Across Bacterial Phyla, Distantly-Related Genomes with Similar Genomic GC Content Have Similar Patterns of Amino Acid Usage
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Leaf-Associated Shifts in Bacterial and Fungal Communities in Response to Chicken Rearing Under Moso Bamboo Forests in Subtropical China
Article Leaf-Associated Shifts in Bacterial and Fungal Communities in Response to Chicken Rearing Under Moso Bamboo Forests in Subtropical China Xiaoping Zhang 1, Zheke Zhong 1,*, Xu Gai 1, Jiafu Ying 2, Weifen Li 2, Xuhua Du 1, Fangyuan Bian 1 and Chuanbao Yang 1 1 China National Bamboo Research Center, Key Laboratory of Resources and Utilization of Bamboo of State Forestry Administration, Hangzhou 310012, China; [email protected] (X.Z.); [email protected] (X.G.); [email protected] (X.D.); [email protected] (F.B.); [email protected] (C.Y.) 2 College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; [email protected] (J.Y.); wfl[email protected] (W.L.) * Correspondence: [email protected]; Tel.: +86-0571-88860734 Received: 25 January 2019; Accepted: 25 February 2019; Published: 1 March 2019 Abstract: Integrated bamboo-chicken farming (BCF) systems are a traditional agroforestry pattern with large economic benefits in subtropical China. However, little is known regarding the effect of this integration on the bamboo leaf-associated microbiome, which can be very important for disease control and nutrient turnover. In the present study, we compared the leaf-associated bacterial and fungal communities of moso bamboo (Phyllostachys edulis) in a BCF system and an adjacent moso bamboo forest (MBF). The results showed that Cyanobacteria and Ascomycota were the predominant microbial phyla associated with bamboo leaves. Chicken farming under the bamboo forest significantly increased the bacterial and fungal alpha diversity (observed operational taxonomic units (OTUs) and Simpson’s index) associated with bamboo leaves. Principal components analysis (PCoA) further confirmed the shifts in the bacterial and fungal communities caused by chicken farming. -
Senegalemassilia Anaerobia Gen. Nov., Sp. Nov
Standards in Genomic Sciences (2013) 7:343-356 DOI:10.4056/sigs.3246665 Non contiguous-finished genome sequence and description of Senegalemassilia anaerobia gen. nov., sp. nov. Jean-Christophe Lagier1, Khalid Elkarkouri1, Romain Rivet1, Carine Couderc1, Didier Raoult1 and Pierre-Edouard Fournier1* 1 Aix-Marseille Université, URMITE, Faculté de médecine, Marseille, France *Corresponding author: Pierre-Edouard Fournier ([email protected]) Keywords: Senegalemassilia anaerobia, genome Senegalemassilia anaerobia strain JC110T sp.nov. is the type strain of Senegalemassilia anaer- obia gen. nov., sp. nov., the type species of a new genus within the Coriobacteriaceae family, Senegalemassilia gen. nov. This strain, whose genome is described here, was isolated from the fecal flora of a healthy Senegalese patient. S. anaerobia is a Gram-positive anaerobic coccobacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,383,131 bp long genome contains 1,932 protein- coding and 58 RNA genes. Introduction Classification and features Senegalemassilia anaerobia strain JC110T (= CSUR A stool sample was collected from a healthy 16- P147 = DSMZ 25959) is the type strain of S. anaer- year-old male Senegalese volunteer patient living obia gen. nov., sp. nov. This bacterium was isolat- in Dielmo (rural village in the Guinean-Sudanian ed from the feces of a healthy Senegalese patient. zone in Senegal), who was included in a research It is a Gram-positive, anaerobic, indole-negative protocol. Written assent was obtained from this coccobacillus. Classically, the polyphasic taxono- individual. No written consent was needed from his my is used to classify the prokaryotes by associat- guardians for this study because he was older than ing phenotypic and genotypic characteristics [1]. -
Miami1132247140.Pdf (3.72
