Gram Negative Bacteria in Brewing
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Indoor Microbiome, Environmental Characteristics and Asthma Among Junior High
Indoor microbiome, environmental characteristics and asthma among junior high school students in Johor Bahru, Malaysia Xi Fu1, Dan Norbäck2, Qianqian Yuan3,4, Yanling Li3,4, Xunhua Zhu3,4,Yiqun Deng3,4, Jamal Hisham Hashim5,6, Zailina Hashim7, Yi-Wu Zheng8, Xu-Xin Lai8, Michael Dho Spangfort8, Yu Sun3,4 * 1Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou, PR China. 2Occupational and Environmental Medicine, Dept. of Medical Science, University Hospital, Uppsala University, 75237 Uppsala, Sweden. 3Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China. 4Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China. 5United Nations University-International Institute for Global Health, Kuala Lumpur, Malaysia, 6Department of Community Health, National University of Malaysia, Kuala Lumpur, Malaysia 7Department of Environmental and Occupational Health, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM, Serdang, Selangor, Malaysia 8Asia Pacific Research, ALK-Abello A/S, Guanzhou, China *To whom corresponds should be addressed: Yu Sun [email protected], Key words: bacteria, fungi, microbial community, absolute quantity, wheezing, breathlessness, adolescence, dampness/visible mold Abstract Indoor microbial diversity and composition are suggested to affect the prevalence and severity of asthma, but no microbial association study has been conducted in tropical countries. In this study, we collected floor dust and environmental characteristics from 21 classrooms, and health data related to asthma symptoms from 309 students, in junior high schools in Johor Bahru, Malaysia. -
Acetobacter Sacchari Sp. Nov., for a Plant Growth-Promoting Acetic Acid Bacterium Isolated in Vietnam
Annals of Microbiology (2019) 69:1155–11631163 https://doi.org/10.1007/s13213-019-01497-0 ORIGINAL ARTICLE Acetobacter sacchari sp. nov., for a plant growth-promoting acetic acid bacterium isolated in Vietnam Huong Thi Lan Vu1,2 & Pattaraporn Yukphan3 & Van Thi Thu Bui1 & Piyanat Charoenyingcharoen3 & Sukunphat Malimas4 & Linh Khanh Nguyen1 & Yuki Muramatsu5 & Naoto Tanaka6 & Somboon Tanasupawat7 & Binh Thanh Le2 & Yasuyoshi Nakagawa5 & Yuzo Yamada3,8,9 Received: 21 January 2019 /Accepted: 7 July 2019 /Published online: 18 July 2019 # Università degli studi di Milano 2019 Abstract Purpose Two bacterial strains, designated as isolates VTH-Ai14T and VTH-Ai15, that have plant growth-promoting ability were isolated during the study on acetic acid bacteria diversity in Vietnam. The phylogenetic analysis based on 16S rRNA gene sequences showed that the two isolates were located closely to Acetobacter nitrogenifigens RG1T but formed an independent cluster. Methods The phylogenetic analysis based on 16S rRNA gene and three housekeeping genes’ (dnaK, groEL, and rpoB) sequences were analyzed. The genomic DNA of the two isolates, VTH-Ai14T and VTH-Ai15, Acetobacter nitrogenifigens RG1T, the closest phylogenetic species, and Acetobacter aceti NBRC 14818T were hybridized and calculated the %similarity. Then, phenotypic and chemotaxonomic characteristics were determined for species’ description using the conventional method. Results The 16S rRNA gene and concatenated of the three housekeeping genes phylogenetic analysis suggests that the two isolates were constituted in a species separated from Acetobacter nitrogenifigens, Acetobacter aceti,andAcetobacter sicerae. The two isolates VTH-Ai14T and VTH-Ai15 showed 99.65% and 98.65% similarity of 16S rRNA gene when compared with Acetobacter nitrogenifigens and Acetobacter aceti and they were so different from Acetobacter nitrogenifigens RG1T with 56.99 ± 3.6 and 68.15 ± 1.8% in DNA-DNA hybridization, when isolates VTH-Ai14T and VTH-Ai15 were respectively labeled. -
Metal Transformation by a Novel Pelosinus Isolate from a Subsurface Environment
