DOCSLIB.ORG

John D. Kriesel, Preetida Bhetariya, Cheryl Palmer, and Kael Fischer University of Utah School of Medicine, Salt Lake City, Utah, USA

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
John D. Kriesel, Preetida Bhetariya, Cheryl Palmer, and Kael Fischer University of Utah School of Medicine, Salt Lake City, Utah, USA Microbial Sequences in Multiple Sclerosis Brain Specimens John D. Kriesel, Preetida Bhetariya, Cheryl Palmer, and Kael Fischer University of Utah School of Medicine, Salt Lake City, Utah, USA Session: 243. Host-Pathogen Interactions Presentation Number 2206 ABSTRACT RESULTS Table 2. MS Microbial Candidate List Background: Our group has developed RNA sequencing and analysis for Figure 2 Normalized Hit Rate Sum MS Group the identification of microbes in diseased brain tissue. Hierarchical Cluster 3.0 Analysis. Phylum1 Contributing Families2 Raw Hits3 # Specimens Increased4 Growth Conditions Methods: Twelve primary demyelination (MS) biopsy and 15 control Log2 transformed normalized Euryarchaeota Methanobacteriaceae 162 3 Anaerobic epilepsy surgical human brain specimens were studied. RNA was hit rates (in pairs per million (archeae) Methanosarcinaceae 96 1 Anaerobic extracted and quantified from the formalin-fixed paraffin-embedded reads, PPM) were centered for all Unclassified (NC10) Unclassified 66 4 n/a specimens, subjected to quality control, and then deep sequenced. The microbial families where at least Acidobacteria Acidobacteriaceae 1266 5 Aerobic reads were filtered and aligned against a panmicrobial database of 1.3 one MS samples was significantly Atopobiaceae 1588 2 Anaerobic Coriobacteriaceae 562 3 Anaerobic million (M) sequence records representing 10,654 species. Microbial overrepresented (FDR, q < 0.05) relative to the set of controls. The Actinobacteria Eggerthellaceae 578 6 Anaerobic reads and human gene expression were compared between the groups. Rubrobacteraceae 472 3 Aerobic, 60˚C. MS (N=12) and epilepsy control Results:100-300M high-quality 125 bp paired-end reads were derived Unclassified 76 4 n/a (N=15) sample values (columns) from each brain specimen. 6.4M read pairs (0.1% of total), from both the Porphyromonadaceae 4330 4 Anaerobic MS and control specimens, aligned to the panmicrobial database. Outlier were used to center the data Bacteroidetes Rikenellaceae 3574 2 Anaerobic analysis, corrected for multiple comparisons, identified significantly for display. The mean HR value Flammeovirgaceae 218 2 Aerobic increased microbial sequence in 11/12 MS brain specimens. 43 genera for each microbial family was Flavobacteriaceae 84 2 Anaerobic and 36 families from 11 microbial phyla (archaea 2, unclassified 1, subtracted from each cell in the Cyanobacteria Gomontiellaceae 284 2 Aerobic Leuconostocaceae 194 2 Aerobic bacteria 11, fungi 2, viruses 1) were overrepresented in at least one of row to provide a visual display of distance from the mean, expressed Clostridiales Family XVII 94 4 Anaerobic the MS brain samples. Many of the MS candidate microbes are anaerobic Firmicutes Lachnospiraceae 866 2 Anaerobic (Alistipes, Akkermansia), noncultivable (Candidatus), or extremophiles as log2 increases (yellow) or decreases (blue) from the mean Peptococcaceae 480 1 Anaerobic (Lawsonia). Gene expression analysis showed that several immune Thermoanaerobacterales 90 5 Anaerobic, 55˚C value (black). A clustering of system pathways are significantly increased in the MS brain specimens. Erysipelotrichaceae 996 2 Aerobic candidate MS microbial families Conclusions: The sequencing data shows that most of the MS brain Fusobacteria Fusobacteriaceae 230 1 Anaerobic among 6 MS brain specimens can Nitrospirae Nitrospiraceae 230 2 Aerobic with nitrite specimens studied contain a set of microbial sequences that are be seen in the upper right corner. significantly different than the controls. This suggests that MS lesions Planctomycetes Planctomycetaceae 156 2 Aerobic Rhodospirillaceae 412 2 Aerobic or anaerobic may be related to the invasion of a diverse set of microbes into the brain, Anaplasmataceae 166 3 Chicken embryo or to a disturbance of preexisting microbes within brain tissue. Human Figure 3. Bacterial Antigen in Human Brain