutefar Shyntum1, Ntombikayise Nkomo1,2, Alessandro Rino Gricia1,2, Ntwanano 6 Luann Shigange1, Daniel Bellieny-Rabelo1 and Lucy Novungayo Moleleki1, 2* 7 1Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lunnon 8 Road, Pretoria, South Africa, 0028 9 2Forestry, Agriculture and Biotechnology Institute, University of Pretoria, Lunnon Road, 10 Pretoria, South Africa, 0028 11 12 *Corresponding author 13 E-mail: [email protected] 14 Tel: +27(0)12 4204662 15 Fax: +27(0)12 4203266 16 1 bioRxiv preprint doi: https://doi.org/10.1101/497016; this version posted December 17, 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. 17 Abstract 18 Plant microbial communities’ complexity provide a rich model for investigation on biochemical and 19 regulatory strategies involved in interbacterial competition. -
YÖK Tez No: 479704
EGE ÜNİVE RSİTESİ DOKTORA TEZİ Ü Ü S S Ü Ü T T İ İ BALÇOVA YÜZEYSEL TERMAL SU T T S S KAYNAKLARINDAN ARSENİK METABOLİZE N N E E EDEN BAKTERİLERİN İZOLASYONU VE İ İ İDENTİFİKASYONU R R E E L L M M Ece SÖKMEN YILMAZ İ İ L L Tez Danışmanı: Prof. Dr. İsmail KARABOZ İ İ B B Biyoloji Anabilim Dalı N N E E Sunuş Tarihi: 17 .05.2017 F F . Ü Ü . E E Bornova-İZMİR 2017 EGE ÜNİVERSİTESİ FEN BİLİMLERİ ENSTİTÜSÜ (DOKTORA TEZİ) BALÇOVA YÜZEYSEL TERMAL SU KAYNAKLARINDAN ARSENİK METABOLİZE EDEN BAKTERİLERİN İZOLASYONU VE İDENTİFİKASYONU Ece SÖKMEN YILMAZ Tez Danışmanı: Prof. Dr. İsmail KARABOZ Biyoloji Anabilim Dalı Sunuş Tarihi: 17.05.2017 Bornova-İZMİR 2017 vii ÖZET BALÇOVA YÜZEYSEL TERMAL SU KAYNAKLARINDAN ARSENİK METABOLİZE EDEN BAKTERİLERİN İZOLASYONU VE İDENTİFİKASYONU SÖKMEN YILMAZ, Ece Doktora Tezi, Biyoloji Anabilim Dalı Tez Danışmanı: Prof. Dr. İsmail KARABOZ Mayıs 2017, 96 sayfa Bakteriyel arsenik metabolizması son yıllarda ilgi çeken konulardandır. Ağır metaller termal sularda boldur. İzmir Balçova’daki termal sularının karıştığı yüzey sularından izole edilen arsenik dirençli bakteriler üzerine bilenenler yok denecek kadar azdır. Bu çalışmanın amacı bu bakterileri tanımlamak ve literatürdeki arsenik metabolizma deneylerini uygulayarak ileriye yönelik veri elde edilmesini sağlamaktır. Bu çalışmada 500 mM arsenat içeren PCA’da üreyebilen on iki izolat tanımlanmıştır. Api 50 CH ve Api 20 E ile fenotipik karekterizasyonları belirlenen izolatların kısmi 16S rDNA dizi benzerliklerine göre birer tanesi Rhodococcus sp., Pannonibacter phragmitetus, Micrococcus sp., Enterobacter sp., Microbacterium sp. iken yedisi Pseudomonas sp.’dir. LB sıvı besiyerleri kullanılarak yüksek değerde arsenik MİK’leri saptandı. -
Enterobacter Pulveris Sp. Nov., Isolated from Fruit Powder, Infant Formula and an Infant Formula Production Environment
Zurich Open Repository and Archive University of Zurich Main Library Strickhofstrasse 39 CH-8057 Zurich www.zora.uzh.ch Year: 2008 Enterobacter pulveris, sp. nov. isolated from fruit powder, infant formula and infant formula production environment. Stephan, Roger ; Van Trappen, S ; Cleenwerck, I ; Iversen, C ; Joosten, H ; De Vos, P ; Lehner, Angelika Abstract: Six Gram-negative, facultative anaerobic, non-spore-forming isolates of coccoid rods were ob- tained from fruit powder (n=3), infant formula (n=2) and infant formula production environment (n=1) and investigated in a polyphasic taxonomic study. Comparative 16S rRNA gene sequence analysis com- bined with rpoB sequence analysis, allocated the isolates to the Enterobacteriaceae. The highest rpoB se- quence similarities (91.2-95.8 %) were obtained with