INL/JOU-08-14091-Revision-0 Metal Transformation by a Novel Pelosinus Isolate From a Subsurface Environment Allison E. Ray, Peter P. Sheridan, Andrew L. Neal, Yoshiko Fujita, David E. Cummings, Timothy S. Magnuson August 2018 The INL is a U.S. Department of Energy National Laboratory operated by Battelle Energy Alliance INL/JOU-08-14091-Revision-0 Metal Transformation by a Novel Pelosinus Isolate From a Subsurface Environment Allison E. Ray, Peter P. Sheridan, Andrew L. Neal, Yoshiko Fujita, David E. Cummings, Timothy S. Magnuson August 2018 Idaho National Laboratory Idaho Falls, Idaho 83415 http://www.inl.gov Prepared for the U.S. Department of Energy Office of Nuclear Energy Under DOE Idaho Operations Office Contract DE-AC07-05ID14517 fmicb-09-01689 July 25, 2018 Time: 20:42 # 1 ORIGINAL RESEARCH published: xx July 2018 doi: 10.3389/fmicb.2018.01689 1 58 2 59 3 60 4 61 5 62 6 63 7 64 8 65 9 Metal Transformation by a Novel 66 10 67 11 Pelosinus Isolate From a Subsurface 68 12 69 13 Environment 70 14 71 15 Allison E. Ray1,2, Stephanie A. Connon1,3, Andrew L. Neal4†, Yoshiko Fujita2, 72 5 2† 1 16 David E. Cummings , Jani C. Ingram and Timothy S. Magnuson * 73 17 74 1 Department of Biological Sciences, Idaho State University, Pocatello, ID, United States, 2 Bioenergy Technologies, Idaho 18 3 75 Edited by: National Laboratory, Idaho Falls, ID, United States, California Institute of Technology, Pasadena, CA, United States, 19 4 5 76 Pankaj Kumar Arora, Savannah River Ecology Laboratory, University of Georgia, Aiken, SC, United States, Department of Biology, Point Loma 20 77 Babasaheb Bhimrao Ambedkar Nazarene University, San Diego, CA, United States 21 University, India 78 22 79 Reviewed by: The capability of microorganisms to alter metal speciation offers potential for 23 80 Ramprasad E.V.V., the development of new strategies for immobilization of toxic metals in the 24 University of Hyderabad, India 81 25 Bärbel Ulrike Fösel, environment. -
Electronic Supplementary Information
Electronic Supplementary Material (ESI) for Environmental Science: Water Research & Technology. This journal is © The Royal Society of Chemistry 2019 Electronic Supplementary Information Microbial community and antibiotic resistance profiles of biomass and effluent are distinctly affected by antibiotic addition to an anaerobic membrane bioreactor Ali Zarei-Baygi*, Moustapha Harb#,*, Phillip Wang*, Lauren Stadler^, and Adam L. Smith*† * Astani Department of Civil and Environmental Engineering, University of Southern California, 3620 South Vermont Avenue, Los Angeles, CA 90089, USA # Department of Civil and Environmental Engineering, Lebanese American University, 309 Bassil Building, Byblos, Lebanon ^ Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, Houston, TX 77005, USA †Corresponding author (Adam L. Smith) Phone: +1 213.740.0473 Email: [email protected] Number of pages: 15 Number of figures: 6 Number of tables: 6 S1 Quantification of antibiotics by LC-MS For antibiotics quantification, 10 mL samples were collected for each sampling time point from the influent and effluent of the AnMBR. Both collected samples and standard solutions were filtered through 0.2 µm PTFE syringe filters (Whatman) using 10 mL syringes with Luer lock tips and stored in certified 2 mL amber LC vials (Agilent) at 4 ºC refrigerator for no more than 3 days prior to analysis. Stock solutions of sulfamethoxazole and erythromycin were prepared in HPLC-grade methanol at concentrations of 20 mg/L and stored at -20 ºC. Ampicillin stock solution was prepared in HPLC-grade water at 4 mg/L due to its lack of solubility in methanol and stored at 4 ºC. For each antibiotic, a six-point standard calibration curve was constructed within the appropriate range (i.e., 0.1-30 µg/L to target effluent antibiotics and 30- 400 µg/L to target influent antibiotics). -
Microbes from Sequencing 16S Ribosomal DNA and Internal Transcribed Spacer 2 Cancan Cheng†, Jingjing Sun†, Fen Zheng, Kuihai Wu and Yongyu Rui*