Specimens. Brain specimens were stained with the mouse mAb M995 against bacterial Proteobacteria Desulfovibrionaceae 126 2 Anaerobic gene expression in these brain specimens supports a role for a bacterial Cystobacteraceae 498 1 Aerobic pathogenesis of MS. Studies are in progress to visualize specific MS peptidoglycan, or the macrophage/microglia anti-CD68 Ab, or no primary Ab (control). Magnification is 125x. Tenericutes Acholeplasmataceae 206 2 n/a candidate microbes within the brain tissue specimens. Mycoplasmataceae 152 1 Aerobic MS-019 anti-PG C-40 anti-PG Brain Abscess anti-PG Verrucomicrobia Akkermansiaceae 25094 1 Anaerobic Ascomycota Saccharomycetaceae 242 1 Aerobic Figure 1. Sequencing and Alignments. Basidiomycota Ustilaginaceae 1080 3 Aerobic Viruses Bromoviridae 486 2 n/a Table 2 Footnotes 1 As classified in NCBI Taxonomy. 2 Genera within the phylum that had the HR from one or more MS samples significantly increased over the set of controls (N=15). To be listed here, the sum of normalized HRs over the entire MS group (N=12) had to exceed 1.0 pair per million read-pairs. 3 Concordant read pairs aligning to this genus summed over the entire MS group (N=12) 4 Number of MS brain specimens that had HRs significantly greater (one-tailed q<.05) than the set of controls (N=15). CONCLUSIONS MS-019 control C-40 control MS019 anti-CD68 1. Certain microbial sequences, representing microbial RNA, are significantly enriched in many of the MS brain specimens compared to a set of 15 epilepsy control brain specimens. 2. No single microbial family, genus, or species was specific to MS. However, a cluster analysis shows that a set of diverse anaerobic and extremophile microbes are associated with 6 of the 12 MS cases we studied. 3. The presence of bacterial antigen was confirmed by immunohistochemistry in all the MS brain specimens where there was sufficient specimen for analysis (N=4). 4. The human gene expression analysis revealed overexpression of immune system related genes in the MS group compared to controls. Some of the overexpressed genes are consistent with an anti-bacterial immune response (e.g. TLR2, TLR4). 5. Additional studies are in progress to determine the significance of these findings..
Load more

Recommended publications
  • Bacterial Communities of the Upper Respiratory Tract of Turkeys
    www.nature.com/scientificreports OPEN Bacterial communities of the upper respiratory tract of turkeys Olimpia Kursa1*, Grzegorz Tomczyk1, Anna Sawicka‑Durkalec1, Aleksandra Giza2 & Magdalena Słomiany‑Szwarc2 The respiratory tracts of turkeys play important roles in the overall health and performance of the birds. Understanding the bacterial communities present in the respiratory tracts of turkeys can be helpful to better understand the interactions between commensal or symbiotic microorganisms and other pathogenic bacteria or viral infections. The aim of this study was the characterization of the bacterial communities of upper respiratory tracks in commercial turkeys using NGS sequencing by the amplifcation of 16S rRNA gene with primers designed for hypervariable regions V3 and V4 (MiSeq, Illumina). From 10 phyla identifed in upper respiratory tract in turkeys, the most dominated phyla were Firmicutes and Proteobacteria. Diferences in composition of bacterial diversity were found at the family and genus level. At the genus level, the turkey sequences present in respiratory tract represent 144 established bacteria. Several respiratory pathogens that contribute to the development of infections in the respiratory system of birds were identifed, including the presence of Ornithobacterium and Mycoplasma OTUs. These results obtained in this study supply information about bacterial composition and diversity of the turkey upper respiratory tract. Knowledge about bacteria present in the respiratory tract and the roles they can play in infections can be useful in controlling, diagnosing and treating commercial turkey focks. Next-generation sequencing has resulted in a marked increase in culture-independent studies characterizing the microbiome of humans and animals1–6. Much of these works have been focused on the gut microbiome of humans and other production animals 7–11.
