DOCSLIB.ORG

Download (PDF)

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

A) Sm B) Sw C) Ss D) N1 114, Nitrospira 114, Nitrospira 24, Sytrophobacteraceae 146, Propionibacterineae 323, Firmicutes 26, Sytrophobacteraceae 161, Spirochaetaceae 228, Chloroflexi 333, Lactobacillales 67, KSB3 132, Acidobacteria 23, Sytrophobacteraceae 21, TM6 23, Sytrophobacteraceae 143, Actinobacteridae 209, Chloroflexi 132, Acidobacteria 85, Bacteroidales 348, Firmicutes 10, Rhodocyclales 301, Firmicutes 114, Nitrospira 146, Propionibacterineae 79, Bacteroidales 23, Sytrophobacteraceae 61, Epsilon proteobacteria 224, Chloroflexi 146, Propionibacterineae 85, Bacteroidales 209, Chloroflexi 87, Bacteroidales 152, Propionibacterineae 113, Flexibacteraceae 351, OD2 208, Chloroflexi 85, Bacteroidales 128, Planctomycetes 146, Propionibacterineae 213, Chloroflexi 186, Chlorobi 161, Spirochaetaceae 79, Bacteroidales 280, Clostridiaceae 250, Lachnospiraceae 138, others 196, Chloroflexi 114, Nitrospira 262, Lachnospiraceae 183, Chlorobi 213, Chloroflexi 24, Sytrophobacteraceae 340, Acidaminococcaceae 231, Chloroflexi 218, Chloroflexi 228, Chloroflexi 25, Sytrophobacteraceae 15, Rhodobacterales 333, Lactobacillales 25, Sytrophobacteraceae 13, Methylophilales 55, Desulfovibrionales 165, Spirochaetaceae 55, Desulfovibrionales 23, Sytrophobacteraceae 173, Spirochaetaceae 65, others 61, Epsilonproteobacteria 116, Verrucomicrobia-Chlamydiae 148, Propionibacterineae 1, Shewanella 132, Acidobacteria 158, Rubrobacteridae 157, Rubrobacteridae 2, Pseudomonadaceae 143, Actinobacteridae 83, Bacteroidales 85, Bacteroidales 3, Pseudomonadaceae 157, Rubrobacteridae 92, Bacteroidales 104, Bacteroidales 161, Spirochaetaceae 198, Chloroflexi 97, Bacteroidales 109, Flavobacteriales 71, Bacteroidales 199, Chloroflexi 98, Bacteroidales 110, Flavobacteriales 95, Bacteroidales 202, Chloroflexi 99, Bacteroidales 193, Chloroflexi 111, Flavobacteriales 106, Bacteroidales 205, Chloroflexi 195, Chloroflexi 184, Chlorobi 203, Chloroflexi 209, Chloroflexi 216, Chloroflexi 198, Chloroflexi 223, Chloroflexi 240, Chloroflexi 217, Chloroflexi 204, Chloroflexi 232, Chloroflexi 218, Chloroflexi 213, Chloroflexi 242, Chloroflexi 234, Chloroflexi 216, Chloroflexi 264, Lachnospiraceae 236, Chloroflexi 230, Chloroflexi 222, Chloroflexi 320, Firmicutes 237, Chloroflexi 233, Chloroflexi 226, Chloroflexi 325, Firmicutes 241, Chloroflexi 287, Firmicutes 240, Chloroflexi 344, Acidaminococcaceae 274, Lachnospiraceae 292, Firmicutes 261, Lachnospiraceae 30, TA-1 296, Firmicutes 313, Peptostreptococcaceae 268, Lachnospiraceae 49, Myxococcales 313, Peptostreptococcaceae 315, Peptostreptococcaceae 325, Firmicutes 345, Acidaminococcaceae 278, Lachnospiraceae 52, Desulfuromonadales 280, Clostridiaceae 341, Acidaminococcaceae 18, Sphingomonadales 58, Desulfovibrionales 281, Clostridiaceae 343, Acidaminococcaceae 5, Comamonadaceae 14, Moraxellaceae 282, Clostridiaceae 115, Nitrospira 8, Comamonadaceae 2, Pseudomonadaceae 292, Firmicutes 19, Alphaproteobacteria 27, Sytrophobacteraceae 3, Pseudomonadaceae 296, Firmicutes 20, Rhodospirillaceae 28, Sytrophobacteraceae 163, Spirochaetaceae 304, Firmicutes 7, Comamonadaceae 61, Epsilon proteobacteria 11, Nitrosomonadales 