MIAMI UNIVERSITY The Graduate School CERTIFICATE FOR APPROVING THE DISSERTATION We hereby approve the Dissertation Of Brian Junior Henson Candidate for the Degree: Doctor of Philosophy Advisor ______________________ (Susan R. Barnum) Advisor ______________________ (Linda E. Watson) Reader ______________________ (David A. Francko) Reader ______________________ (John Z. Kiss) Grad School Representative ______________________ (Luis A. Actis) Abstract EVOLUTION, VARIATION, AND EXCISION OF DEVELOPMENTALLY REGULATED DNA ELEMENTS IN THE HETEROCYSTOUS CYANOBACTERIA by Brian Junior Henson In some cyanobacteria, heterocyst differentiation is accompanied by developmentally regulated DNA rearrangements that occur within the nifD, fdxN, and hupL genes, referred to as the nifD, fdxN, and hupL elements. These elements are excised from the genome by site-specific recombination during the latter stages of heterocyst differentiation. In this dissertation, two major questions are addressed: 1) what is the evolutionary history of the nifD and hupL elements and 2) how is the nifD element excised? To answer the first question, full length nifD and hupL element sequences were characterized and compared; and xisA and xisC sequences (which encode the recombinases that excise the nifD and hupL elements, respectively) were phylogenetically analyzed. Results indicated extensive structural and compositional variation within the nifD and hupL elements. The data suggests that the nifD and hupL elements are of viral origin and that they have variable patterns of evolution in the cyanobacteria. To answer the second question, a recombination system was devised where the ability of XisA to excise or recombine variants of the nifD element (substrate plasmids) was tested. Using PCR directed mutagenesis, specific nucleotides within the flanking regions of the nifD element were altered and the effects on recombination determined. -
Evolutionary Origin of Insect–Wolbachia Nutritional Mutualism
Evolutionary origin of insect–Wolbachia nutritional mutualism Naruo Nikoha,1, Takahiro Hosokawab,1, Minoru Moriyamab,1, Kenshiro Oshimac, Masahira Hattoric, and Takema Fukatsub,2 aDepartment of Liberal Arts, The Open University of Japan, Chiba 261-8586, Japan; bBioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan; and cCenter for Omics and Bioinformatics, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277-8561, Japan Edited by Nancy A. Moran, University of Texas at Austin, Austin, TX, and approved June 3, 2014 (received for review May 20, 2014) Obligate insect–bacterium nutritional mutualism is among the insects, generally conferring negative fitness consequences to most sophisticated forms of symbiosis, wherein the host and the their hosts and often causing hosts’ reproductive aberrations to symbiont are integrated into a coherent biological entity and un- enhance their own transmission in a selfish manner (7, 8). Re- able to survive without the partnership. Originally, however, such cently, however, a Wolbachia strain associated with the bedbug obligate symbiotic bacteria must have been derived from free-living Cimex lectularius,designatedaswCle, was shown to be es- bacteria. How highly specialized obligate mutualisms have arisen sential for normal growth and reproduction of the blood- from less specialized associations is of interest. Here we address this sucking insect host via provisioning of B vitamins (9). Hence, it –Wolbachia evolutionary -
Bacterial Community Structure in High-Arctic Snow and Freshwater As Revealed by Pyrosequencing of 16S Rrna Genes and Cultivation Annette K
RESEARCH/REVIEW ARTICLE Bacterial community structure in High-Arctic snow and freshwater as revealed by pyrosequencing of 16S rRNA genes and cultivation Annette K. Møller,1 Ditte A. Søborg,1 Waleed Abu Al-Soud,2 Søren J. Sørensen2 & Niels Kroer1 1 Department of Environmental Science, Aarhus University, Frederiksborgvej 399, DK-4000 Roskilde, Denmark 2 Department of Biology, University of Copenhagen, Sølvgade 83H, DK-1307 K Copenhagen, Denmark Keywords Abstract Taxonomic diversity; microbial assemblages; bacterial density; DOC. The bacterial community structures in High-Arctic snow over sea ice and an ice-covered freshwater lake were examined by pyrosequencing of 16S rRNA Correspondence genes and 16S rRNA gene sequencing of cultivated isolates. Both the Niels Kroer, pyrosequence and cultivation data indicated that the phylogenetic composition Department of Environmental Science, of the microbial assemblages was different within the snow layers and between Aarhus University, snow and freshwater. The highest diversity was seen in snow. In the middle Frederiksborgvej 399, and top snow layers, , and dominated, DK-4000 Roskilde, Denmark. Proteobacteria Bacteroidetes Cyanobacteria E-mail: [email protected] although Actinobacteria and Firmicutes were relatively abundant also. High numbers of