    [Show full text]
  • Global Metagenomic Survey Reveals a New Bacterial Candidate Phylum in Geothermal Springs
    ARTICLE Received 13 Aug 2015 | Accepted 7 Dec 2015 | Published 27 Jan 2016 DOI: 10.1038/ncomms10476 OPEN Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs Emiley A. Eloe-Fadrosh1, David Paez-Espino1, Jessica Jarett1, Peter F. Dunfield2, Brian P. Hedlund3, Anne E. Dekas4, Stephen E. Grasby5, Allyson L. Brady6, Hailiang Dong7, Brandon R. Briggs8, Wen-Jun Li9, Danielle Goudeau1, Rex Malmstrom1, Amrita Pati1, Jennifer Pett-Ridge4, Edward M. Rubin1,10, Tanja Woyke1, Nikos C. Kyrpides1 & Natalia N. Ivanova1 Analysis of the increasing wealth of metagenomic data collected from diverse environments can lead to the discovery of novel branches on the tree of life. Here we analyse 5.2 Tb of metagenomic data collected globally to discover a novel bacterial phylum (‘Candidatus Kryptonia’) found exclusively in high-temperature pH-neutral geothermal springs. This lineage had remained hidden as a taxonomic ‘blind spot’ because of mismatches in the primers commonly used for ribosomal gene surveys. Genome reconstruction from metagenomic data combined with single-cell genomics results in several high-quality genomes representing four genera from the new phylum. Metabolic reconstruction indicates a heterotrophic lifestyle with conspicuous nutritional deficiencies, suggesting the need for metabolic complementarity with other microbes. Co-occurrence patterns identifies a number of putative partners, including an uncultured Armatimonadetes lineage. The discovery of Kryptonia within previously studied geothermal springs underscores the importance of globally sampled metagenomic data in detection of microbial novelty, and highlights the extraordinary diversity of microbial life still awaiting discovery. 1 Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA. 2 Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada.
    [Show full text]
  • MIB–MIP Is a Mycoplasma System That Captures and Cleaves Immunoglobulin G
    MIB–MIP is a mycoplasma system that captures and cleaves immunoglobulin G Yonathan Arfia,b,1, Laetitia Minderc,d, Carmelo Di Primoe,f,g, Aline Le Royh,i,j, Christine Ebelh,i,j, Laurent Coquetk, Stephane Claveroll, Sanjay Vasheem, Joerg Joresn,o, Alain Blancharda,b, and Pascal Sirand-Pugneta,b aINRA (Institut National de la Recherche Agronomique), UMR 1332 Biologie du Fruit et Pathologie, F-33882 Villenave d’Ornon, France; bUniversity of Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33882 Villenave d’Ornon, France; cInstitut Européen de Chimie et Biologie, UMS 3033, University of Bordeaux, 33607 Pessac, France; dInstitut Bergonié, SIRIC BRIO, 33076 Bordeaux, France; eINSERM U1212, ARN Regulation Naturelle et Artificielle, 33607 Pessac, France; fCNRS UMR 5320, ARN Regulation Naturelle et Artificielle, 33607 Pessac, France; gInstitut Européen de Chimie et Biologie, University of Bordeaux, 33607 Pessac, France; hInstitut de Biologie Structurale, University of Grenoble Alpes, F-38044 Grenoble, France; iCNRS, Institut de Biologie Structurale, F-38044 Grenoble, France; jCEA, Institut de Biologie Structurale, F-38044 Grenoble, France; kCNRS UMR 6270, Plateforme PISSARO, Institute for Research and Innovation in Biomedicine - Normandie Rouen, Normandie Université, F-76821 Mont-Saint-Aignan, France; lProteome Platform, Functional Genomic Center of Bordeaux, University of Bordeaux, F-33076 Bordeaux Cedex, France; mJ. Craig Venter Institute, Rockville, MD 20850; nInternational Livestock Research Institute, 00100 Nairobi, Kenya; and oInstitute of Veterinary Bacteriology, University of Bern, CH-3001 Bern, Switzerland Edited by Roy Curtiss III, University of Florida, Gainesville, FL, and approved March 30, 2016 (received for review January 12, 2016) Mycoplasmas are “minimal” bacteria able to infect humans, wildlife, introduced into naive herds (8).