312, Peptostreptococcaceae 373, Deferribacteres 165, Spirochaetaceae 317, Peptostreptococcaceae 36, Delta proteobacteria 374, Deferribacteres 171, Spirochaetaceae 325, Firmicutes 59, Campylobacteraceae 361, others 178, Leptospiraceae 326, Firmicutes 4, Methylomonas 348, Firmicutes 0 5 10 15 20 25 30 175, Spirochaetes 0 1 2 3 4 5 6 7 8 9 10 128, Planctomycetes 119, Verrucomicrobia-Chlamydiae 62, Epsilon proteobacteria 123, Verrucomicrobia-Chlamydiae 171, Spirochaetaceae 350, Caldicellulosiruptor 68, KSB3 66, Caldothrix 140, NKB19 365, OP10 353, OD2 244, OP9 354, OD2 376, Deferribacteres 0 1 2 3 4 5 6 7 8 9 356, WS6 141,others 0 2 4 6 8 10 12 14 16 Fig. S1. Rank abundances of bacterial phylotypes of 12 UASB granular sludges. Sludge samples were collected from the reactors A) Sm, B) Sw, C) Ss, D) N1, E) N2, F), Q, G) Hg, H) Hn, I) Yk, J) Ks, K) Hs, and L) Dt. The vertical axis shows the taxonomic affi liation and number of phylotypes found in the respective clone libraries (382 bacterial phylotypes in total). E) N2 F) Q G) Hg H) Hn 146, Propionibacterineae 182, Chlorobi 52, Desulfuromonadales 114, Nitrospira 23, Sytrophobacteraceae 114, Nitrospira 68, KSB3 138, others 161, Spirochaetaceae 142, others 25, Sytrophobacteraceae 85, Bacteroidales 211, Chloroflexi 213, Chloroflexi 52, Desulfuromonadales 52, Desulfuromonadales 26, Sytrophobacteraceae 224, Chloroflexi 68, KSB3 369, Deferribacteres 179, Leptospiraceae 24, Sytrophobacteraceae 114, Nitrospira 88, Bacteroidales 143, Actinobacteridae 35, Delta proteobacteria 244, OP9 93, Bacteroidales 93, Bacteroidales 130, others 85, Bacteroidales 210, Chloroflexi 126, Planctomycetes 151, Propionibacterineae 191, Chloroflexi 232, Chloroflexi 26, Sytrophobacteraceae 53, Desulfuromonadales 114, Nitrospira 189, Chloroflexi 170, Spirochaetaceae 146, Propionibacterineae 136, OS-K 197 ,Chloroflexi 79, Bacteroidales 79, Bacteroidales 64, others 214, Chloroflexi 88, Bacteroidales 194, Chloroflexi 70, Bacteroidales 227, Chloroflexi 188, Chloroflexi 201, Chloroflexi 85, Bacteroidales 239, Chloroflexi 226, Chloroflexi 229, Chloroflexi 29, TA-1 280, Clostridiaceae 245, Lachnospiraceae 297, Firmicutes 296, Firmicutes 44, Syntrophaceae 271, Lachnospiraceae 50, Myxococcales 347, Syntrophomonadaceae 16, Rhodobacterales 295, Firmicutes 132, Acidobacteria 23, Sytrophobacteraceae 77 ,Bacteroidales 339, Acidaminococcaceae 80, Bacteroidales 48, Myxococcales 37, Syntrophaceae 79, Bacteroidales 88, Bacteroidales 118, Verrucomicrobia-Chlamydiae 46, Syntrophaceae 81, Bacteroidales 90, Bacteroidales 373, Deferribacteres 375, Deferribacteres 85, Bacteroidales 105, Bacteroidales 146, Propionibacterineae 382, Thermotogae 91, Bacteroidales 185, Chlorobi 160, Coriobacteridae 142, others 201, Chloroflexi 154, Rubrobacteridae 206, Chloroflexi 132, Acidobacteria 209, Chloroflexi 78, Bacteroidales 215, Chloroflexi 145, Cellulomonadaceae 217, Chloroflexi 103, Bacteroidales 226, Chloroflexi 159, Rubrobacteridae 218, Chloroflexi 198, Chloroflexi 242, Chloroflexi 200, Chloroflexi 181, Chlorobi 225, Chloroflexi 252, Lachnospiraceae 208, Chloroflexi 191, Chloroflexi 228, Chloroflexi 321, Firmicutes 212, Chloroflexi 201, Chloroflexi 235, Chloroflexi 326, Firmicutes 213, Chloroflexi 328, Firmicutes 