Cheng et al. Annals of Clinical Microbiology and Antimicrobials 2014, 13:1 http://www.ann-clinmicrob.com/content/13/1/1 RESEARCH Open Access Molecular identification of clinical “difficult-to-identify” microbes from sequencing 16S ribosomal DNA and internal transcribed spacer 2 Cancan Cheng†, Jingjing Sun†, Fen Zheng, Kuihai Wu and Yongyu Rui* Abstract Background: Clinical microbiology laboratories have to accurately identify clinical microbes. However, some isolates are difficult to identify by the automated biochemical text platforms, which are called “difficult-to-identify” microbes in this study. Therefore, the ability of 16S ribosomal DNA (16S rDNA) and internal transcribed spacer 2 (ITS2) sequencing to identify these “difficult-to-identify” bacteria and fungi was assessed in this study. Methods: Samples obtained from a teaching hospital over the past three years were examined. The 16S rDNA of four standard strains, 18 clinical common isolates, and 47 “difficult-to-identify” clinical bacteria were amplified by PCR and sequenced. The ITS2 of eight standard strains and 31 “difficult-to-identify” clinical fungi were also amplified by PCR and sequenced. The sequences of 16S rDNA and ITS2 were compared to reference data available in GenBank by using the BLASTN program. These microbes were identified according to the percentage of similarity to reference sequences of strains in GenBank. Results: The results from molecular sequencing methods correlated well with automated microbiological identification systems for common clinical isolates. Sequencing results of the standard strains were consistent with their known phenotype. Overall, 47 “difficult-to-identify” clinical bacteria were identified as 35 genera or species by sequence analysis (with 10 of these identified isolates first reported in clinical specimens in China and two first identified in the international literature). -
Characterization of Bacterial Communities Associated
www.nature.com/scientificreports OPEN Characterization of bacterial communities associated with blood‑fed and starved tropical bed bugs, Cimex hemipterus (F.) (Hemiptera): a high throughput metabarcoding analysis Li Lim & Abdul Hafz Ab Majid* With the development of new metagenomic techniques, the microbial community structure of common bed bugs, Cimex lectularius, is well‑studied, while information regarding the constituents of the bacterial communities associated with tropical bed bugs, Cimex hemipterus, is lacking. In this study, the bacteria communities in the blood‑fed and starved tropical bed bugs were analysed and characterized by amplifying the v3‑v4 hypervariable region of the 16S rRNA gene region, followed by MiSeq Illumina sequencing. Across all samples, Proteobacteria made up more than 99% of the microbial community. An alpha‑proteobacterium Wolbachia and gamma‑proteobacterium, including Dickeya chrysanthemi and Pseudomonas, were the dominant OTUs at the genus level. Although the dominant OTUs of bacterial communities of blood‑fed and starved bed bugs were the same, bacterial genera present in lower numbers were varied. The bacteria load in starved bed bugs was also higher than blood‑fed bed bugs. Cimex hemipterus Fabricus (Hemiptera), also known as tropical bed bugs, is an obligate blood-feeding insect throughout their entire developmental cycle, has made a recent resurgence probably due to increased worldwide travel, climate change, and resistance to insecticides1–3. Distribution of tropical bed bugs is inclined to tropical regions, and infestation usually occurs in human dwellings such as dormitories and hotels 1,2. Bed bugs are a nuisance pest to humans as people that are bitten by this insect may experience allergic reactions, iron defciency, and secondary bacterial infection from bite sores4,5. -
Electrochemical Startup Increases 1,3-Propanediol Titers in Mixed-Culture Glycerol Fermentations
G Model PRBI-10464; No. of Pages 10 ARTICLE IN PRESS Process Biochemistry xxx (2015) xxx–xxx Contents lists available at ScienceDirect Process Biochemistry jo urnal homepage: www.elsevier.com/locate/procbio Electrochemical startup increases 1,3-propanediol titers in mixed-culture glycerol fermentations a,∗ a,b a Nikolaos Xafenias , MarySandra Oluchi Anunobi , Valeria Mapelli a Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE-41296, Sweden b School of Engineering, University of Aberdeen, Aberdeen AB243 UE, United Kingdom a r a t i b s c t l e i n f o r a c t Article history: In this study we investigated the use of electric potential to bioelectrochemically ferment glycerol, a Received 13 May 2015 cheap by-product of biodiesel production, into valuable 1,3-propanediol (1,3-PDO). The 1,3-PDO