From Genotype to Phenotype: Inferring Relationships Between Microbial Traits and Genomic Components
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Effects of Dietary Supplementation with Hainanmycin on Protein Degradation and Populations of Ammonia-Producing Bacteria in Vitro
668 Asian Australas. J. Anim. Sci. Vol. 26, No. 5 : 668-674 May 2013 http://dx.doi.org/10.5713/ajas.2012.12589 www.ajas.info pISSN 1011-2367 eISSN 1976-5517 Effects of Dietary Supplementation with Hainanmycin on Protein Degradation and Populations of Ammonia-producing Bacteria In vitro Z. B. Wang1,2,a, H. S. Xin1,a, M. J. Wang1, Z. Y. Li1, Y. L. Qu2, S. J. Miao2 and Y. G. Zhang1,* 1 College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, Heilongjiang, China ABSTRACT: An in vitro fermentation was conducted to determine the effects of hainanmycin on protein degradation and populations of ammonia-producing bacteria. The substrates (DM basis) for in vitro fermentation consisted of alfalfa hay (31.7%), Chinese wild rye grass hay (28.3%), ground corn grain (24.5%), soybean meal (15.5%) with a forage: concentrate of 60:40. Treatments were the control (no additive) and hainanmycin supplemented at 0.1 (H0.1), 1 (H1), 10 (H10), and 100 mg/kg (H100) of the substrates. After 24 h of fermentation, the highest addition level of hainanmycin decreased total VFA concentration and increased the final pH. The high addition level of hainanmycin (H1, H10, and H100) reduced (p<0.05) branched-chain VFA concentration, the molar proportion of acetate and butyrate, and ratio of acetate to propionate; and increased the molar proportion of propionate, except that for H1 the in molar proportion of acetate and isobutyrate was not changed (p>0.05). After 24 h of fermentation, H10 and H100 increased (p<0.05) concentrations of peptide nitrogen and AA nitrogen and proteinase activity, and decreased (p<0.05) NH3-N concentration and deaminase activity compared with control. -
Comparison of Enzymatic Activities and Proteomic Profiles Of
Sechovcová et al. Proteome Science (2019) 17:2 https://doi.org/10.1186/s12953-019-0150-3 RESEARCH Open Access Comparison of enzymatic activities and proteomic profiles of Butyrivibrio fibrisolvens grown on different carbon sources Hana Sechovcová1,5* , Lucie Kulhavá2,4, Kateřina Fliegerová1, Mária Trundová3, Daniel Morais6, Jakub Mrázek1 and Jan Kopečný1 Abstract Background: The rumen microbiota is one of the most complex consortia of anaerobes, involving archaea, bacteria, protozoa, fungi and phages. They are very effective at utilizing plant polysaccharides, especially cellulose and hemicelluloses. The most important hemicellulose decomposers are clustered with the genus Butyrivibrio.As the related species differ in their range of hydrolytic activities and substrate preferences, Butyrivibrio fibrisolvens was selected as one of the most effective isolates and thus suitable for proteomic studies on substrate comparisons in the extracellular fraction. The B. fibrisolvens genome is the biggest in the butyrivibria cluster and is focused on “environmental information processing” and “carbohydrate metabolism”. Methods: The study of the effect of carbon source on B. fibrisolvens 3071 was based on cultures grown on four substrates: xylose, glucose, xylan, xylan with 25% glucose. The enzymatic activities were studied by spectrophotometric and zymogram methods. Proteomic study was based on genomics, 2D electrophoresis and nLC/MS (Bruker Daltonics) analysis. Results: Extracellular β-endoxylanase as well as xylan β-xylosidase activities were induced with xylan. The presence of the xylan polymer induced hemicellulolytic enzymes and increased the protein fraction in the interval from 40 to 80 kDa. 2D electrophoresis with nLC/MS analysis of extracellular B. fibrisolvens 3071 proteins found 14 diverse proteins with significantly different expression on the tested substrates. -