265, Lachnospiraceae 220, Chloroflexi 329, Firmicutes 331, Lactobacillales 332, Lactobacillales 27, Sytrophobacteraceae 238, Chloroflexi 251, Lachnospiraceae 333, Lactobacillales 334, Lactobacillales 30, TA-1 257, Lachnospiraceae 341, Acidaminococcaceae 17, Rhodobacterales 46, Syntrophaceae 292, Firmicutes 342, Acidaminococcaceae 25, Sytrophobacteraceae 162, Spirochaetaceae 293, Firmicutes 12, Methylophilales 56, Desulfovibrionales 172, Spirochaetaceae 297, Firmicutes 27, Sytrophobacteraceae 61, Epsilonproteobacteria 121, Verrucomicrobia-Chlamydiae 300, Firmicutes 29, TA-1 374, Deferribacteres 377, Deferribacteres 308, Peptostreptococcaceae 31, TA-1 379, Deferribacteres 63, Gemmatimonadetes 311, Peptostreptococcaceae 366, OP10 364, OP10 320, Firmicutes 39, Syntrophaceae 367, OP10 137, OP8 322, Firmicutes 45, Syntrophaceae 324, Firmicutes 357, TM7 65, others 162, Spirochaetaceae 325, Firmicutes 122, Verrucomicrobia-Chlamydiae 336, Firmicutes 0 5 10 15 20 25 30 35 40 0 2 4 6 8 10 12 14 16 244, OP9 35, Deltaproteobacteria 37, Syntrophaceae 131, others 53, Desulfuromonadales 0 5 10 15 20 25 30 35 164, Spirochaetaceae 177, Leptospiraceae 180, Leptospiraceae Verrucomicrobia-Chlamydiae Deferribacteres Deferribacteres Deferribacteres others others others 0 2 4 6 8 10 12 14 16 Fig. S1 (continued).Fig. S1. (continued). Narihiro et al. I) Yk J) Ks K) Hs L) Dt 59, Campylobacteraceae 27, Sytrophobacteraceae 90, Bacteroidales 368, Deferribacteres 322, Firmicutes 377, Deferribacteres 190, Chloroflexi 149, Propionibacterineae 318, Firmicutes 95, Bacteroidales 102, Bacteroidales 80, Bacteroidales 2, Pseudomonadaceae 26, Sytrophobacteraceae 187, Chloroflexi 377, Deferribacteres 335, Firmicutes 74, Bacteroidales 297, Firmicutes 150, Propionibacterineae 253, Lachnospiraceae 45, Syntrophaceae 26, Sytrophobacteraceae 292, Firmicutes 9, Oxalobacteraceae 369, Deferribacteres 54, Desulfuromonadales 373, Deferribacteres 73, Bacteroidales 138, others 164, Spirochaetaceae 208, Chloroflexi 256, Lachnospiraceae 79, Bacteroidales 283, Firmicutes 266, Lachnospiraceae 290, Firmicutes 16, Rhodobacterales 181, Chlorobi 296, Firmicutes 284, Firmicutes 306, Peptostreptococcaceae 146, Propionibacterineae 297, Firmicutes 319, Firmicutes 51, Bdellovibrionales 85, Bacteroidales 330, Firmicutes 51, Bdellovibrionales 162, Spirochaetaceae 41, Syntrophaceae 57, Desulfovibrionales 154, Rubrobacteridae 258, Lachnospiraceae 144, Cellulomonadaceae 371, Deferribacteres 155, Rubrobacteridae 275, Lachnospiraceae 221, Chloroflexi 359, Termite group I 33, TA-1 296, Firmicutes 323, Firmicutes 265, Lachnospiraceae 147, Propionibacterineae 176, Spirochaetes 69, Bacteroidales 243, OP9 330, Firmicutes 285, Firmicutes 16, Rhodobacterales 72, Bacteroidales 244, OP9 21, TM6 30, TA-1 86, Bacteroidales 156, Rubrobacteridae 133, Acidobacteria 37, Syntrophaceae 94, Bacteroidales 75, Bacteroidales 134, Acidobacteria 41, Syntrophaceae 245, Lachnospiraceae 76, Bacteroidales 47, Myxococcales 153, Propionibacterineae 247, Lachnospiraceae 88, Bacteroidales 58, Desulfovibrionales 82, Bacteroidales 248, Lachnospiraceae 89, Bacteroidales 373, Deferribacteres 84, Bacteroidales 249, Lachnospiraceae 91, Bacteroidales
Recommended publications
  • Battistuzzi2009chap07.Pdf

