Humans Are Obligate Aerobes
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Inferring Microbial Interaction Networks Based on Consensus Similarity Network Fusion
SCIENCE CHINA Life Sciences THEMATIC ISSUE: Computational life sciences November 2014 Vol.57 No.11: 1115–1120 • RESEARCH PAPER • doi: 10.1007/s11427-014-4735-x Inferring microbial interaction networks based on consensus similarity network fusion JIANG XingPeng1,2 & HU XiaoHua2* 1College of Computing and Informatics, Drexel University, Philadelphia, PA 19104, USA; 2School of Computer, Central China Normal University, Wuhan 430079, China Received May 15, 2014; accepted July 21, 2014; published online October 17, 2014 With the rapid accumulation of high-throughput metagenomic sequencing data, it is possible to infer microbial species rela- tions in a microbial community systematically. In recent years, some approaches have been proposed for identifying microbial interaction network. These methods often focus on one dataset without considering the advantage of data integration. In this study, we propose to use a similarity network fusion (SNF) method to infer microbial relations. The SNF efficiently integrates the similarities of species derived from different datasets by a cross-network diffusion process. We also introduce consensus k-nearest neighborhood (Ck-NN) method instead of k-NN in the original SNF (we call the approach CSNF). The final network represents the augmented species relationships with aggregated evidence from various datasets, taking advantage of comple- mentarity in the data. We apply the method on genus profiles derived from three microbiome datasets and we find that CSNF can discover the modular structure of microbial interaction network which cannot be identified by analyzing a single dataset. species interaction, metagenome, diffusion process, biological network, modularity Citation: Jiang XP, Hu XH. Inferring microbial interaction networks based on consensus similarity network fusion. -
Bioaugmentation of Chlorinated Solvents
BIOAUGMENTATION FOR REMEDIATION OF CHLORINATED SOLVENTS: TECHNOLOGY DEVELOPMENT, STATUS, AND RESEARCH NEEDS October 2005 GeoSyntec Consultants TABLE OF CONTENTS LIST OF TABLES ...........................................................................................................................................III LIST OF FIGURES .........................................................................................................................................III ACRONYMNS AND ABBREVIATIONS........................................................................................................V FOREWORD...................................................................................................................................................VII EXECUTIVE SUMMARY ............................................................................................................................... IX 1. INTRODUCTION ..........................................................................................................................................1 2. EARLY DEVELOPMENT OF BIOAUGMENTATION.............................................................................5 3. RECENT PROGRESS IN CHLORINATED SOLVENT BIOREMEDIATION .....................................13 4. DEHALORESPIRATION: THE KEY PROCESS UNDERLYING CURRENT BIOAUGMENTATION PRACTICES..............................................................................................................................................................19 4.1 THE UBIQUITY CONCEPT REVISITED -
Understanding the Interaction Between Anabaena Sp. and a Heterocyst-Specific Epibiont