Enterobacter helveticus, Enterobacter radicincitans, Enterobacter turicensis and Enterobacter sakazakii and the phylogenetic branch formed by these species is supported by a high bootstrap value. Biochemical data revealed that the isolates could be differentiated from their nearest neighbours by the positive utilization of -D-melibiose, sucrose, D-arabitol, mucate and 1-0-methyl--galacto-pyranoside as well as negative tests for D-sorbitol, and the Voges-Proskauer reac- tion. On the basis of the phylogenetic analyses, DNA-DNA hybridizations and the unique physiological and biochemical characteristics, it is proposed that the isolates represent a novel Enterobacter species, Enterobacter pulveris sp. nov. The type strain is 601/05T (= LMG 24057T = DSM 19144T). DOI: https://doi.org/10.1099/ijs.0.65427-0 Posted at the Zurich Open Repository and Archive, University of Zurich ZORA URL: https://doi.org/10.5167/uzh-5093 Journal Article Originally published at: Stephan, Roger; Van Trappen, S; Cleenwerck, I; Iversen, C; Joosten, H; De Vos, P; Lehner, Angelika (2008). -
Evaluation of FISH for Blood Cultures Under Diagnostic Real-Life Conditions
Original Research Paper Evaluation of FISH for Blood Cultures under Diagnostic Real-Life Conditions Annalena Reitz1, Sven Poppert2,3, Melanie Rieker4 and Hagen Frickmann5,6* 1University Hospital of the Goethe University, Frankfurt/Main, Germany 2Swiss Tropical and Public Health Institute, Basel, Switzerland 3Faculty of Medicine, University Basel, Basel, Switzerland 4MVZ Humangenetik Ulm, Ulm, Germany 5Department of Microbiology and Hospital Hygiene, Bundeswehr Hospital Hamburg, Hamburg, Germany 6Institute for Medical Microbiology, Virology and Hygiene, University Hospital Rostock, Rostock, Germany Received: 04 September 2018; accepted: 18 September 2018 Background: The study assessed a spectrum of previously published in-house fluorescence in-situ hybridization (FISH) probes in a combined approach regarding their diagnostic performance with incubated blood culture materials. Methods: Within a two-year interval, positive blood culture materials were assessed with Gram and FISH staining. Previously described and new FISH probes were combined to panels for Gram-positive cocci in grape-like clusters and in chains, as well as for Gram-negative rod-shaped bacteria. Covered pathogens comprised Staphylococcus spp., such as S. aureus, Micrococcus spp., Enterococcus spp., including E. faecium, E. faecalis, and E. gallinarum, Streptococcus spp., like S. pyogenes, S. agalactiae, and S. pneumoniae, Enterobacteriaceae, such as Escherichia coli, Klebsiella pneumoniae and Salmonella spp., Pseudomonas aeruginosa, Stenotrophomonas maltophilia, and Bacteroides spp. Results: A total of 955 blood culture materials were assessed with FISH. In 21 (2.2%) instances, FISH reaction led to non-interpretable results. With few exemptions, the tested FISH probes showed acceptable test characteristics even in the routine setting, with a sensitivity ranging from 28.6% (Bacteroides spp.) to 100% (6 probes) and a spec- ificity of >95% in all instances. -
Thi Na Utaliblat in Un Minune Talk