    Battistuzzi2009chap07.Pdf

    Eubacteria Fabia U. Battistuzzia,b,* and S. Blair Hedgesa shown increasing support for lower-level phylogenetic Department of Biology, 208 Mueller Laboratory, The Pennsylvania clusters (e.g., classes and below), they have also shown the State University, University Park, PA 16802-5301, USA; bCurrent susceptibility of eubacterial phylogeny to biases such as address: Center for Evolutionary Functional Genomics, The Biodesign horizontal gene transfer (HGT) (20, 21). Institute, Arizona State University, Tempe, AZ 85287-5301, USA In recent years, three major approaches have been used *To whom correspondence should be addressed (Fabia.Battistuzzi@ asu.edu) for studying prokaryote phylogeny with data from com- plete genomes: (i) combining gene sequences in a single analysis of multiple genes (e.g., 7, 9, 10), (ii) combining Abstract trees from individual gene analyses into a single “super- tree” (e.g., 22, 23), and (iii) using the presence or absence The ~9400 recognized species of prokaryotes in the of genes (“gene content”) as the raw data to investigate Superkingdom Eubacteria are placed in 25 phyla. Their relationships (e.g., 17, 18). While the results of these dif- relationships have been diffi cult to establish, although ferent approaches have not agreed on many details of some major groups are emerging from genome analyses. relationships, there have been some points of agreement, A molecular timetree, estimated here, indicates that most such as support for the monophyly of all major classes (85%) of the phyla and classes arose in the Archean Eon and some phyla (e.g., Proteobacteria and Firmicutes). (4000−2500 million years ago, Ma) whereas most (95%) of 7 ese A ndings, although criticized by some (e.g., 24, 25), the families arose in the Proterozoic Eon (2500−542 Ma).
  • Bacterial Communities Associated with the Pine Wilt Disease Vector Monochamus Alternatus (Coleoptera: Cerambycidae) During Different Larval Instars

    Bacterial Communities Associated with the Pine Wilt Disease Vector Monochamus Alternatus (Coleoptera: Cerambycidae) During Different Larval Instars

    Journal of Insect Science, (2017)17(6): 115; 1–7 doi: 10.1093/jisesa/iex089 Research Article Bacterial Communities Associated With the Pine Wilt Disease Vector Monochamus alternatus (Coleoptera: Cerambycidae) During Different Larval Instars Xia Hu,1 Ming Li,1 Kenneth F. Raffa,2 Qiaoyu Luo,1 Huijing Fu,1 Songqing Wu,1 Guanghong Liang,1 Rong Wang,1 and Feiping Zhang1,3 1College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China, 2Department of Entomology, University of Wisconsin-Madison, 345 Russell Labs 1630 Linden Dr., Madison, WI 53706, and 3Corresponding author, e-mail: [email protected] Subject Editor: Campbell Mary and Lancette Josh Received 14 June 2017; Editorial decision 20 September 2017 Abstract We investigated the influence of larval instar on the structure of the gut bacterial community in the Japanese pine sawyer, Monochamus alternatus (Hope; Coleoptera: Cerambycidae). The diversity of the gut bacterial community in early, phloem-feeding larvae is significantly higher than in later, wood-feeding larvae. Many of these associates were assigned into a few taxonomic groups, of which Enterobacteriaceae was the most abundant order. The predominant bacterial genus varied during the five instars of larval development.Erwinia was the most abundant genus in the first and fifth instars,Enterobacter was predominant in the third and fourth instars, and the predominant genus in the second instars was in the Enterobacteriaceae (genus unclassified). Actinobacteria were reported in association with M. alternatus for the first time in this study. Cellulomonadaceae (Actinobacteria) was the second most abundant family in the first instar larvae (10.6%). These data contribute to our understanding of the relationships among gut bacteria and M.
  • Genomics 98 (2011) 370–375