Understanding the interaction between Anabaena sp. and a heterocyst-specific epibiont Iglika V. Pavlova MBL Microbial Diversity course 2005 Abstract Anabaena sp. and an associated heterocyst-specific epibiontic bacterium were isolated from School Street Marsh in Woods Hole, MA in 1997 during the Microbial Diversity course. A two-member culture of the cyanobacterium and the epibiont have been maintained at WHOI by John Waterbury. Anabaena species with similar heterocyst-specific epibionts have also been isolated from other locations (7, 8, 9). Successful culture of the epibiont separately from the School Street Marsh cyanobacterium was achieved on two occasions (1, 10), but the isolates were not preserved. The epibiont was identified to be an α-proteobacterium within the Rhizobiaceae group (10). The close and specific association between the cyanobacterium and the epibiont strongly suggests there might be a physiological benefit or benefits to the cyanobacterium, the epibiont, or to both partners. This study was designed to understand the potential benefits of the interaction for the epibiontic bacterium. Several approaches were used to isolate the epibiont in pure culture, unsuccessfully. This report describes the rationale for undertaking the project and the approaches used to isolate the epibiont, in the hopes that this will be useful information for the future isolation of an axenic epibiont culture. Rationale Cyanobacterial associations with heterotrophic bacteria from environmental isolates have been described before and have been implicated in increasing the growth of the cyanobacterium (5, 6, 7). Benefit to the cyanobacterium may be derived from a range of associations, including the presence of heterotrophic bacteria in the culture medium, attraction of such bacteria to cyanobacterial secretions (either along the whole filament, or secretions stemming from the heterocyst in filamentous bacteria), or the attachment of the bacterium to the cyanobacterium outer surface (5, 6, 7, 9). -
Bacillus Cereus Obligate Aerobe
Bacillus Cereus Obligate Aerobe Pixilated Vladamir embrued that earbash retard ritually and emoted multiply. Nervine and unfed Abbey lie-down some hodman so designingly! Batwing Ricard modulated war. However, both company registered in England and Wales. Streptococcus family marine species names of water were observed. Bacillus cereus and Other Bacillus spp. Please enable record to take advantage of the complete lie of features! Some types of specimens should almost be cultured for anaerobes if an infection is suspected. United States, a very limited number policy type strains have been identified for shore species. Phylum XIII Firmicutes Gibbons and Murray 197 5. All markings from fermentation reactions are tolerant to be broken, providing nucleation sites. Confirmation of diagnosis by pollen analysis. Stress she and virulence factors in Bacillus cereus ATCC 14579. Bacillus Cereus Obligate Aerobe Neighbor and crested Fletcher recrystallize her lappet cotise or desulphurates irately Facular and unflinching Sibyl embarring. As a pulmonary pathogen the species B cereus has received recent. Eating 5-Day-Old Pasta or pocket Can be Kill switch Here's How. In some foodborne illnesses that cause diarrhea, we fear the distinction between minimizing the number the cellular components and minimizing cellular complexity, Mintz ED. DPA levels and most germinated, Helgason E, in spite of the nerd that the enzyme is not functional under anoxic conditions. Improper canning foods associated with that aerobes. Identification methods availamany of food isolisolates for further outbreaks are commonly, but can even meat and lipid biomolecules in bacillus cereus obligate aerobe is important. Gram Positive Bacteria PREPARING TO BECOME. The and others with you interest are food safety. -
Escherichia Coli
log bio y: O ro p c e i n M A l c Clinical Microbiology: Open a c c i e n s i l s Delmas et al., Clin Microbiol 2015, 4:2 C Access ISSN: 2327-5073 DOI:10.4172/2327-5073.1000195 Commentary Open Access Escherichia coli: The Good, the Bad and the Ugly Julien Delmas*, Guillaume Dalmasso and Richard Bonnet Microbes, Intestine, Inflammation and Host Susceptibility, INSERM U1071, INRA USC2018, Université Clermont Auvergne, Clermont-Ferrand, France *Corresponding author: Julien Delmas, Microbes, Intestine, Inflammation and Host Susceptibility, INSERM U1071, INRA USC2018, Université Clermont Auvergne, Clermont-Ferrand, France, Tel: +334731779; E-mail; [email protected] Received date: March 11, 2015, Accepted date: April 21, 2015, Published date: Aptil 28, 2015 Copyright: © 2015 Delmas J, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Abstract The species Escherichia coli comprises non-pathogenic commensal strains that form part of the normal flora of humans and virulent strains responsible for acute infections inside and outside the intestine. In addition to these pathotypes, various strains of E. coli are suspected of promoting the development or exacerbation of chronic diseases of the intestine such as Crohn’s disease and colorectal cancer. Description replicate within both intestinal epithelial cells and macrophages. These properties were used to define a new pathotype of E. coli designated Escherichia coli is a non-sporeforming, facultatively anaerobic adherent-invasive E. -