THI NA UTALIBLATUS010064900B2 IN UN MINUNE TALK (12 ) United States Patent ( 10 ) Patent No. : US 10 , 064 ,900 B2 Von Maltzahn et al . ( 45 ) Date of Patent: * Sep . 4 , 2018 ( 54 ) METHODS OF POPULATING A (51 ) Int. CI. GASTROINTESTINAL TRACT A61K 35 / 741 (2015 . 01 ) A61K 9 / 00 ( 2006 .01 ) (71 ) Applicant: Seres Therapeutics, Inc. , Cambridge , (Continued ) MA (US ) (52 ) U . S . CI. CPC .. A61K 35 / 741 ( 2013 .01 ) ; A61K 9 /0053 ( 72 ) Inventors : Geoffrey Von Maltzahn , Boston , MA ( 2013. 01 ); A61K 9 /48 ( 2013 . 01 ) ; (US ) ; Matthew R . Henn , Somerville , (Continued ) MA (US ) ; David N . Cook , Brooklyn , (58 ) Field of Classification Search NY (US ) ; David Arthur Berry , None Brookline, MA (US ) ; Noubar B . See application file for complete search history . Afeyan , Lexington , MA (US ) ; Brian Goodman , Boston , MA (US ) ; ( 56 ) References Cited Mary - Jane Lombardo McKenzie , Arlington , MA (US ); Marin Vulic , U . S . PATENT DOCUMENTS Boston , MA (US ) 3 ,009 ,864 A 11/ 1961 Gordon - Aldterton et al. 3 ,228 ,838 A 1 / 1966 Rinfret (73 ) Assignee : Seres Therapeutics , Inc ., Cambridge , ( Continued ) MA (US ) FOREIGN PATENT DOCUMENTS ( * ) Notice : Subject to any disclaimer , the term of this patent is extended or adjusted under 35 CN 102131928 A 7 /2011 EA 006847 B1 4 / 2006 U .S . C . 154 (b ) by 0 days. (Continued ) This patent is subject to a terminal dis claimer. OTHER PUBLICATIONS ( 21) Appl . No. : 14 / 765 , 810 Aas, J ., Gessert, C . E ., and Bakken , J. S . ( 2003) . Recurrent Clostridium difficile colitis : case series involving 18 patients treated ( 22 ) PCT Filed : Feb . 4 , 2014 with donor stool administered via a nasogastric tube . -
A Report of 31 Unrecorded Bacterial Species in South Korea Belonging to the Class Gammaproteobacteria
Journal188 of Species Research 5(1):188-200, 2016JOURNAL OF SPECIES RESEARCH Vol. 5, No. 1 A report of 31 unrecorded bacterial species in South Korea belonging to the class Gammaproteobacteria Yong-Taek Jung1, Jin-Woo Bae2, Che Ok Jeon3, Kiseong Joh4, Chi Nam Seong5, Kwang Yeop Jahng6, Jang-Cheon Cho7, Chang-Jun Cha8, Wan-Taek Im9, Seung Bum Kim10 and Jung-Hoon Yoon1,* 1Department of Food Science and Biotechnology, Sungkyunkwan University, Suwon 16419, Korea 2Department of Biology, Kyung Hee University, Seoul 02447, Korea 3Department of Life Science, Chung-Ang University, Seoul 06974, Korea 4Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Korea 5Department of Biology, Sunchon National University, Suncheon 57922, Korea 6Department of Life Sciences, Chonbuk National University, Jeonju-si 54896, Korea 7Department of Biological Sciences, Inha University, Incheon 22212, Korea 8Department of Biotechnology, Chung-Ang University, Anseong 17546, Korea 9Department of Biotechnology, Hankyong National University, Anseong 17579, Korea 10Department of Microbiology, Chungnam National University, Daejeon 34134, Korea *Correspondent: [email protected] During recent screening to discover indigenous prokaryotic species in South Korea, a total of 31 bacterial strains assigned to the class Gammaproteobacteria were isolated from a variety of environmental samples including soil, tidal flat, freshwater, seawater, and plant roots. From the high 16S rRNA gene sequence similarity (>98.7%) and formation of a robust -
Invasive Lactuca Serriola Seeds Contain Endophytic Bacteria That Contribute to Drought Tolerance Seorin Jeong, Tae‑Min Kim, Byungwook Choi, Yousuk Kim & Eunsuk Kim *