    [Show full text]
  • Supplementary Information for Microbial Electrochemical Systems Outperform Fixed-Bed Biofilters for Cleaning-Up Urban Wastewater
    Electronic Supplementary Material (ESI) for Environmental Science: Water Research & Technology. This journal is © The Royal Society of Chemistry 2016 Supplementary information for Microbial Electrochemical Systems outperform fixed-bed biofilters for cleaning-up urban wastewater AUTHORS: Arantxa Aguirre-Sierraa, Tristano Bacchetti De Gregorisb, Antonio Berná, Juan José Salasc, Carlos Aragónc, Abraham Esteve-Núñezab* Fig.1S Total nitrogen (A), ammonia (B) and nitrate (C) influent and effluent average values of the coke and the gravel biofilters. Error bars represent 95% confidence interval. Fig. 2S Influent and effluent COD (A) and BOD5 (B) average values of the hybrid biofilter and the hybrid polarized biofilter. Error bars represent 95% confidence interval. Fig. 3S Redox potential measured in the coke and the gravel biofilters Fig. 4S Rarefaction curves calculated for each sample based on the OTU computations. Fig. 5S Correspondence analysis biplot of classes’ distribution from pyrosequencing analysis. Fig. 6S. Relative abundance of classes of the category ‘other’ at class level. Table 1S Influent pre-treated wastewater and effluents characteristics. Averages ± SD HRT (d) 4.0 3.4 1.7 0.8 0.5 Influent COD (mg L-1) 246 ± 114 330 ± 107 457 ± 92 318 ± 143 393 ± 101 -1 BOD5 (mg L ) 136 ± 86 235 ± 36 268 ± 81 176 ± 127 213 ± 112 TN (mg L-1) 45.0 ± 17.4 60.6 ± 7.5 57.7 ± 3.9 43.7 ± 16.5 54.8 ± 10.1 -1 NH4-N (mg L ) 32.7 ± 18.7 51.6 ± 6.5 49.0 ± 2.3 36.6 ± 15.9 47.0 ± 8.8 -1 NO3-N (mg L ) 2.3 ± 3.6 1.0 ± 1.6 0.8 ± 0.6 1.5 ± 2.0 0.9 ± 0.6 TP (mg
    [Show full text]
  • Table S4. Phylogenetic Distribution of Bacterial and Archaea Genomes in Groups A, B, C, D, and X
    Table S4. Phylogenetic distribution of bacterial and archaea genomes in groups A, B, C, D, and X. Group A a: Total number of genomes in the taxon b: Number of group A genomes in the taxon c: Percentage of group A genomes in the taxon a b c cellular organisms 5007 2974 59.4 |__ Bacteria 4769 2935 61.5 | |__ Proteobacteria 1854 1570 84.7 | | |__ Gammaproteobacteria 711 631 88.7 | | | |__ Enterobacterales 112 97 86.6 | | | | |__ Enterobacteriaceae 41 32 78.0 | | | | | |__ unclassified Enterobacteriaceae 13 7 53.8 | | | | |__ Erwiniaceae 30 28 93.3 | | | | | |__ Erwinia 10 10 100.0 | | | | | |__ Buchnera 8 8 100.0 | | | | | | |__ Buchnera aphidicola 8 8 100.0 | | | | | |__ Pantoea 8 8 100.0 | | | | |__ Yersiniaceae 14 14 100.0 | | | | | |__ Serratia 8 8 100.0 | | | | |__ Morganellaceae 13 10 76.9 | | | | |__ Pectobacteriaceae 8 8 100.0 | | | |__ Alteromonadales 94 94 100.0 | | | | |__ Alteromonadaceae 34 34 100.0 | | | | | |__ Marinobacter 12 12 100.0 | | | | |__ Shewanellaceae 17 17 100.0 | | | | | |__ Shewanella 17 17 100.0 | | | | |__ Pseudoalteromonadaceae 16 16 100.0 | | | | | |__ Pseudoalteromonas 15 15 100.0 | | | | |__ Idiomarinaceae 9 9 100.0 | | | | | |__ Idiomarina 9 9 100.0 | | | | |__ Colwelliaceae 6 6 100.0 | | | |__ Pseudomonadales 81 81 100.0 | | | | |__ Moraxellaceae 41 41 100.0 | | | | | |__ Acinetobacter 25 25 100.0 | | | | | |__ Psychrobacter 8 8 100.0 | | | | | |__ Moraxella 6 6 100.0 | | | | |__ Pseudomonadaceae 40 40 100.0 | | | | | |__ Pseudomonas 38 38 100.0 | | | |__ Oceanospirillales 73 72 98.6 | | | | |__ Oceanospirillaceae
    [Show full text]
  • Extensive Microbial Diversity Within the Chicken Gut Microbiome Revealed by Metagenomics and Culture
    Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture Rachel Gilroy1, Anuradha Ravi1, Maria Getino2, Isabella Pursley2, Daniel L. Horton2, Nabil-Fareed Alikhan1, Dave Baker1, Karim Gharbi3, Neil Hall3,4, Mick Watson5, Evelien M. Adriaenssens1, Ebenezer Foster-Nyarko1, Sheikh Jarju6, Arss Secka7, Martin Antonio6, Aharon Oren8, Roy R. Chaudhuri9, Roberto La Ragione2, Falk Hildebrand1,3 and Mark J. Pallen1,2,4 1 Quadram Institute Bioscience, Norwich, UK 2 School of Veterinary Medicine, University of Surrey, Guildford, UK 3 Earlham Institute, Norwich Research Park, Norwich, UK 4 University of East Anglia, Norwich, UK 5 Roslin Institute, University of Edinburgh, Edinburgh, UK 6 Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Banjul, The Gambia 7 West Africa Livestock Innovation Centre, Banjul, The Gambia 8 Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, Edmond J. Safra Campus, Hebrew University of Jerusalem, Jerusalem, Israel 9 Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK ABSTRACT Background: The chicken is the most abundant food animal in the world. However, despite its importance, the chicken gut microbiome remains largely undefined. Here, we exploit culture-independent and culture-dependent approaches to reveal extensive taxonomic diversity within this complex microbial community. Results: We performed metagenomic sequencing of fifty chicken faecal samples from Submitted 4 December 2020 two breeds and analysed these, alongside all (n = 582) relevant publicly available Accepted 22 January 2021 chicken metagenomes, to cluster over 20 million non-redundant genes and to Published 6 April 2021 construct over 5,500 metagenome-assembled bacterial genomes.
    [Show full text]
  • Pathogen Challenge and Dietary Shift Alter Microbiota Composition And
    fmicb-12-703421 July 19, 2021 Time: 11:40 # 1 ORIGINAL RESEARCH published: 19 July 2021 doi: 10.3389/fmicb.2021.703421 Pathogen Challenge and Dietary Shift Alter Microbiota Composition and Activity in a Mucin-Associated in vitro Model of the Piglet Colon (MPigut-IVM) Simulating Weaning Transition Raphaële Gresse1,2, Frédérique Chaucheyras-Durand1,2, Juan J. Garrido3, Sylvain Denis1, Angeles Jiménez-Marín3, Martin Beaumont4, Tom Van de Wiele5, Evelyne Forano1 and Stéphanie Blanquet-Diot1* 1 INRAE, UMR 454 MEDIS, Université Clermont Auvergne, Clermont-Ferrand, France, 2 Lallemand SAS, Blagnac, France, 3 Grupo de Genómica y Mejora Animal, Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain, 4 GenPhySE, INRAE, ENVT, Université de Toulouse, Castanet-Tolosan, France, 5 Center for Microbial Ecology and Technology, Ghent University, Ghent, Belgium Edited by: Wakako Ikeda-Ohtsubo, Tohoku University, Japan Enterotoxigenic Escherichia coli (ETEC) is the principal pathogen responsible for post- Reviewed by: weaning diarrhea in newly weaned piglets. Expansion of ETEC at weaning is thought to Katie Lynn Summers, be the consequence of various stress factors such as transient anorexia, dietary change United States Department or increase in intestinal inflammation and permeability, but the exact mechanisms remain of Agriculture (USDA), United States Åsa Sjöling, to be elucidated. As the use of animal experiments raise more and more ethical Karolinska Institutet (KI), Sweden concerns, we used a recently developed in vitro model of piglet colonic microbiome *Correspondence: and mucobiome, the MPigut-IVM, to evaluate the effects of a simulated weaning Stéphanie Blanquet-Diot [email protected] transition and pathogen challenge at weaning.