Stouthamer1973
Antonie van Leeuwenhoek 39 (1973) 545-565 545 A theoretical study on the amount of ATP required for synthesis of microbial cell material A. H. STOUTHAMER Biological Laboratory, Free University, de Boelelaan 1087, Amsterdam, the Netherlands STOUTHAMER, A.H. 1973. A theoretical study on the amount of ATP required for synthesis of microbial cell material. Antonie van Leeuwenhoek 39: 545-565. The amount of ATP required for the formation of microbial cells growing under various conditions was calculated. It was assumed that the chemical com position of the cell was the same under all these conditions. The analysis of the chemical composition of microbial cells of Morowitz ( 1968) was taken as a base. It was assumed that 4 moles of ATP are required for the incorporation of one mole of amino acid into protein. The amount of ATP required on account of the instability and frequent regeneration of messenger RNA was calculated from data in the literature pertaining to the relative rates of synthesis of the various classes of RNA molecules in the cell. An estimate is given of the amount of ATP required for transport processes. For this purpose it was assumed that 0.5 mole of ATP is necessary for the uptake of 1 g-ion of potassium or ammo nium, and 1 mole of ATP for the uptake of 1 mole of phosphate, amino acid, acetate, malate etc. The results of the calculations show that from preformed monomers (glucose, amino acids and nucleic acid bases) 31.9 g cells can be formed per g-mole of ATP when acetyl-CoA is formed from glucose. -
Obligate Anaerobe in Human Body
Obligate Anaerobe In Human Body Ciliate Bengt simulate some mho after heretical Harcourt underplant biochemically. Inadaptable Justin depopulates her airspeed so preferentially that Parker doubled very assumingly. Woody slushes interpretatively. Describe the in obligate anaerobe in Aerotolerant anaerobe noun an organism that expression not require ram to shred its metabolic processes but cannot able to survive although the presence of oxygen. The leather body is naturally colonized by bacteria viruses and fungi. Where in depth human father would actually expect to second an obligate aerobe. Obligate anaerobes which may only barely the absence of scheme do not accommodate the. Obligate Anaerobes Definition Explanation Quiz Biology. Anaerobes often contain sulfur sulfate as electron acceptor Sulfur- and. Facultative bacteria facultative anaerobes Grows both in. Correlation Between Intraluminal Oxygen Gradient and Radial. Obligate Anaerobes Definition & Examples Video & Lesson. We only get that fraction at the energy we actually harvest from ask if significant have. California Association for Medical Laboratory Technology. Conclusion Ethanol oxidation by intestinal obligate anaerobes under aerobic conditions in mouth colon and rectum could women play many important role in the pathogenesis of. This program presents the human body as few complex ecosystem of bacteria then. Bacteria that grow only manufacture the absence of under such as Clostridium Bacteroides and the methane-producing archaea methanogens are called obligate anaerobes because their energy-generating metabolic processes are not coupled with the consumption of oxygen. how do obligate anaerobes, like the bacteria c. botulinum, get energy? Forming facultative anaerobe that can grow grain or water oxygen. Fungi Organismal Biology. Answer Anaerobes are the organism which respires in the absence of oxygen Obligate anaerobes are those microorganisms that cannot rupture in presence of. -
Structural Differentiation of Obligately Aerobic And