A Putative Cystathionine Beta-Synthase Homolog of Mycolicibacterium Smegmatis Is Involved in De Novo Cysteine Biosynthesis
University of Arkansas, Fayetteville ScholarWorks@UARK Theses and Dissertations 5-2020 A Putative Cystathionine Beta-Synthase Homolog of Mycolicibacterium smegmatis is Involved in de novo Cysteine Biosynthesis Saroj Kumar Mahato University of Arkansas, Fayetteville Follow this and additional works at: https://scholarworks.uark.edu/etd Part of the Cell Biology Commons, Molecular Biology Commons, and the Pathogenic Microbiology Commons Citation Mahato, S. K. (2020). A Putative Cystathionine Beta-Synthase Homolog of Mycolicibacterium smegmatis is Involved in de novo Cysteine Biosynthesis. Theses and Dissertations Retrieved from https://scholarworks.uark.edu/etd/3639 This Thesis is brought to you for free and open access by ScholarWorks@UARK. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of ScholarWorks@UARK. For more information, please contact [email protected]. A Putative Cystathionine Beta-Synthase Homolog of Mycolicibacterium smegmatis is Involved in de novo Cysteine Biosynthesis A thesis submitted in partial fulfillment of the requirement for the degree of Master of Science in Cell and Molecular Biology by Saroj Kumar Mahato Purbanchal University Bachelor of Science in Biotechnology, 2016 May 2020 University of Arkansas This thesis is approved for recommendation to the Graduate Council. ___________________________________ Young Min Kwon, Ph.D. Thesis Director ___________________________________ ___________________________________ Suresh Thallapuranam, Ph.D. Inés Pinto, Ph.D. Committee Member Committee Member ABSTRACT Mycobacteria include serious pathogens of humans and animals. Mycolicibacterium smegmatis is a non-pathogenic model that is widely used to study core mycobacterial metabolism. This thesis explores mycobacterial pathways of cysteine biosynthesis by generating and study of genetic mutants of M. smegmatis. Published in vitro biochemical studies had revealed three independent routes to cysteine synthesis in mycobacteria involving separate homologs of cysteine synthase, namely CysK1, CysK2, and CysM. -
Effects of Zinc and Menthol-Based Diets on Co-Selection of Antibiotic Resistance Among E
animals Article Effects of Zinc and Menthol-Based Diets on Co-Selection of Antibiotic Resistance among E. coli and Enterococcus spp. in Beef Cattle Sarah A. Murray 1, Raghavendra G. Amachawadi 2 , Keri N. Norman 3 , Sara D. Lawhon 1, Tiruvoor G. Nagaraja 4 , James S. Drouillard 5 and Harvey M. Scott 1,* 1 Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843, USA; [email protected] (S.A.M.); [email protected] (S.D.L.) 2 Department of Clinical Sciences, Kansas State University, Manhattan, KS 66506, USA; [email protected] 3 Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA; [email protected] 4 Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, KS 66506, USA; [email protected] 5 Department of Animal Sciences and Industry, Kansas State University, Manhattan, KS 66506, USA; [email protected] * Correspondence: [email protected]; Tel.: +1-(979)-847-6197 Simple Summary: As antibiotic resistance increases globally, alternatives to antibiotics are increas- ingly being investigated as growth promoters, as well as preventive and therapeutic agents, partic- ularly in agriculture. Equally important is the need for investigation into the effects of antibiotic Citation: Murray, S.A.; Amachawadi, alternatives on antibiotic resistance and particularly their risk for co-selection. In this study, we R.G.; Norman, K.N.; Lawhon, S.D.; explored the prevalence of antibiotic-resistant Escherichia coli and Enterococcus spp. in cattle fed zinc, Nagaraja, T.G.; Drouillard, J.S.; Scott, menthol or a combination of the two. -
Microbial Community Structure Dynamics in Ohio River Sediments During Reductive Dechlorination of Pcbs