chloroplasts were also observed. In the deepest snow layer, large percentages of Firmicutes and Fusobacteria were seen. In freshwater, Bacter- oidetes, Actinobacteria and Verrucomicrobia were the most abundant phyla while relatively few Proteobacteria and Cyanobacteria were present. Possibly, light intensity controlled the distribution of the Cyanobacteria and algae in the snow while carbon and nitrogen fixed by these autotrophs in turn fed the heterotrophic bacteria. In the lake, a probable lower light input relative to snow resulted in low numbers of Cyanobacteria and chloroplasts and, hence, limited input of organic carbon and nitrogen to the heterotrophic bacteria. -
Within-Arctic Horizontal Gene Transfer As a Driver of Convergent Evolution in Distantly Related 2 Microalgae
bioRxiv preprint doi: https://doi.org/10.1101/2021.07.31.454568; this version posted August 2, 2021. 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 Within-Arctic horizontal gene transfer as a driver of convergent evolution in distantly related 2 microalgae 3 Richard G. Dorrell*+1,2, Alan Kuo3*, Zoltan Füssy4, Elisabeth Richardson5,6, Asaf Salamov3, Nikola 4 Zarevski,1,2,7 Nastasia J. Freyria8, Federico M. Ibarbalz1,2,9, Jerry Jenkins3,10, Juan Jose Pierella 5 Karlusich1,2, Andrei Stecca Steindorff3, Robyn E. Edgar8, Lori Handley10, Kathleen Lail3, Anna Lipzen3, 6 Vincent Lombard11, John McFarlane5, Charlotte Nef1,2, Anna M.G. Novák Vanclová1,2, Yi Peng3, Chris 7 Plott10, Marianne Potvin8, Fabio Rocha Jimenez Vieira1,2, Kerrie Barry3, Joel B. Dacks5, Colomban de 8 Vargas2,12, Bernard Henrissat11,13, Eric Pelletier2,14, Jeremy Schmutz3,10, Patrick Wincker2,14, Chris 9 Bowler1,2, Igor V. Grigoriev3,15, and Connie Lovejoy+8 10 11 1 Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, 12 INSERM, Université PSL, 75005 Paris, France 13 2CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, 14 FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France 15 3 US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 16 Cyclotron Road, Berkeley, -
Validation of the Generic Name Gloeobacter Rippka Et Al. 1974, Cyanophyceae
Cryptogamie, Algologie, 2013, 34 (3): 255-262 © 2013 Adac. Tous droits réservés Validation of the generic name Gloeobacter Rippka et al. 1974, Cyanophyceae Jan MARE≤ a,b*, Ji÷í KOMÁREK a,b, Pierre COMPÈRE c & Aharon OREN d a University of South Bohemia, Faculty of Science, Brani≠ovká 31, CZ-37005 Ωeské Bud{jovice, Czech Republic b Czech Academy of Sciences, Institute of Botany, Dukelská 135, CZ-37982 T÷ebo≈, Czech Republic c National Botanic Garden of Belgium, Domein van Bouchout, B-1860 Meise, Belgium d Department of Plant and Environmental Sciences, the Institute of Life Sciences, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel Abstract – The genus name Gloeobacter with the single (= type) species Gloeobacter violaceus (Cyanophyta, Cyanoprokaryota, Cyanobacteria) was described by Rippka, Water- bury et Cohen-Bazire (Arch. Microbiol. 100: 419-436, 1974). However, this is not a validly published name and so it currently has no standing under the botanical International Code of Nomenclature (ICN, Mc Neil et al. 2012) or the International Code of Nomenclature of Prokaryotes (ICNB/ICNP, Lapage et al. 1992). The lack of valid publication of the genus name causes many problems in the taxonomy of this phylogenetically and experimentally important cyanophyte/cyanobacterium. The lack of thylakoids, a feature unique among all known cyanobacteria, as well as the phylogenetic position of the representative of this genus, warrant valid publication of this generic name. The type strain was deposited in the collection PCC in Paris under the number PCC 7421 and later introduced into numerous other strain collections; however, the dried specimens were not yet conserved. -
The Two-Domain Tree of Life Is Linked to a New Root for the Archaea