pro- Received in revised form 7 June 2015 duction rates were increased up to 6 times in electrofermentations, compared to non-electrochemical Accepted 22 June 2015 fermentations, and high concentrations up to 42 g 1,3-PDO/l were achieved in fed-batch mode. Extensive Available online xxx growth of the well-known 1,3-PDO producers Clostridiaceae (55–57%) was observed when an appro- priate potential (−1.1 V vs. SHE) was constantly applied since the start. Potential propionate producers Keywords: (Veillonellaceae) were also among the dominant families (20–21%); however, surprisingly enough, propio- 1,3-Propanediol nate production was not observed. On the contrary, Clostridiaceae were absent, Veillonellaceae dominated Bioelectrochemical systems Bioelectrosynthesis (56–72%), and propionate was produced when electric potential was not sufficient for current produc- Fermentation tion since the beginning. -
Integrating Taxonomic, Functional, and Strain-Level Profiling of Diverse
TOOLS AND RESOURCES Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 Francesco Beghini1†, Lauren J McIver2†, Aitor Blanco-Mı´guez1, Leonard Dubois1, Francesco Asnicar1, Sagun Maharjan2,3, Ana Mailyan2,3, Paolo Manghi1, Matthias Scholz4, Andrew Maltez Thomas1, Mireia Valles-Colomer1, George Weingart2,3, Yancong Zhang2,3, Moreno Zolfo1, Curtis Huttenhower2,3*, Eric A Franzosa2,3*, Nicola Segata1,5* 1Department CIBIO, University of Trento, Trento, Italy; 2Harvard T.H. Chan School of Public Health, Boston, United States; 3The Broad Institute of MIT and Harvard, Cambridge, United States; 4Department of Food Quality and Nutrition, Research and Innovation Center, Edmund Mach Foundation, San Michele all’Adige, Italy; 5IEO, European Institute of Oncology IRCCS, Milan, Italy Abstract Culture-independent analyses of microbial communities have progressed dramatically in the last decade, particularly due to advances in methods for biological profiling via shotgun metagenomics. Opportunities for improvement continue to accelerate, with greater access to multi-omics, microbial reference genomes, and strain-level diversity. To leverage these, we present bioBakery 3, a set of integrated, improved methods for taxonomic, strain-level, functional, and *For correspondence: phylogenetic profiling of metagenomes newly developed to build on the largest set of reference [email protected] (CH); sequences now available. Compared to current alternatives, MetaPhlAn 3 increases the accuracy of [email protected] (EAF); taxonomic profiling, and HUMAnN 3 improves that of functional potential and activity. These [email protected] (NS) methods detected novel disease-microbiome links in applications to CRC (1262 metagenomes) and †These authors contributed IBD (1635 metagenomes and 817 metatranscriptomes). -
Biodegradation Treatment of Petrochemical Wastewaters
UNIVERSIDADE DE LISBOA FACULDADE DE CIÊNCIAS DEPARTAMENTO DE BIOLOGIA VEGETAL Biodegradation treatment of petrochemical wastewaters Catarina Isabel Nunes Alexandre Dissertação Mestrado em Microbiologia Aplicada Orientadores Doutora Sandra Sanches Professora Doutora Lélia Chambel 2015 Biodegradation treatment of petrochemical wastewaters Catarina Isabel Nunes Alexandre 2015 This thesis was fully performed at the Institute of Experimental and Technologic Biology (IBET) of Instituto de Tecnologia Química e Bioquímica (ITQB) under the direct supervision of Drª Sandra Sanches in the scope of the Master in Applied Microbiology of the Faculty of Sciences of the University of Lisbon. Prof. Drª Lélia Chambel was the internal designated supervisor in the scope of the Master in Applied Microbiology of the Faculty of Sciences of the University of Lisbon. Agradecimentos Gostaria de agradecer a todas as pessoas que estiveram directamente ou indirectamente envolvidas na execução da minha tese de mestrado, pois sem eles a sua realização não teria sido possível. Queria começar por agradecer à Doutora Sandra Sanches, que se demonstrou sempre disponível para esclarecer dúvidas quando precisei, e que fez questão de me ensinar de forma rigorosa e exigente. À Doutora Maria Teresa Crespo, que assim que lhe pedi para me orientar me disse que sim imediatamente, fez questão de me treinar em vários contextos e sempre estimulou o meu envolvimento nas rotinas do laboratório. À Professora Doutora Lélia Chambel, que sempre me esclareceu dúvidas sobre processos burocráticos, me deu conselhos quando eu mais precisei e que me apoiou durante toda a minha tese. Queria também agradecer à Doutora Dulce Brito, que sempre se mostrou disponível para ajudar quando a nossa equipa mais precisava dela, e sempre me ajudou a realizar as tarefas mais básicas do meu trabalho até eu ter ganho a minha autonomia no laboratório. -