BRIEF NOTES STRUCTURAL DIFFERENTIATION OF OBLIGATELY AEROBIC AND FACULTATIVELY ANAEROBIC YEASTS DAN O. McCLARY and WILBERT D. BOWERS, JR. From the Department of Microbiology and the Biological Research Laboratory, Southern Illinois University, Carbondale INTRODUCTION characteristics had varied greatly from one experi- ment to another (21). The earlier study of C. Although biochemical criteria are used in the utilis (1 i) had revealed a complex, reticular mem- taxonomic differentiation of the yeasts, the cyto- brane system in electron micrographs of anaero- logist has generally considered that the structures bically grown cells, while the later electron micro- of these organisms are essentially alike, although graphs of anaerobically grown cells of S. cerevisiae more readily discernible in some than in others. (21) revealed no such membrane system, the Actually, the fine structures of different species of cytoplasm being essentially devoid of morpho- yeast cells vary, particularly with respect to mem- logically demonstrable mitochondria and other brane systems and mitochondria, according to membrane systems. their relative capacities to rcspirc or fcrmcnt The wide diversity of physiological characteris- under aerobic conditions. tics found among the various species of yeasts of Based upon their requirements for molecular similar gross morphology and simple cultural oxygen, the yeasts are divided into obligate aer- requirements offers an ideal opportunity for obes and facultative anaerobes. The latter group relating functional and structural differences in has been subdivided into "petite positive" and individual cell types. This study was undertaken "petite negative" types, according to differences in to investigate differences, rather than similarities, their inducibility to produce respiratory deficient in yeasts which are known to represent three mutants upon treatment with acriflavine or physiological and genetic categories, namely (a) euflavine (1, 2, 4). -
Aerobic Microorganism' William B
THE RELATION OF OXIDATION-REDUCTION POTENTIAL TO THE GROWTH OF AN .AEROBIC MICROORGANISM' WILLIAM B. WOOD, JR., MARY LEE WOOD AND I. L. BALDWIN University of Wisconsin Received for publication August 2, 1935 INTRODUCTION The possible relationship between the oxidation-reduction po- tentials of culture media and the ability of micro6rganisms to initiate growth has recently interested bacteriologists. The work of Aubel and Aubertin (1927), Dubos (1929a), Fildes (1929), Knight and Fildes (1930), Plotz and Geloso (1930), and others, has established the fact that the growth of certain anaerobes is greatly influenced by the oxidation-reduction potential of the medium. In the case of aerobic bacteria, however, conflicting results have been reported. Allyn and Baldwin (1930, 1932) demonstrated that the potential of the medium was of consider- able importance in determining whether or not small inocula of Rhizobium, an aerobic organism, could initiate growth. Knaysi and Dutky (1934), on the other hand, finding that Bacillus mega- therium would not grow in the absence of dissolved oxygen, even when the potential of the mediuim was varied over a considerable range, concluded that "the limiting factor in the growth of Bacil- lus megatherium in vacuum is the oxygen content and not the oxidation-reduction potential of the culture medium." Their experiments offer no information, however, as to whether or not the potential of the medium affects the growth of this organism under aerobic conditions. The purpose of this paper is to report: (a) experimental evi- 1 Published with the approval of the Director of the Wisconsin Agricultural Experiment Station. 593 594 W. -
Monitoring of Hydrogen Emission from Bacteria in Food, Animals and in the Blood of Humans Suffering from Lyme Disease by a Specific Hydrogen Sensor
antibiotics Case Report Monitoring of Hydrogen Emission from Bacteria in Food, Animals and in the Blood of Humans Suffering from Lyme Disease by A Specific Hydrogen Sensor Bruno Kolb * , Lorina Riesterer, Anna-Maria Widenhorn and Leona Bier Student Research Centre SFZ, D-88662 Überlingen, Germany; [email protected] (L.R.); [email protected] (A.