www.nature.com/scientificreports OPEN Invasive Lactuca serriola seeds contain endophytic bacteria that contribute to drought tolerance Seorin Jeong, Tae‑Min Kim, Byungwook Choi, Yousuk Kim & Eunsuk Kim * The mutualistic relationship between alien plant species and microorganisms is proposed to facilitate or hinder invasive success, depending on whether plants can form novel associations with microorganisms in the introduced habitats. However, this hypothesis has not considered seed endophytes that would move together with plant propagules. Little information is available on the seed endophytic bacteria of invasive species and their efects on plant performance. We isolated the seed endophytic bacteria of a xerophytic invasive plant, Lactuca serriola, and examined their plant growth‑promoting traits. In addition, we assessed whether these seed endophytes contributed to plant drought tolerance. Forty‑two bacterial species were isolated from seeds, and all of them exhibited at least one plant growth‑promoting trait. Kosakonia cowanii occurred in all four tested plant populations and produced a high concentration of exopolysaccharides in media with a highly negative water potential. Notably, applying K. cowanii GG1 to Arabidopsis thaliana stimulated plant growth under drought conditions. It also reduced soil water loss under drought conditions, suggesting bacterial production of exopolysaccharides might contribute to the maintenance of soil water content. These results imply that invasive plants can disperse along with benefcial bacterial symbionts, which potentially improve plant ftness and help to establish alien plant species. Endophytic bacteria are non-pathogenic microbes that occur within plant tissues, including the stems, seeds, leaves, and fruits1,2. Endophytic bacteria have received considerable attention because they stimulate plant growth by producing plant growth-promoting (PGP) molecules or increasing plant resistance to biotic and abiotic envi- ronmental stresses3–6. -
Prevalence of Bacterial Contamination in Uncooked Sticky Rice Samples from Markets in Japan
Original Article Prevalence of bacterial contamination in uncooked sticky rice samples from markets in Japan Kazuko Kato1 Noriko Komagome1 Machiko Mineki1 Sumalee Boonmar2 Yukio Morita3* Abstract We investigated the prevalence of bacterial contamination in uncooked sticky rice samples obtained from markets in Japan. Between June and August, 2019, a total of 25 sticky rice samples were purchased from shops in the Tokyo area. Twenty-two (88.0%) and 10 (40.0%) of 25 sticky rice samples harbored 3.06±0.54 log spc/g of standard plates counts and 2.17±0.23 log cfu/g of enterobacteriaceae bacteria counts, respectively. Three species of Enterobacteriaceae, Pantoea dispersa, P. ananati, and Kosakonia cowanii, were identified by MALDI-TOFMS-based test. Three (12.0%) of 25 sticky rice samples harbored 2.00 log cfu/g of Bacillus species. Bacillus spp. was not isolated after heat treatment (98 °C for 20 min.) of sample homogenates. Two isolates were identified B. cereus by both API 50 CH and MALDI-TOFMS based test. However, one isolate was B. mycoides by API 50 CH, but B. cereus by MALDI-TOF MS based test. These 3 Bacillus strains harbored no gene encoding the enzyme responsible for cereulide synthesis and had not produced enterotoxin. Our study suggested that some uncooked sticky rice has Enterobacteriaceae bacteria and Bacillus spp. contamination, however there is no isolate from heat treatment samples in this study. Isolated P. dispersa, P. ananati, and K. cowanii, are usually in the environment and these organisms have been isolated from patients with opportunistic infections. Preventing cross-contamination, from sticky rice to cooked food may be important during preparation and storage in kitchen. -
UNIVERSITY of CALIFORNIA Los Angeles