University of Kentucky UKnowledge University of Kentucky Doctoral Dissertations Graduate School 2008 MICROBIAL COMMUNITY STRUCTURE DYNAMICS IN OHIO RIVER SEDIMENTS DURING REDUCTIVE DECHLORINATION OF PCBS Andres Enrique Nunez University of Kentucky Right click to open a feedback form in a new tab to let us know how this document benefits ou.y Recommended Citation Nunez, Andres Enrique, "MICROBIAL COMMUNITY STRUCTURE DYNAMICS IN OHIO RIVER SEDIMENTS DURING REDUCTIVE DECHLORINATION OF PCBS" (2008). University of Kentucky Doctoral Dissertations. 679. https://uknowledge.uky.edu/gradschool_diss/679 This Dissertation is brought to you for free and open access by the Graduate School at UKnowledge. It has been accepted for inclusion in University of Kentucky Doctoral Dissertations by an authorized administrator of UKnowledge. For more information, please contact [email protected]. ABSTRACT OF DISSERTATION Andres Enrique Nunez The Graduate School University of Kentucky 2008 MICROBIAL COMMUNITY STRUCTURE DYNAMICS IN OHIO RIVER SEDIMENTS DURING REDUCTIVE DECHLORINATION OF PCBS ABSTRACT OF DISSERTATION A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the College of Agriculture at the University of Kentucky By Andres Enrique Nunez Director: Dr. Elisa M. D’Angelo Lexington, KY 2008 Copyright © Andres Enrique Nunez 2008 ABSTRACT OF DISSERTATION MICROBIAL COMMUNITY STRUCTURE DYNAMICS IN OHIO RIVER SEDIMENTS DURING REDUCTIVE DECHLORINATION OF PCBS The entire stretch of the Ohio River is under fish consumption advisories due to contamination with polychlorinated biphenyls (PCBs). In this study, natural attenuation and biostimulation of PCBs and microbial communities responsible for PCB transformations were investigated in Ohio River sediments. Natural attenuation of PCBs was negligible in sediments, which was likely attributed to low temperature conditions during most of the year, as well as low amounts of available nitrogen, phosphorus, and organic carbon. -
Microbial Diversity of Non-Flooded High Temperature Petroleum Reservoir in South of Iran
Archive of SID Biological Journal of Microorganism th 8 Year, Vol. 8, No. 32, Winter 2020 Received: November 18, 2018/ Accepted: May 21, 2019. Page: 15-231- 8 Microbial Diversity of Non-flooded High Temperature Petroleum Reservoir in South of Iran Mohsen Pournia Department of Microbiology, Shiraz Branch, Islamic Azad University, Shiraz, Iran, [email protected] Nima Bahador * Department of Microbiology, Shiraz Branch, Islamic Azad University, Shiraz, Iran, [email protected] Meisam Tabatabaei Biofuel Research Team (BRTeam), Karaj, Iran, [email protected] Reza Azarbayjani Molecular bank, Iranian Biological Resource Center, ACECR, Karaj, Iran, [email protected] Ghassem Hosseni Salekdeh Department of Biology, Agricultural Biotechnology Research Institute, Karaj, Iran, [email protected] Abstract Introduction: Although bacteria and archaea are able to grow and adapted to the petrol reservoirs during several years, there are no results from microbial diversity of oilfields with high temperature in Iran. Hence, the present study tried to identify microbial community in non-water flooding Zeilaei (ZZ) oil reservoir. Materials and methods: In this study, for the first time, non-water flooded high temperature Zeilaei oilfield was analyzed for its microbial community based on next generation sequencing of 16S rRNA genes. Results: The results obtained from this study indicated that the most abundant bacterial community belonged to phylum of Firmicutes (Bacilli ) and Thermotoga, while other phyla (Proteobacteria , Actinobacteria and Synergistetes ) were much less abundant. Bacillus subtilis , B. licheniformis , Petrotoga mobilis , P. miotherma, Fervidobacterium pennivorans , and Thermotoga subterranea were observed with high frequency. In addition, the most abundant archaea were Methanothermobacter thermautotrophicus . Discussion and conclusion: Although there are many reports on the microbial community of oil filed reservoirs, this is the first report of large quantities of Bacillus spp. -