    [Show full text]
  • Dose-Responses Relationship in Glucose Lowering and Gut
    microorganisms Article Dose-Responses Relationship in Glucose Lowering and Gut Dysbiosis to Saskatoon Berry Powder Supplementation in High Fat-High Sucrose Diet-Induced Insulin Resistant Mice Ruozhi Zhao 1, Fei Huang 1 and Garry X. Shen 1,2,* 1 Department of Internal Medicine, University of Manitoba, Winnipeg, MB R3E 3P4, Canada; [email protected] (R.Z.); [email protected] (F.H.) 2 Department of Food and Human Nutritional Sciences, University of Manitoba, Winnipeg, MB R3E 3P4, Canada * Correspondence: [email protected]; Tel.: +1-204-789-3816; Fax: +1-204-789-3987 Abstract: Administration of freeze-dried powder of Saskatoon berry (SB), a popular fruit enriched with antioxidants, reduced glucose level, inflammatory markers and gut microbiota disorder in high fat-high sucrose (HFHS) diet-induced insulin resistant mice. The present study examined the dose-response relationship in metabolic, inflammatory and gut microbiotic variables to SB power (SBp) supplementation in HFHS diet-fed mice. Male C57 BL/6J mice were fed with HFHS diet supplemented with 0, 1%, 2.5% or 5% SBp for 11 weeks. HFHS diet significantly increased the levels of fast plasma glucose (FPG), cholesterol, triglycerides, insulin, homeostatic model assessment of insulin resistance (HOMA-IR), tumor necrosis factor-α, monocyte chemotactic protein-1 and plasminogen activator inhibitor-1, but decreased fecal Bacteroidetes phylum bacteria and Muribaculaceae family bacteria compared to low fat diet. SBp dose-dependently reduced metabolic and inflammatory Citation: Zhao, R.; Huang, F.; Shen, variables and gut dysbiosis in mice compared with mice receiving HFHS diet alone. Significant G.X. Dose-Responses Relationship in ≥ Glucose Lowering and Gut Dysbiosis attenuation of HFHS diet-induced biochemical disorders were detected in mice receiving 1% SBp.
    [Show full text]
  • Prokaryotic Gene Start Prediction: Algorithms for Genomes and Metagenomes
    PROKARYOTIC GENE START PREDICTION: ALGORITHMS FOR GENOMES AND METAGENOMES A Dissertation Presented to The Academic Faculty By Karl Gemayel In Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the School of Computational Science and Engineering Georgia Institute of Technology December 2020 © Karl Gemayel 2020 PROKARYOTIC GENE START PREDICTION: ALGORITHMS FOR GENOMES AND METAGENOMES Thesis committee: Dr. Mark Borodovsky Dr. Polo Chau School of Computational Science and En- School of Computational Science and En- gineering and Department of Biomedical gineering Engineering Georgia Institute of Technology Georgia Institute of Technology Dr. Umit¨ C¸atalyurek¨ Dr. King Jordan School of Computational Science and En- School of Biological Sciences gineering Georgia Institute of Technology Georgia Institute of Technology Dr. Pen Qui Department of Biomedical Engineering Georgia Institute of Technology Date approved: October 31, 2020 Wooster: “There are moments, Jeeves, when one asks oneself, ‘Do trousers matter?’” Jeeves: “The mood will pass, sir.” P.G. Wodehouse, The Code Of The Woosters To Mom and Dad, all my ancestors, and the first self-replicating molecule. Without you, this work would literally not have been possible. ACKNOWLEDGMENTS I am bound to forget someone or something and so, in fairness to all, I will forget most things and keep this vague and terse, though not necessarily short. I was very much at the right place at the right time to do this work, a time where these problems had not yet been solved. To the driven students who graduated early enough before such ideas came to them, thank you for being considerate. To my advisor Mark Borodovsky, who insisted that a lack of community funding for prokaryotic gene finding does not mean that the problem has actually been solved, thank you for continuously pushing for rigorous science that questions accepted beliefs.