UNIVERSITY OF CALIFORNIA Los Angeles Inflammatory Bowel Disease-associated Dysbiosis and Immune Gardening of the Intestinal Microbiome A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Cellular and Molecular Pathology by Jonathan Patrick Jacobs 2015 ABSTRACT OF THE DISSERTATION Inflammatory Bowel Disease-associated Dysbiosis and Immune Gardening of the Intestinal Microbiome by Jonathan Patrick Jacobs Doctor of Philosophy in Cellular and Molecular Pathology University of California, Los Angeles, 2015 Professor Jonathan Braun, Chair Inflammatory bowel disease (IBD) – comprised of Crohn’s disease (CD) and ulcerative colitis (UC) – is believed to arise from a combination of genetic susceptibility and environmental factors that trigger an inappropriate mucosal immune response to constituents of the intestinal microbiome. There is now an extensive literature demonstrating that the microbiome has profound effects on immune function and, conversely, that the immune system can shape the microbiome. I hypothesized that genetic variation in mucosal immune gardening of the intestinal microbiome can result in pro-inflammatory dysbiosis, which acts as a risk factor for overt IBD. To evaluate whether individuals at risk for IBD develop dysbiosis prior to the onset of disease, a family based study was performed to characterize the microbiome and metabolome of pediatric IBD patients and their first degree relatives. These relatives are at higher risk for dysbiosis than the general population due to shared genetic and environmental factors with the IBD proband. A ii subset of healthy relatives in this cohort had dysbiosis with fecal metabolomic profiles (metabotypes) shared with IBD patients. The effect of the transcription factor RORγt on the intestinal microbiome was then investigated as a model of how perturbation of immune gardening could result in dysbiosis. -
Rhabdomyolysis Due to Bacteremia from Enterobacter Cowanii Caused by a Rose Thorn Prick
Kobe University Repository : Kernel タイトル Rhabdomyolysis due to bacteremia from Enterobacter cowanii caused Title by a rose thorn prick 著者 Washio, Ken / Yamamoto, Go / Ikemachi, Mami / Fujii, Shotaro / Author(s) Ohnuma, Kenichiro / Masaki, Taro 掲載誌・巻号・ページ JOURNAL OF DERMATOLOGY,45(11):e313-e314 Citation 刊行日 2018-11 Issue date 資源タイプ Journal Article / 学術雑誌論文 Resource Type 版区分 author Resource Version 権利 Rights DOI 10.1111/1346-8138.14341 JaLCDOI URL http://www.lib.kobe-u.ac.jp/handle_kernel/90006665 PDF issue: 2021-10-04 1 1 Rhabdomyolysis due to bacteremia from Enterobacter cowanii caused by a rose 2 thorn prick 3 4 Running head 5 Rhabdomyolysis by Enterobacter cowanii 6 7 Ken Washio1, Go Yamamoto2, Mami Ikemachi2, Shotaro Fujii1, Kenichiro Ohnuma3, and 8 Taro Masaki1 9 10 1) Department of Dermatology, Kobe City Nishi-Kobe Medical Center, Japan. 11 2) Department of Clinical Laboratory, Kobe City Nishi-Kobe Medical Center, Japan. 12 3) Department of Clinical Laboratory, Kobe University Hospital, Japan. 13 14 Correspondence: 15 Ken Washio, M.D., Ph.D., Department of Dermatology, Kobe City Nishi-Kobe Medical 16 Center, Japan. 17 5-7-1, Koji-Dai, Nishi-ku, Kobe, 651-2273 Japan. 18 E-mail: [email protected] 19 Tel: +81-78-997-2200 20 Fax: +81-78-993-3728 21 22 2 23 Manuscript word, table, and figure counts 24 Words: 489 25 Tables: 0 26 Figures: 1 27 References: 5 28 Supplemental Figures: 1 29 Supplemental Tables: 3 30 3 31 Dear Editor, 32 Rose bush thorns can be dangerous to human health.