Identification of Functional Lsrb-Like Autoinducer-2 Receptors
Swarthmore College Works Chemistry & Biochemistry Faculty Works Chemistry & Biochemistry 11-15-2009 Identification Of unctionalF LsrB-Like Autoinducer-2 Receptors C. S. Pereira Anna Katherine De Regt , '09 P. H. Brito Stephen T. Miller Swarthmore College, [email protected] K. B. Xavier Follow this and additional works at: https://works.swarthmore.edu/fac-chemistry Part of the Biochemistry Commons Let us know how access to these works benefits ouy Recommended Citation C. S. Pereira; Anna Katherine De Regt , '09; P. H. Brito; Stephen T. Miller; and K. B. Xavier. (2009). "Identification Of unctionalF LsrB-Like Autoinducer-2 Receptors". Journal Of Bacteriology. Volume 191, Issue 22. 6975-6987. DOI: 10.1128/JB.00976-09 https://works.swarthmore.edu/fac-chemistry/52 This work is brought to you for free by Swarthmore College Libraries' Works. It has been accepted for inclusion in Chemistry & Biochemistry Faculty Works by an authorized administrator of Works. For more information, please contact [email protected]. Identification of Functional LsrB-Like Autoinducer-2 Receptors Catarina S. Pereira, Anna K. de Regt, Patrícia H. Brito, Stephen T. Miller and Karina B. Xavier J. Bacteriol. 2009, 191(22):6975. DOI: 10.1128/JB.00976-09. Published Ahead of Print 11 September 2009. Downloaded from Updated information and services can be found at: http://jb.asm.org/content/191/22/6975 http://jb.asm.org/ These include: SUPPLEMENTAL MATERIAL Supplemental material REFERENCES This article cites 65 articles, 29 of which can be accessed free on September 10, 2014 by SWARTHMORE COLLEGE at: http://jb.asm.org/content/191/22/6975#ref-list-1 CONTENT ALERTS Receive: RSS Feeds, eTOCs, free email alerts (when new articles cite this article), more» Information about commercial reprint orders: http://journals.asm.org/site/misc/reprints.xhtml To subscribe to to another ASM Journal go to: http://journals.asm.org/site/subscriptions/ JOURNAL OF BACTERIOLOGY, Nov. -
Potential for and Distribution of Enzymatic Biodegradation of Polystyrene by Environmental Microorganisms
materials Communication Potential for and Distribution of Enzymatic Biodegradation of Polystyrene by Environmental Microorganisms Liyuan Hou and Erica L.-W. Majumder * Department of Chemistry, SUNY College of Environmental Science and Forestry, Syracuse, NY 13210, USA; [email protected] * Correspondence: [email protected] or [email protected]; Tel.: +1-3154706854 Abstract: Polystyrene (PS) is one of the main polymer types of plastic wastes and is known to be resistant to biodegradation, resulting in PS waste persistence in the environment. Although previous studies have reported that some microorganisms can degrade PS, enzymes and mechanisms of microorganism PS biodegradation are still unknown. In this study, we summarized microbial species that have been identified to degrade PS. By screening the available genome information of microorganisms that have been reported to degrade PS for enzymes with functional potential to depolymerize PS, we predicted target PS-degrading enzymes. We found that cytochrome P4500s, alkane hydroxylases and monooxygenases ranked as the top potential enzyme classes that can degrade PS since they can break C–C bonds. Ring-hydroxylating dioxygenases may be able to break the side-chain of PS and oxidize the aromatic ring compounds generated from the decomposition of PS. These target enzymes were distributed in Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes, suggesting a broad potential for PS biodegradation in various earth environments and microbiomes. Our results provide insight into the enzymatic degradation of PS and suggestions for realizing the biodegradation of this recalcitrant plastic. Citation: Hou, L.; Majumder, E.L. Keywords: plastics; polystyrene biodegradation; enzymatic biodegradation; monooxygenase; alkane Potential for and Distribution of hydroxylase; cytochrome P450 Enzymatic Biodegradation of Polystyrene by Environmental Microorganisms. -