The two-domain tree of life is linked to a new root for the Archaea Kasie Raymanna, Céline Brochier-Armanetb, and Simonetta Gribaldoa,1 aInstitut Pasteur, Department of Microbiology, Unit Biologie Moléculaire du Gène chez les Extrêmophiles, 75015 Paris, France; and bUniversité de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, 69622 Villeurbanne, France Edited by W. Ford Doolittle, Dalhousie University, Halifax, NS, Canada, and approved April 17, 2015 (received for review November 02, 2014) One of the most fundamental questions in evolutionary biology is restricted taxonomic sampling, notably for the outgroup, may also the origin of the lineage leading to eukaryotes. Recent phyloge- generate or mask potential tree reconstruction artifacts (16). All nomic analyses have indicated an emergence of eukaryotes from these considerations emphasize that we have not yet found a way within the radiation of modern Archaea and specifically from a group out of the phylogenomic impasse caused by the use of universal comprising Thaumarchaeota/“Aigarchaeota” (candidate phylum)/ trees to investigate the relationships among Archaea and eu- Crenarchaeota/Korarchaeota (TACK). Despite their major im- karyotes (12). plications, these studies were all based on the reconstruction of Here, we have applied an original two-step strategy that we universal trees and left the exact placement of eukaryotes with re- proposed a few years ago which involves separately analyzing the spect to the TACK lineage unclear. Here we have applied an original markers shared between Archaea and eukaryotes and between two-step approach that involves the separate analysis of markers Archaea and Bacteria (12). This strategy allowed us to use a larger shared between Archaea and eukaryotes and between Archaea and taxonomic sampling, more markers and thus more positions, have Bacteria. -
ESCMID Online Lecture Library © by Author
The order Rickettsiales Pathogenesis of “ehrlichia” (Anaplasmataceae) infections of humans •Family Rickettsiaceae • Genera Rickettsia, Orientia •Family Anaplasmatacea • Ehrlichia, Anaplasma, others J. Stephen Dumler, M.D. •obligate intracellular bacteria • -proteobacteria phylogeny by small Departments of Pathology and Microbiology & Immunology subunit RNA genes (rrs) University of Maryland School of Medicine • contain DNA, RNA, ribosomes And Departments of Pathology and Molecular Microbiology & Immunology • divide by binary fission The Johns Hopkins Medical Institutions • Gram-negative cell wall Baltimore, MD USA •life cycle within arthropod host [email protected] •Bartonella (and former Rochalimaea) and Coxiella not in Rickettsiales Phylogeny of Rickettsiales (rrs) Ehrlichia and Anaplasma species infections α-proteobacteria E chaffeensis E ewingii pathogenesis A phagocytophilum E muris R prowazekii R australis • attachment R typhi R akari R felis R honei • endosomal entry R rickettsii Neoehrlichia mikurensis R conorii R parkeri W pipientis R africae R sibirica • avoidance of immediate intracellular killing (signaling) – phagolysosome fusion inhibition - doxycycline sensitive O tsutsugamushi Anaplasmataceae – subversion of autophagy Rickettsiaceae – detoxification of oxidative killing mechanisms • regulation and perturbation of host cell functions N sennetsu (gene expression) – downregulation of innate or early immune responses B quintana – cell cycle perturbations / apoptosis B henselae E coli – inhibition of intracellular trafficking -
Various Complexes of the Oral Microbial Flora in Periodontal Disease
ISSN: 2394-8418 DOI: https://doi.org/10.17352/jdps CLINICAL GROUP Received: 01 April, 2021 Short Communication Accepted: 08 April, 2021 Published: 10 April, 2021 *Corresponding author: Dr. Sukhvinder Singh Oberoi, Various complexes of the oral BDS, MDS, Associate Professor, Public Health Den- tistry, ESIC Dental College and Hospital, Rohini, Guru microbial fl ora in periodontal Gobind Singh Indraprastha University, India, E-mail: disease Keywords: Periodontal diseases; Red complex; Orange complex Sukhvinder Singh Oberoi1*, Shabina Sachdeva2 and https://www.peertechzpublications.com Shibani Grover3 1Associate Professor, Public Health Dentistry, ESIC Dental College and Hospital, Rohini, Guru Gobind Singh Indraprastha University, India 2Professor, Prosthodontics, Faculty of Dentistry, Jamia Milia Islamia, India 3Dean and Director Professor, Conservative Dentistry and Endodontics, ESIC Dental College and Hospital, Rohini, Guru Gobind Singh Indraprastha University, India Abstract Periodontal diseases, is the infection of the periodontal tissues which eventually can lead to loss of teeth, is a form of aberrant infl ammation resulting from a complex biofi lm of friendly commensal and periodontopathic bacteria and their products, triggering the human infl ammatory response. The cluster analysis has shown that 6 closely associated bacterial complexes are associated with it which are designated with different color codes. The early colonizers are “Blue complex” consisting of Actinomyces species, “Yellow complex” comprising of various Streptococci, “Green complex” comprising Eiknella corrodens and Capnocytophaga species, and “Purple complex” comprising Veillonella parvula and Actinomyces odontolyticus. The late colonizers are “Orange complex” comprising Prevotella, Fusobacterium, Campylobacter and other bacteria and the “Red complex” chiefl y consisting of Porphyromonas gingivalis, Tannerella forsythia, and Treponema Denticola. Periodontal disease is the commonest oral disease affecting are facultative, spirochetes and motile rods. -