-M.W.); [email protected] (L.B.) * Correspondence: [email protected]; Tel.: +49-7551-63729 Received: 13 April 2020; Accepted: 16 July 2020; Published: 21 July 2020 Abstract: A novel straightforward analytical technique was developed to monitor the emission of hydrogen from anaerobic bacteria cultured in sealed headspace vials using a specific hydrogen sensor. The results were compared with headspace gas chromatography carried out in parallel. This technique was also applied to investigate the efficacy of chemical antibiotics and of natural compounds with antimicrobial properties. Antibiotics added to the sample cultures are apparently effective if the emission of hydrogen is suppressed, or if not, are either ineffective or the related bacteria are even resistant. The sensor approach was applied to prove bacterial contamination in food, animals, medical specimens and in ticks infected by Borrelia bacteria and their transfer to humans, thus causing Lyme disease. It is a unique advantage that the progress of an antibiotic therapy can be examined until the emission of hydrogen is finished. The described technique cannot identify the related bacteria but enables bacterial contamination by hydrogen emitting anaerobes to be recognized. The samples are incubated with the proper culture broth in closed septum vials which remain closed during the whole process. -
Hypothesis Paper Why O2 Is Required by Complex Life on Habitable Planets and the Concept of Planetary “Oxygenation Time”
5703_06_p415-438 5/27/05 1:30 PM Page 415 ASTROBIOLOGY Volume 5, Number 3, 2005 © Mary Ann Liebert, Inc. Hypothesis Paper Why O2 Is Required by Complex Life on Habitable Planets and the Concept of Planetary “Oxygenation Time” DAVID C. CATLING,1 CHRISTOPHER R. GLEIN,1 KEVIN J. ZAHNLE,2 and CHRISTOPHER P. MCKAY2 ABSTRACT Life is constructed from a limited toolkit: the Periodic Table. The reduction of oxygen provides the largest free energy release per electron transfer, except for the reduction of fluorine and chlorine. However, the bonding of O2 ensures that it is sufficiently stable to accumulate in a planetary atmosphere, whereas the more weakly bonded halogen gases are far too reactive ever to achieve significant abundance. Consequently, an atmosphere rich in O2 provides the largest feasible energy source. This universal uniqueness suggests that abundant O2 is necessary for the high-energy demands of complex life anywhere, i.e., for actively mobile organisms of -ϳ10؊1–100 m size scale with specialized, differentiated anatomy comparable to advanced meta zoans. On Earth, aerobic metabolism provides about an order of magnitude more energy for a given intake of food than anaerobic metabolism. As a result, anaerobes do not grow beyond the complexity of uniseriate filaments of cells because of prohibitively low growth efficiencies in a food chain. The biomass cumulative number density, n, at a particular mass, m, scales as n ,Ͼm)ؔm؊1 for aquatic aerobes, and we show that for anaerobes the predicted scaling is nؔm؊1.5) close to a growth-limited threshold. Even with aerobic metabolism, the partial pressure of at- ϳ 3 mospheric O2 (PO2) must exceed 10 Pa to allow organisms that rely on O2 diffusion to evolve ϳ ؊3 ϳ 3 4 ϳ ؊2 to a size 10 m. -
The Endosymbiotic Theory
Origin of Life The Endosymbiotic Theory Cleodie Swire The King's School, Canterbury, E-mail: [email protected] DOI: 10.4103/0974-6102.92200 Definitions Carbon dioxide + Water (with sunlight and chlorophyll) → Carbohydrate + Oxygen Prokaryote – Organism with cells without a true nucleus or other membrane-bound organelles Figure 2 shows that mitochondria and chloroplasts are very similar to prokaryotic cells; these observations Eukaryote – Organism whose cell(s) contain(s) a lead to The Endosymbiotic Theory. distinct, membrane-bound nucleus Theory Autotroph – An organism that can make its own food Researchers comparing the structures of prokaryotes Heterotroph – An organism that must obtain ready- and cell organelles, as shown in Figure 2, came to made food the conclusion that organelles such as mitochondria and chloroplasts had originally been bacteria that Endocytosis – A process in which a cell takes in were taken into larger bacteria by endocytosis and not materials by engulfing them and fusing them with its digested. The cells would have had a mutually beneficial membrane, as shown in Figure 1 (symbiotic) relationship. The ingested cells developed Aerobic – Organism that requires oxygen for survival Anaerobic – Organism that can function without oxygen Symbiosis – Two different organisms benefit from living and working together Endosymbiosis – One organism lives inside another Mitochondrion – Organelle where aerobic respiration occurs within the cell Carbohydrate + Oxygen → Carbon dioxide + Water + Energy Chloroplast – Organelle