Upper and Lower Case Letters to Be Used
Isolation, characterization and genome sequencing of a soil-borne Citrobacter freundii strain capable of detoxifying trichothecene mycotoxins by Rafiqul Islam A Thesis Presented to The University of Guelph In Partial Fulfilment of Requirements for the Degree of Doctor of Philosophy in Plant Agriculture Guelph, Ontario, Canada © Rafiqul Islam, April, 2012 ABSTRACT ISOLATION, CHARACTERIZATION AND GENOME SEQUENCING OF A SOIL- BORNE CITROBACTER FREUNDII STRAIN CAPABLE OF DETOXIFIYING TRICHOTHECENE MYCOTOXINS Rafiqul Islam Advisors: University of Guelph, 2012 Dr. K. Peter Pauls Dr. Ting Zhou Cereals are frequently contaminated with tricthothecene mycotoxins, like deoxynivalenol (DON, vomitoxin), which are toxic to humans, animals and plants. The goals of the research were to discover and characterize microbes capable of detoxifying DON under aerobic conditions and moderate temperatures. To identify microbes capable of detoxifying DON, five soil samples collected from Southern Ontario crop fields were tested for the ability to convert DON to a de-epoxidized derivative. One soil sample showed DON de-epoxidation activity under aerobic conditions at 22-24°C. To isolate the microbes responsible for DON detoxification (de-epoxidation) activity, the mixed culture was grown with antibiotics at 50ºC for 1.5 h and high concentrations of DON. The treatments resulted in the isolation of a pure DON de-epoxidating bacterial strain, ADS47, and phenotypic and molecular analyses identified the bacterium as Citrobacter freundii. The bacterium was also able to de-epoxidize and/or de-acetylate 10 other food-contaminating trichothecene mycotoxins. A fosmid genomic DNA library of strain ADS47 was prepared in E. coli and screened for DON detoxification activity. However, no library clone was found with DON detoxification activity. -
Heat Resistant Thermophilic Endospores in Cold Estuarine Sediments
Heat resistant thermophilic endospores in cold estuarine sediments Emma Bell Thesis submitted for the degree of Doctor of Philosophy School of Civil Engineering and Geosciences Faculty of Science, Agriculture and Engineering February 2016 Abstract Microbial biogeography explores the spatial and temporal distribution of microorganisms at multiple scales and is influenced by environmental selection and passive dispersal. Understanding the relative contribution of these factors can be challenging as their effects can be difficult to differentiate. Dormant thermophilic endospores in cold sediments offer a natural model for studies focusing on passive dispersal. Understanding distributions of these endospores is not confounded by the influence of environmental selection; rather their occurrence is due exclusively to passive transport. Sediment heating experiments were designed to investigate the dispersal histories of various thermophilic spore-forming Firmicutes in the River Tyne, a tidal estuary in North East England linking inland tributaries with the North Sea. Microcosm incubations at 50-80°C were monitored for sulfate reduction and enriched bacterial populations were characterised using denaturing gradient gel electrophoresis, functional gene clone libraries and high-throughput sequencing. The distribution of thermophilic endospores among different locations along the estuary was spatially variable, indicating that dispersal vectors originating in both warm terrestrial and marine habitats contribute to microbial diversity in estuarine and marine environments. In addition to their persistence in cold sediments, some endospores displayed a remarkable heat-resistance surviving multiple rounds of autoclaving. These extremely heat-resistant endospores are genetically similar to those detected in deep subsurface environments, including geothermal groundwater investigated from a nearby terrestrial borehole drilled to >1800 m depth with bottom temperatures in excess of 70°C. -