    Genomics 98 (2011) 370–375

    Genomics 98 (2011) 370–375 Contents lists available at ScienceDirect Genomics journal homepage: www.elsevier.com/locate/ygeno Whole-genome comparison clarifies close phylogenetic relationships between the phyla Dictyoglomi and Thermotogae Hiromi Nishida a,⁎, Teruhiko Beppu b, Kenji Ueda b a Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan b Life Science Research Center, College of Bioresource Sciences, Nihon University, Fujisawa, Japan article info abstract Article history: The anaerobic thermophilic bacterial genus Dictyoglomus is characterized by the ability to produce useful Received 2 June 2011 enzymes such as amylase, mannanase, and xylanase. Despite the significance, the phylogenetic position of Accepted 1 August 2011 Dictyoglomus has not yet been clarified, since it exhibits ambiguous phylogenetic positions in a single gene Available online 7 August 2011 sequence comparison-based analysis. The number of substitutions at the diverging point of Dictyoglomus is insufficient to show the relationships in a single gene comparison-based analysis. Hence, we studied its Keywords: evolutionary trait based on whole-genome comparison. Both gene content and orthologous protein sequence Whole-genome comparison Dictyoglomus comparisons indicated that Dictyoglomus is most closely related to the phylum Thermotogae and it forms a Bacterial systematics monophyletic group with Coprothermobacter proteolyticus (a constituent of the phylum Firmicutes) and Coprothermobacter proteolyticus Thermotogae. Our findings indicate that C. proteolyticus does not belong to the phylum Firmicutes and that the Thermotogae phylum Dictyoglomi is not closely related to either the phylum Firmicutes or Synergistetes but to the phylum Thermotogae. © 2011 Elsevier Inc.
  • Online Supplementary Figures of Chapter 3

    Online Supplementary Figures of Chapter 3

    Online Supplementary Figures of Chapter 3 Fabio Gori Figures 1-30 contain pie charts showing the population characterization re- sulting from the taxonomic assignment computed by the methods. On the simulated datasets the true population distribution is also shown. 1 MTR Bacillales (47.11%) Thermoanaerobacterales (0.76%) Clostridiales (33.58%) Lactobacillales (7.99%) Others (10.55%) LCA Bacillales (48.38%) Thermoanaerobacterales (0.57%) Clostridiales (32.14%) Lactobacillales (10.07%) Others (8.84%) True Distribution 333 386 Prochlorales (5.84%) 535 Bacillales (34.61%) Halanaerobiales (4.37%) Thermoanaerobacterales (10.29%) Clostridiales (28.75%) Lactobacillales (9.38%) 1974 Herpetosiphonales (6.77%) 1640 249 587 Figure 1: Population distributions (rank Order) of M1, coverage 0.1x, by MTR and LCA, and the true population distribution. 2 MTR Bacillus (47.34%) Clostridium (14.61%) Lactobacillus (8.71%) Anaerocellum (11.41%) Alkaliphilus (5.14%) Others (12.79%) LCA Bacillus (51.41%) Clostridium (8.08%) Lactobacillus (9.23%) Anaerocellum (15.79%) Alkaliphilus (5.17%) Others (10.31%) True Distribution 386 552 Herpetosiphon (6.77%) 333 Prochlorococcus (5.84%) 587 Bacillus (34.61%) Clostridium (19.07%) Lactobacillus (9.38%) 249 Halothermothrix (4.37%) Caldicellulosiruptor (10.29%) Alkaliphilus (9.68%) 535 1974 1088 Figure 2: Population distributions (rank Genus) of M1, coverage 0.1x, by MTR and LCA, and the true population distribution. 3 MTR Prochlorales (0.07%) Bacillales (47.97%) Thermoanaerobacterales (0.66%) Clostridiales (32.18%) Lactobacillales (7.76%) Others (11.35%) LCA Prochlorales (0.10%) Bacillales (49.02%) Thermoanaerobacterales (0.59%) Clostridiales (30.62%) Lactobacillales (9.50%) Others (10.16%) True Distribution 3293 3950 Prochlorales (5.65%) 5263 Bacillales (36.68%) Halanaerobiales (3.98%) Thermoanaerobacterales (10.56%) Clostridiales (27.34%) Lactobacillales (9.03%) 21382 Herpetosiphonales (6.78%) 15936 2320 6154 Figure 3: Population distributions (rank Order) of M1, coverage 1x, by MTR and LCA, and the true population distribution.
  • Information to Users