Human Babesiosis and Ehrlichiosis Current Status
IgeneX_v1_A4_A4_2011 27/04/2012 17:26 Page 49 Tick-borne Infectious Disease Human Babesiosis and Ehrlichiosis – Current Status Jyotsna S Shah,1 Richard Horowitz2 and Nick S Harris3 1. Vice President, IGeneX Inc., California; 2. Medical Director, Hudson Valley Healing Arts Center, New York; 3. CEO and President, IGeneX Inc., California, US Abstract Lyme disease (LD), caused by the Borrelia burgdorferi complex, is the most frequently reported arthropod-borne infection in North America and Europe. The ticks that transmit LD also carry other pathogens. The two most common co-infections in patients with LD are babesiosis and ehrlichiosis. Human babesiosis is caused by protozoan parasites of the genus Babesia including Babesia microti, Babesia duncani, Babesia divergens, Babesia divergens-like (also known as Babesia MOI), Babesia EU1 and Babesia KO1. Ehrlichiosis includes human sennetsu ehrlichiosis (HSE), human granulocytic anaplasmosis (HGA), human monocytic ehrlichiosis (HME), human ewingii ehrlichiosis (HEE) and the recently discovered human ehrlichiosis Wisconsin–Minnesota (HWME). The resulting illnesses vary from asymptomatic to severe, leading to significant morbidity and mortality, particularly in immunocompromised patients. Clinical signs and symptoms are often non-specific and require the medical provider to have a high degree of suspicion of these infections in order to be recognised. In this article, the causative agents, geographical distribution, clinical findings, diagnosis and treatment protocols are discussed for both babesiosis and ehrlichiosis. Keywords Babesia, Ehrlichia, babesiosis, ehrlichiosis, human, Borrelia Disclosure: Jyotsna Shah and Nick Harris are employees of IGeneX. Richard Horowitz is an employee of Hudson Valley Healing Arts Center. Acknowledgements: The authors would like to thank Eddie Caoili, and Sohini Stone, for providing technical assistance. -
Oxygenic Photosynthesis
JWBS121-c02 JWBS121-Razeghifard Printer: Yet to Come July 30, 2013 8:16 Trim: 6.125in × 9.25in CHAPTER 2 Oxygenic Photosynthesis DMITRIY SHEVELA, LARS OLOF BJORN,¨ and GOVINDJEE 2.1 INTRODUCTION 2.1.1 Importance of Photosynthesis: Why Study Photosynthesis? In a general sense the term photosynthesis is synthesis of chemical compounds by the use of light. In the more restricted sense, as we shall use it here, it stands for the process by which plants, algae, cyanobacteria, and phototrophic bacteria convert light energy to chemical forms of energy. Most photosynthesis is coupled to assimilation of carbon in the form of carbon dioxide or bicarbonate ions, but there exists also assimilation of CO2 that is not coupled to photosynthesis, as well as photosynthesis that is not coupled to assimilation of carbon. All life on Earth, with some exceptions, is completely dependent on photosynthe- sis. Most organisms that do not live directly by photosynthesis depend on the organic compounds formed by photosynthesis and, in many cases, also on the molecular oxy- gen formed by the most important type of photosynthesis, oxygenic photosynthesis. Even much of the energy fueling the ecosystems at deep-water hydrothermal vents depends on photosynthesis, since it is made available to organisms using molecular oxygen of photosynthetic origin. In addition, photosynthesis is biologically impor- tant in a number of more indirect ways. The stratospheric ozone layer protecting the biosphere from dangerous ultraviolet radiation from the sun is formed from photosynthesis-derived oxygen by a photochemical process. The photosynthetic as- similation of CO2, and associated processes such as formation of carbonate shells by aquatic organisms, has (so far) helped to maintain the climate of our planet in a life-sustainable state.