1471-2180-13-114.Pdf (2.637Mb)
Baseline survey of the anatomical microbial ecology of an important food plant: Solanum lycopersicum (tomato) Ottesen et al. Ottesen et al. BMC Microbiology 2013, 13:114 http://www.biomedcentral.com/1471-2180/13/114 Ottesen et al. BMC Microbiology 2013, 13:114 http://www.biomedcentral.com/1471-2180/13/114 RESEARCH ARTICLE Open Access Baseline survey of the anatomical microbial ecology of an important food plant: Solanum lycopersicum (tomato) Andrea R Ottesen1*, Antonio González Peña3, James R White2, James B Pettengill1, Cong Li1, Sarah Allard1, Steven Rideout4, Marc Allard1, Thomas Hill1, Peter Evans1, Errol Strain1, Steven Musser1, Rob Knight3 and Eric Brown1 Abstract Background: Research to understand and control microbiological risks associated with the consumption of fresh fruits and vegetables has examined many environments in the farm to fork continuum. An important data gap however, that remains poorly studied is the baseline description of microflora that may be associated with plant anatomy either endemically or in response to environmental pressures. Specific anatomical niches of plants may contribute to persistence of human pathogens in agricultural environments in ways we have yet to describe. Tomatoes have been implicated in outbreaks of Salmonella at least 17 times during the years spanning 1990 to 2010. Our research seeks to provide a baseline description of the tomato microbiome and possibly identify whether or not there is something distinctive about tomatoes or their growing ecology that contributes to persistence of Salmonella in this important food crop. Results: DNA was recovered from washes of epiphytic surfaces of tomato anatomical organs; leaves, stems, roots, flowers and fruits of Solanum lycopersicum (BHN602), grown at a site in close proximity to commercial farms previously implicated in tomato-Salmonella outbreaks. -
Mycobacterium Gilvum Spyr1
Standards in Genomic Sciences (2011) 5:144-153 DOI:10.4056/sigs.2265047 Complete genome sequence of Mycobacterium sp. strain (Spyr1) and reclassification to Mycobacterium gilvum Spyr1 Aristeidis Kallimanis1, Eugenia Karabika1, Kostantinos Mavromatis2, Alla Lapidus2, Kurt M. LaButti2, Konstantinos Liolios2, Natalia Ivanova2, Lynne Goodwin2,3, Tanja Woyke2, Athana- sios D. Velentzas4, Angelos Perisynakis1, Christos C. Ouzounis5§, Nikos C. Kyrpides2, Anna I. Koukkou1*, and Constantin Drainas1† 1 Sector of Organic Chemistry and Biochemistry, University of Ioannina, 45110 Ioannina, Greece 2 DOE Joint Genome Institute, Walnut Creek, California, USA 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 4 Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, 15701, Athens, Greece 5 Centre for Bioinformatics, Department of Informatics, School of Natural & Mathematical Sciences, King's College London (KCL), London WC2R 2LS, UK § Present address: Computational Genomics Unit, Institute of Agrobiotechnology, Center for Research & Technology Hellas (CERTH), GR-57001 Thessaloniki, Greece & Donnelly Cen- tre for Cellular & Biomolecular Research, University of Toronto, 160 College Street, To- ronto, Ontario M5S 3E1, Canada *Corresponding author: Anna I. Koukkou, email: [email protected] † In memory of professor Constantin Drainas who lost his life in a car accident on July 5th, 2011. Mycobacterium sp.Spyr1 is a newly isolated strain that occurs in a creosote contaminated site in Greece. It was isolated by an enrichment method using pyrene as sole carbon and energy source and is capable of degrading a wide range of PAH substrates including pyrene, fluoran- thene, fluorene, anthracene and acenapthene. Here we describe the genomic features of this organism, together with the complete sequence and annotation.