    Information to Users

    INFORMATION TO USERS This manuscript bas been reproJuced from the microfilm master. UMI films the text directly ftom the original or copy submitted. Thus, sorne thesis and dissertation copies are in typewriter face, while others may be itom any type ofcomputer printer. The quality oftbis reproduction is depeDdeDt apoD the quality of the copy sablDitted. Broken or indistinct print, colored or poor quality illustrations and photographs, print bleedthlough, substandard margins, and improper alignment can adversely affect reproduction. In the unlikely event that the author did not send UMI a complete manuscript and there are missing pages, these will he noted. Also, if unauthorized copyright material had to be removed, a note will indicate the deletion. Oversize materials (e.g., maps, drawings, charts) are reproduced by sectioning the original, beginning at the upper left-hand corner and continuing trom left to right in equal sections with sma1l overlaps. Each original is a1so photographed in one exposure and is included in reduced fonn at the back orthe book. Photographs ineluded in the original manuscript have been reproduced xerographically in this copy. Higher quality 6" x 9" black and white photographie prints are available for any photographs or illustrations appearing in this copy for an additional charge. Contact UMI directly to order. UMI A Bell & Howell Information Company 300 North Zeeb Raad, ADn AJbor MI 48106-1346 USA 313n61-4700 8OO1S21~ NOTE TO USERS The original manuscript received by UMI contains pages with slanted print. Pages were microfilmed as received. This reproduction is the best copy available UMI Oral spirochetes: contribution to oral malodor and formation ofspherical bodies by Angela De Ciccio A thesis submitted to the Faculty ofGraduate Studies and Research, McGill University, in partial fulfillment ofthe requirements for the degree ofMaster ofScience.
  • Thitiwut Vongkampang WEBB

    Thitiwut Vongkampang WEBB

    Exploring strategies to improve volumetric hydrogen productivities of Caldicellulosiruptor species Vongkampang, Thitiwut 2021 Document Version: Publisher's PDF, also known as Version of record Link to publication Citation for published version (APA): Vongkampang, T. (2021). Exploring strategies to improve volumetric hydrogen productivities of Caldicellulosiruptor species. Department of Applied Microbiology, Lund University. Total number of authors: 1 General rights Unless other specific re-use rights are stated the following general rights apply: Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal Read more about Creative commons licenses: https://creativecommons.org/licenses/ Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. LUND UNIVERSITY PO Box 117 221 00 Lund +46 46-222 00 00 Exploring strategies to improve volumetric hydrogen productivities of Caldicellulosiruptor species THITIWUT VONGKAMPANG | APPLIED MICROBIOLOGY | LUND UNIVERSITY AN ECOLABEL 3041 0903 NORDIC SW ryck, Lund 2021 Printed by Media-T Mer de Glace is the largest glacier in France’s alpine, covering 30.4 sq.
  • Alpine Soil Bacterial Community and Environmental Filters Bahar Shahnavaz