EXPERIMENTAL STUDIES on FERMENTATIVE FIRMICUTES from ANOXIC ENVIRONMENTS: ISOLATION, EVOLUTION, and THEIR GEOCHEMICAL IMPACTS By
EXPERIMENTAL STUDIES ON FERMENTATIVE FIRMICUTES FROM ANOXIC ENVIRONMENTS: ISOLATION, EVOLUTION, AND THEIR GEOCHEMICAL IMPACTS By JESSICA KEE EUN CHOI A dissertation submitted to the School of Graduate Studies Rutgers, The State University of New Jersey In partial fulfillment of the requirements For the degree of Doctor of Philosophy Graduate Program in Microbial Biology Written under the direction of Nathan Yee And approved by _______________________________________________________ _______________________________________________________ _______________________________________________________ _______________________________________________________ New Brunswick, New Jersey October 2017 ABSTRACT OF THE DISSERTATION Experimental studies on fermentative Firmicutes from anoxic environments: isolation, evolution and their geochemical impacts by JESSICA KEE EUN CHOI Dissertation director: Nathan Yee Fermentative microorganisms from the bacterial phylum Firmicutes are quite ubiquitous in subsurface environments and play an important biogeochemical role. For instance, fermenters have the ability to take complex molecules and break them into simpler compounds that serve as growth substrates for other organisms. The research presented here focuses on two groups of fermentative Firmicutes, one from the genus Clostridium and the other from the class Negativicutes. Clostridium species are well-known fermenters. Laboratory studies done so far have also displayed the capability to reduce Fe(III), yet the mechanism of this activity has not been investigated -
Supplementary Figure Legends for Rands Et Al. 2019
Supplementary Figure legends for Rands et al. 2019 Figure S1: Display of all 485 prophage genome maps predicted from Gram-Negative Firmicutes. Each horizontal line corresponds to an individual prophage shown to scale and color-coded for annotated phage genes according to the key displayed in the right- side Box. The left vertical Bar indicates the Bacterial host in a colour code. Figure S2: Projection of virome sequences from 183 human stool samples on A. Acidaminococcus intestini RYC-MR95, and B. Veillonella parvula UTDB1-3. The first panel shows the read coverage (Y-axis) across the complete Bacterial genome sequence (X-axis; with bp coordinates). Predicted prophage regions are marked with red triangles and magnified in the suBsequent panels. Virome reads projected outside of prophage prediction are listed in Table S4. Figure S3: The same display of virome sequences projected onto Bacterial genomes as in Figure S2, But for two different Negativicute species: A. Dialister Marseille, and B. Negativicoccus massiliensis. For non-phage peak annotations, see Table S4. Figure S4: Gene flanking analysis for the lysis module from all prophages predicted in all the different Bacterial clades (Table S2), a total of 3,462 prophages. The lysis module is generally located next to the tail module in Firmicute prophages, But adjacent to the packaging (terminase) module in Escherichia phages. 1 Figure S5: Candidate Mu-like prophage in the Negativicute Propionispora vibrioides. Phage-related genes (arrows indicate transcription direction) are coloured and show characteristics of Mu-like genome organization. Figure S6: The genome maps of Negativicute prophages harbouring candidate antiBiotic resistance genes MBL (top three Veillonella prophages) and tet(32) (bottom Selenomonas prophage remnant); excludes the ACI-1 prophage harbouring example characterised previously (Rands et al., 2018). -
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.