    [Show full text]
  • Data Sheet on Spiroplasma Citri
    Prepared by CABI and EPPO for the EU under Contract 90/399003 Data Sheets on Quarantine Pests Spiroplasma citri The vectors of Spiroplasma citri are individually included in EU Directive 77/93. Since their importance only arises in relation to S. citri, they are covered in this data sheet. IDENTITY • Spiroplasma citri Name: Spiroplasma citri Saglio et al. Taxonomic position: Bacteria: Tenericutes: Mollicutes Common names: Stubborn, little leaf (English) Stubborn (French) Bayer computer code: SPIRCI EU Annex designation: II/A2 • Circulifer tenellus Name: Circulifer tenellus (Baker) Synonyms: Neoaliturus tenellus (Baker) Eutettix tenellus Baker Taxonomic position: Insecta: Hemiptera: Homoptera: Cicadellidae Common names: Beet leafhopper (English) Cicadelle de la betterave (French) Saltahojas de la remolacha (Spanish) Notes on taxonomy and nomenclature: Oman (1970) argues for the retention of Circulifer and Neoaliturus as separate genera; in his concept both tenellus and haematoceps are placed in Circulifer. Nast (1972) treats the two genera as Neoaliturus notwithstanding Oman's (1970) arguments for the retention of the two genera. He includes 17 species in the Palaearctic region of which 14 are recorded from the Mediterranean Basin. The two species, tenellus and haematoceps, are both included in Circulifer by della Giustina (1989), who reports that tenellus is confirmed in Corsica. Bayer computer code: CIRCTE EU Annex designation: II/A2 • Neoaliturus haematoceps Name: Neoaliturus haematoceps (Mulsant & Rey) Synonyms: Circulifer haematoceps (Mulsant & Rey) Jassus haematoceps Mulsant & Rey Taxonomic position: Insecta: Hemiptera: Homoptera: Cicadellidae Bayer computer code: NEOAHA EU Annex designation: II/A2 (under the name Circulifer haematoceps) HOSTS • Spiroplasma citri The principal economic hosts of S. citri are susceptible Citrus spp.
    [Show full text]
  • Downloaded from Genome Website
    bioRxiv preprint doi: https://doi.org/10.1101/2020.11.18.388454; this version posted November 19, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Characterization of the first cultured free-living representative of 2 Candidatus Izimaplasma uncovers its unique biology 3 Rikuan Zheng1,2,3,4, Rui Liu1,2,4, Yeqi Shan1,2,3,4, Ruining Cai1,2,3,4, Ge Liu1,2,4, Chaomin Sun1,2,4* 1 4 CAS Key Laboratory of Experimental Marine Biology & Center of Deep Sea 5 Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China 2 6 Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory 7 for Marine Science and Technology, Qingdao, China 3 8 College of Earth Science, University of Chinese Academy of Sciences, Beijing, 9 China 10 4Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China 11 12 * Corresponding author 13 Chaomin Sun Tel.: +86 532 82898857; fax: +86 532 82898857. 14 E-mail address: [email protected] 15 16 17 Key words: Candidatus Izimaplasma, uncultivation, biogeochemical cycling, 18 extracellular DNA, in situ, deep sea 19 Running title: Characterization of the first cultured Izimaplasma 20 21 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.11.18.388454; this version posted November 19, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 22 Abstract 23 Candidatus Izimaplasma, an intermediate in the reductive evolution from Firmicutes 24 to Mollicutes, was proposed to represent a novel class of free-living wall-less bacteria 25 within the phylum Tenericutes found in deep-sea methane seeps.
    [Show full text]
  • Lists of Names of Prokaryotic Candidatus Taxa
    NOTIFICATION LIST: CANDIDATUS LIST NO. 1 Oren et al., Int. J. Syst. Evol. Microbiol. DOI 10.1099/ijsem.0.003789 Lists of names of prokaryotic Candidatus taxa Aharon Oren1,*, George M. Garrity2,3, Charles T. Parker3, Maria Chuvochina4 and Martha E. Trujillo5 Abstract We here present annotated lists of names of Candidatus taxa of prokaryotes with ranks between subspecies and class, pro- posed between the mid- 1990s, when the provisional status of Candidatus taxa was first established, and the end of 2018. Where necessary, corrected names are proposed that comply with the current provisions of the International Code of Nomenclature of Prokaryotes and its Orthography appendix. These lists, as well as updated lists of newly published names of Candidatus taxa with additions and corrections to the current lists to be published periodically in the International Journal of Systematic and Evo- lutionary Microbiology, may serve as the basis for the valid publication of the Candidatus names if and when the current propos- als to expand the type material for naming of prokaryotes to also include gene sequences of yet-uncultivated taxa is accepted by the International Committee on Systematics of Prokaryotes. Introduction of the category called Candidatus was first pro- morphology, basis of assignment as Candidatus, habitat, posed by Murray and Schleifer in 1994 [1]. The provisional metabolism and more. However, no such lists have yet been status Candidatus was intended for putative taxa of any rank published in the journal. that could not be described in sufficient details to warrant Currently, the nomenclature of Candidatus taxa is not covered establishment of a novel taxon, usually because of the absence by the rules of the Prokaryotic Code.
    [Show full text]