    Alpine Soil Bacterial Community and Environmental Filters Bahar Shahnavaz

    Alpine soil bacterial community and environmental filters Bahar Shahnavaz To cite this version: Bahar Shahnavaz. Alpine soil bacterial community and environmental filters. Other [q-bio.OT]. Université Joseph-Fourier - Grenoble I, 2009. English. tel-00515414 HAL Id: tel-00515414 https://tel.archives-ouvertes.fr/tel-00515414 Submitted on 6 Sep 2010 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. THÈSE Pour l’obtention du titre de l'Université Joseph-Fourier - Grenoble 1 École Doctorale : Chimie et Sciences du Vivant Spécialité : Biodiversité, Écologie, Environnement Communautés bactériennes de sols alpins et filtres environnementaux Par Bahar SHAHNAVAZ Soutenue devant jury le 25 Septembre 2009 Composition du jury Dr. Thierry HEULIN Rapporteur Dr. Christian JEANTHON Rapporteur Dr. Sylvie NAZARET Examinateur Dr. Jean MARTIN Examinateur Dr. Yves JOUANNEAU Président du jury Dr. Roberto GEREMIA Directeur de thèse Thèse préparée au sien du Laboratoire d’Ecologie Alpine (LECA, UMR UJF- CNRS 5553) THÈSE Pour l’obtention du titre de Docteur de l’Université de Grenoble École Doctorale : Chimie et Sciences du Vivant Spécialité : Biodiversité, Écologie, Environnement Communautés bactériennes de sols alpins et filtres environnementaux Bahar SHAHNAVAZ Directeur : Roberto GEREMIA Soutenue devant jury le 25 Septembre 2009 Composition du jury Dr.
  • Sporulation Evolution and Specialization in Bacillus

    Sporulation Evolution and Specialization in Bacillus

    bioRxiv preprint doi: https://doi.org/10.1101/473793; this version posted March 11, 2019. 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 4.0 International license. Research article From root to tips: sporulation evolution and specialization in Bacillus subtilis and the intestinal pathogen Clostridioides difficile Paula Ramos-Silva1*, Mónica Serrano2, Adriano O. Henriques2 1Instituto Gulbenkian de Ciência, Oeiras, Portugal 2Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal *Corresponding author: Present address: Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands Phone: 0031 717519283 Email: [email protected] (Paula Ramos-Silva) Running title: Sporulation from root to tips Keywords: sporulation, bacterial genome evolution, horizontal gene transfer, taxon- specific genes, Bacillus subtilis, Clostridioides difficile 1 bioRxiv preprint doi: https://doi.org/10.1101/473793; this version posted March 11, 2019. 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 4.0 International license. Abstract Bacteria of the Firmicutes phylum are able to enter a developmental pathway that culminates with the formation of a highly resistant, dormant spore. Spores allow environmental persistence, dissemination and for pathogens, are infection vehicles. In both the model Bacillus subtilis, an aerobic species, and in the intestinal pathogen Clostridioides difficile, an obligate anaerobe, sporulation mobilizes hundreds of genes.
  • 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

    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
  • Taxonomy JN869023

    Taxonomy JN869023

    Species that differentiate periods of high vs. low species richness in unattached communities Species Taxonomy JN869023 Bacteria; Actinobacteria; Actinobacteria; Actinomycetales; ACK-M1 JN674641 Bacteria; Bacteroidetes; [Saprospirae]; [Saprospirales]; Chitinophagaceae; Sediminibacterium JN869030 Bacteria; Actinobacteria; Actinobacteria; Actinomycetales; ACK-M1 U51104 Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Comamonadaceae; Limnohabitans JN868812 Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Comamonadaceae JN391888 Bacteria; Planctomycetes; Planctomycetia; Planctomycetales; Planctomycetaceae; Planctomyces HM856408 Bacteria; Planctomycetes; Phycisphaerae; Phycisphaerales GQ347385 Bacteria; Verrucomicrobia; [Methylacidiphilae]; Methylacidiphilales; LD19 GU305856 Bacteria; Proteobacteria; Alphaproteobacteria; Rickettsiales; Pelagibacteraceae GQ340302 Bacteria; Actinobacteria; Actinobacteria; Actinomycetales JN869125 Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Comamonadaceae New.ReferenceOTU470 Bacteria; Cyanobacteria; ML635J-21 JN679119 Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Comamonadaceae HM141858 Bacteria; Acidobacteria; Holophagae; Holophagales; Holophagaceae; Geothrix FQ659340 Bacteria; Verrucomicrobia; [Pedosphaerae]; [Pedosphaerales]; auto67_4W AY133074 Bacteria; Elusimicrobia; Elusimicrobia; Elusimicrobiales FJ800541 Bacteria; Verrucomicrobia; [Pedosphaerae]; [Pedosphaerales]; R4-41B JQ346769 Bacteria; Acidobacteria; [Chloracidobacteria]; RB41; Ellin6075
  • Treponema Borrelia Family: Leptospiraceae Genus: Leptospira Gr

    Treponema Borrelia Family: Leptospiraceae Genus: Leptospira Gr

    Bacteriology lecture no.12 Spirochetes 3rd class -The spirochetes: are a large ,heterogeneous group of spiral ,motile bacteria. Although, • there are at least eight genera in this family ,only the genera Treponema,Borrelia,and Leptospira which contain organism pathogenic for humans . -There are some reports of intestinal spirochetes ,that have been isolated from biopsy material ,these are Brachyspira pilosicoli,and Brachyspira aalborgi. *Objectives* Taxonomy Order: Spirochaetales Family: Spirochaetaceae Genus: Treponema Borrelia Family: Leptospiraceae Genus: Leptospira -Gram-negative spirochetes -Spirochete from Greek for “coiled hair "they are : *1*Extremely thin and can be very long *2* Motile by periplasmic flagella (axial fibrils or endoflagella) *3*Outer sheath encloses axial fibrils *4*Axial fibrils originate from insertion pores at both poles of cell 1 Bacteriology lecture no.12 Spirochetes 3rd class Spirochaetales Associated Human Diseases Treponema Main Treponema are: - T. pallidum subspecies pallidum - Syphilis: Venereal (sexual) disease 2 Bacteriology lecture no.12 Spirochetes 3rd class - T. pertenue - Yaws Non venereal - T. carateum - Pinta skin disease All three species are morphologically identical Characteristics of T.pallidum 1-They are long ,slender ,helically coiled ,spiral or cork –screw shaped bacilli. 2-T.pallidum has an outer sheath or glycosaminoglycan contain peptidoglycan and maintain the structural integrity of the organisms. 3-Endoflagella (axial filament ) are the flagella-like organelles in the periplasmic space encased by the outer membranes . 4-The endoflagella begin at each end of the organism and wind around it ,extending to and overlapping at the midpoint. 5- Inside the endoflagella is the inner membrane (cytoplasmic membrane)that provide osmotic stability and cover the protoplasmic cylinders .
  • Phylogenomic Analysis of 589 Metagenome-Assembled Genomes Encompassing All Major Prokaryotic Lineages from the Gut of Higher Termites

    Phylogenomic Analysis of 589 Metagenome-Assembled Genomes Encompassing All Major Prokaryotic Lineages from the Gut of Higher Termites

    Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites Vincent Hervé1, Pengfei Liu1, Carsten Dietrich1, David Sillam-Dussès2, Petr Stiblik3, Jan Šobotník3 and Andreas Brune1 1 Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany 2 Laboratory of Experimental and Comparative Ethology EA 4443, Université Paris 13, Villetaneuse, France 3 Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic ABSTRACT “Higher” termites have been able to colonize all tropical and subtropical regions because of their ability to digest lignocellulose with the aid of their prokaryotic gut microbiota. Over the last decade, numerous studies based on 16S rRNA gene amplicon libraries have largely described both the taxonomy and structure of the prokaryotic communities associated with termite guts. Host diet and microenvironmental conditions have emerged as the main factors structuring the microbial assemblages in the different gut compartments. Additionally, these molecular inventories have revealed the existence of termite-specific clusters that indicate coevolutionary processes in numerous prokaryotic lineages. However, for lack of representative isolates, the functional role of most lineages remains unclear. We reconstructed 589 metagenome-assembled genomes (MAGs) from the different Submitted 29 August 2019 gut compartments of eight higher termite species that encompass 17 prokaryotic